diff --git a/.classpath b/.classpath index f16b26a7a..b98566358 100644 --- a/.classpath +++ b/.classpath @@ -7,23 +7,22 @@ - - - - - - - + + + + + + diff --git a/.settings/org.eclipse.jdt.core.prefs b/.settings/org.eclipse.jdt.core.prefs index 657d9e408..0fee6a9c4 100644 --- a/.settings/org.eclipse.jdt.core.prefs +++ b/.settings/org.eclipse.jdt.core.prefs @@ -1,13 +1,15 @@ eclipse.preferences.version=1 org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate -org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6 +org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8 org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve -org.eclipse.jdt.core.compiler.compliance=1.6 +org.eclipse.jdt.core.compiler.compliance=1.8 org.eclipse.jdt.core.compiler.debug.lineNumber=generate org.eclipse.jdt.core.compiler.debug.localVariable=generate org.eclipse.jdt.core.compiler.debug.sourceFile=generate org.eclipse.jdt.core.compiler.problem.assertIdentifier=error +org.eclipse.jdt.core.compiler.problem.enablePreviewFeatures=disabled org.eclipse.jdt.core.compiler.problem.enumIdentifier=error +org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=warning org.eclipse.jdt.core.compiler.release=disabled -org.eclipse.jdt.core.compiler.source=1.6 +org.eclipse.jdt.core.compiler.source=1.8 diff --git a/Additional Files/Mesquite.exe b/Additional Files/Mesquite.exe deleted file mode 100755 index f3da370b3..000000000 Binary files a/Additional Files/Mesquite.exe and /dev/null differ diff --git a/Additional Files/Mesquite_Start_Script java 1.7.command b/Additional Files/Mesquite_Start_Script java 1.7.command deleted file mode 100755 index 6fa795c1c..000000000 --- a/Additional Files/Mesquite_Start_Script java 1.7.command +++ /dev/null @@ -1,4 +0,0 @@ -dir=`dirname "$0"` -/Library/Java/JavaVirtualMachines/jdk1.7.0_45.jdk/Contents/Home/bin/java -d64 -Xmx4000M -Xss2m -Djava.library.path=lib -Djri.ignore.ule="yes" -cp "$dir" mesquite.Mesquite -#increase the numbers above to enable more than 500M total and 2M per thread for the stack. The latter enables larger trees, e.g. more than 5000 taxa -# add flag -d64 to enable 64 bit support and thus larger memory allocation, e.g. above 2gb diff --git a/Additional Files/Mesquite_Start_Script java 1.8.command b/Additional Files/Mesquite_Start_Script java 1.8.command deleted file mode 100644 index 36a021c48..000000000 --- a/Additional Files/Mesquite_Start_Script java 1.8.command +++ /dev/null @@ -1,4 +0,0 @@ -dir=`dirname "$0"` -/Library/Java/JavaVirtualMachines/jdk1.8.0_101.jdk/Contents/Home/bin/java -d64 -Xmx4000M -Xss2m -Djava.library.path=lib -Djri.ignore.ule="yes" -cp "$dir" mesquite.Mesquite -#increase the numbers above to enable more than 500M total and 2M per thread for the stack. The latter enables larger trees, e.g. more than 5000 taxa -# add flag -d64 to enable 64 bit support and thus larger memory allocation, e.g. above 2gb diff --git a/Additional Files/classpaths.txt b/Additional Files/classpaths.txt deleted file mode 100644 index a4a5bc122..000000000 --- a/Additional Files/classpaths.txt +++ /dev/null @@ -1 +0,0 @@ -../../Cartographer/Mesquite_Folder diff --git a/Additional Files/execsToStartUnderWindows/Mesquite.jar b/Additional Files/execsToStartUnderWindows/Mesquite.jar deleted file mode 100644 index 439933377..000000000 Binary files a/Additional Files/execsToStartUnderWindows/Mesquite.jar and /dev/null differ diff --git a/Additional Files/executables.zip b/Additional Files/executables.zip deleted file mode 100644 index 967f6b2e4..000000000 Binary files a/Additional Files/executables.zip and /dev/null differ diff --git a/Additional Files/jarFileMaking.txt b/Additional Files/jarFileMaking.txt deleted file mode 100644 index 8d7ccf886..000000000 --- a/Additional Files/jarFileMaking.txt +++ /dev/null @@ -1,3 +0,0 @@ -jar cvfm mesquite.jar manifest.txt mesquite org com - -jar cvfm mesquite.jar manifest.txt start diff --git a/Additional Files/jars.zip b/Additional Files/jars.zip deleted file mode 100644 index 067cc0dc3..000000000 Binary files a/Additional Files/jars.zip and /dev/null differ diff --git a/Additional Files/menuSquares.txt b/Additional Files/menuSquares.txt deleted file mode 100644 index 4ec0ff6b9..000000000 --- a/Additional Files/menuSquares.txt +++ /dev/null @@ -1,2 +0,0 @@ -◼ ◻ ❑ ⬒ ▣ -◀ ▶ ◢ ◣ ◥ ◤ ◇ ◆ ◈ ◊ \ No newline at end of file diff --git a/Additional Files/preparingMesquite.html b/Additional Files/preparingMesquite.html deleted file mode 100644 index e9ae3cc54..000000000 --- a/Additional Files/preparingMesquite.html +++ /dev/null @@ -1,54 +0,0 @@ - - - -Preparing a Copy of Mesquite - - - - -

Taking a development copy of Mesquite and preparing a copy that can - be moved onto another machine

-

(Note: step 1 is optional, but recommended.)

-
    -
  1. Open up Eclipse and update all of the projects (to update projects, select - them in the Package Explorer, right click (or control-click) and, in the popup menu, select Team>Update).
    2. -
  2. Quit Eclipse, and find the Eclipse workspace on your hard disk. In the workspace, you should find several folders. One is called Mesquite Project; this is the core of Mesquite. The other - folders are for other Mesquite packages.
    3. -
  3. In Mesquite Project, you will find a "Mesquite_Folder". - Copy that entire folder to another location on your hard disk. This is the Mesquite_Folder that will be able to be moved to another machine. That copy will henceforth be referred to as - the Mesquite_Folder Copy
    4. -
  4. Also in the workspace are the folders for project for other packages. - For example, one is Chromaseq. To add Chromaseq to Mesquite_Folder Copy, open the Chromaseq folder. Inside that you will find a "Mesquite_Folder"; - open that, then "mesquite". In there you will find a folder called "chromaseq". - Copy that folder into the "mesquite" folder within Mesquite_Folder Copy.
    5. -
  5. Repeat #3 for any of the other projects you wish to incorporate.
    6. -
  6. Go into the copy of the Mesquite_Folder Copy you made in step 2, and - delete any files whose names start with "classpath".
    7. -
  7. Open up Mesquite_Folder Copy and start up the copy of Mesquite in there. - If it starts up without errors, you should be fine. If, however, there - are errors, then it might be because the "jars" folder is not fully - set up (this is a problem we haven't managed to get a regular fix for), - or the Mac executibles have been damaged. You should then try the - following: -
      -
    • go into Mesquite Project/Additional Files and copy from there the jars.zip - file into Mesquite Project/Mesquite_Folder
      • -
    • delete the jars folder present in Mesquite Project/Mesquite_Folder
      • -
    • unzip the jars.zip folder in Mesquite Project/Mesquite_Folder
      • -
    • On MacOS X, for reasons that we don't understand - yet, Eclipse seems to damage the executable files that are needed - to launch Mesquite in the standard way. If on a Mac you find Mesquite - does not launch appropriately, then open unzip the file executables.zip - that is contained in the Additional Files folder, and move its contents - into Mesquite_Folder, replacing the existing files of the same name.
      • -
    • Start up Mesquite again to see if the problems are now fixed; if - there are still problems, please contact David Maddison.
      • -
    -
    8. -
  8. If all is well, then zip the Mesquite_Folder copy and you can now move - it onto another machine.
    9. -
-

 

- - - diff --git a/Additional Files/receipts.xml b/Additional Files/receipts.xml deleted file mode 100644 index fa0374e1c..000000000 --- a/Additional Files/receipts.xml +++ /dev/null @@ -1,18 +0,0 @@ - - - 1 - - silk - SILK version 1.1 - SILK provides functions to display images integrated into a character matrix editor - mesquite/silk - 110 - - - pdap - PDAP version 1.1 - PDAP provides functions for comparative analyses with continuous data - mesquite/pdap - 110 - - diff --git a/Executables/All OSs - Scripts and Instructions to Users/Windows/Mesquite_Starter_INSTRUCTIONS_Windows.docx b/Executables/All OSs - Scripts and Instructions to Users/Windows/Mesquite_Starter_INSTRUCTIONS_Windows.docx new file mode 100644 index 000000000..1e0d47c3b Binary files /dev/null and b/Executables/All OSs - Scripts and Instructions to Users/Windows/Mesquite_Starter_INSTRUCTIONS_Windows.docx differ diff --git a/Executables/All OSs - Scripts and Instructions to Users/Windows/Mesquite_Starter_INSTRUCTIONS_Windows.pdf b/Executables/All OSs - Scripts and Instructions to Users/Windows/Mesquite_Starter_INSTRUCTIONS_Windows.pdf new file mode 100644 index 000000000..1c825afa7 Binary files /dev/null and b/Executables/All OSs - Scripts and Instructions to Users/Windows/Mesquite_Starter_INSTRUCTIONS_Windows.pdf differ diff --git a/Additional Files/execsToStartUnderWindows/Mesquite_Start_Script.bat b/Executables/All OSs - Scripts and Instructions to Users/Windows/Mesquite_Starter_SE.bat similarity index 100% rename from Additional Files/execsToStartUnderWindows/Mesquite_Start_Script.bat rename to Executables/All OSs - Scripts and Instructions to Users/Windows/Mesquite_Starter_SE.bat diff --git a/Executables/All OSs - Scripts and Instructions to Users/Windows/Mesquite_Starter_SK.bat b/Executables/All OSs - Scripts and Instructions to Users/Windows/Mesquite_Starter_SK.bat new file mode 100755 index 000000000..9c340523f --- /dev/null +++ b/Executables/All OSs - Scripts and Instructions to Users/Windows/Mesquite_Starter_SK.bat @@ -0,0 +1 @@ +java --add-opens java.base/java.net=ALL-UNNAMED -Xmx1000M -Xss4m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar Mesquite.jar diff --git a/Executables/All OSs - Scripts and Instructions to Users/linux/Mesquite_Starting_INSTRUCTIONS on Linux.txt b/Executables/All OSs - Scripts and Instructions to Users/linux/Mesquite_Starting_INSTRUCTIONS on Linux.txt new file mode 100644 index 000000000..b6608111d --- /dev/null +++ b/Executables/All OSs - Scripts and Instructions to Users/linux/Mesquite_Starting_INSTRUCTIONS on Linux.txt @@ -0,0 +1,30 @@ +To Run Mesquite on Linux + +SYSTEM REQUIREMENTS +To run Mesquite, you need Java installed. The version of Mesquite you have here runs on Java 1.8 or higher. If Mesquite doesn't work, you may need to try different versions of Java. Occasionally a new version of Java is released that has bugs, or adds a requirement that is not backwards-compatible, and Mesquite will be unable to run. + +There is a bug in Oracle Java versions 11 to 16 (at least) on Linux that causes Mesquite to crash during startup with a StackOverflowError. The only workaround we know is to use Mesquite on Linux only with Java version 8 (i.e. 1.8) which is available from java.com. You may need to make adjustments so that your system knows to use Java 8 (e.g., see instructions here http://www.ormbunkar.se/aliview/#java8install, or see below). + +RUNNING MESQUITE +Run Mesquite by double clicking mesquite.sh or running mesquite.sh from the command line like this: + ./mesquite.sh + +You may want to edit this to request more memory using options like "-Xmx1000M -Xss4m" (see below). + +Alternatively, run it from the command line by cd'ing into Mesquite_Folder and then giving a command like this: + + java -Xmx1000M -Xss4m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar Mesquite.jar + +The part -Xmx1000M indicates how much heap memory to give to Mesquite in general. With more heap memory Mesquite can handle more trees, bigger matrices, bigger charts, and so on. + +The part -Xss4m indicates how much stack memory to give to each thread. With more stack memory, Mesquite can handle bigger trees, e.g. more than 5000 taxa. To be able to handle 10000 taxa, you may need to increase this to 4m + +Here is an example configuration: + + java -Xmx4000M -Xss16m -d64 -Djava.library.path=lib -Djri.ignore.ule="yes" -jar Mesquite.jar + +This gives much memory to Mesquite, but 4000 MB (= 4 GB) memory exceeds the ability of 32 bit Java. For that reason the command -d64 was added, to indicate you want to use 64 bit java. + +If you run Mesquite directly from the command line, you can replace java by the full path to the Java 1.8 jre or jdk. That will allow you to have multiple versions of Java on your computer, have Java 16 or some other newer version as the default, but still run Mesquite on Java 1.8. + + diff --git a/Executables/All OSs - Scripts and Instructions to Users/linux/mesquite.sh b/Executables/All OSs - Scripts and Instructions to Users/linux/mesquite.sh new file mode 100755 index 000000000..ff90b9a35 --- /dev/null +++ b/Executables/All OSs - Scripts and Instructions to Users/linux/mesquite.sh @@ -0,0 +1,64 @@ +#!/bin/bash + +#Script to identify java VM. Also modifies classpath on cygwin. +#Written by Travis Wheeler (www.traviswheeler.com) + +#If you find bugs or modify the script to improve functionality, +# please let us know so we can improve the script for everyone + + +# Thanks to William Cook (http://www.cs.utexas.edu/users/wcook/) for the bit that +# identifies the path containing this script, and uses it to set the classpath. +# (the exact site of the work that served as inspiration for this code is lost to antiquity) + +#Note from W. Maddison: to increase memory allocation adjust the following lines: +# java -Djava.library.path=lib -cp "$dir" mesquite.Mesquite $* +# by adding the extra arguments -Xmx and -Xss +# For instance, +# java -Djava.library.path=lib -Xmx500M -Xss4m -cp "$dir" mesquite.Mesquite $* +# will allocate 500M for the heap, which helps with large data and calculations, +# and 4M stack size per thread, which helps with large trees (> 5000 taxa). + +#figure out where java lives +if [ $MESQUITE_JAVA_HOME ] +then + java="$MESQUITE_JAVA_HOME/bin/java" +elif [ $JAVA_HOME ] +then + java="$JAVA_HOME/bin/java" +else + tmp=`java -version 2>&1` + if echo "$tmp" | grep -q "command not found" # no "java", so try "jre" + then + tmp=`jre -version 2>&1` + if echo "$tmp" | grep -q "command not found" + then + echo "Can't find java. Try setting either the JAVA_HOME environment variable" + exit + else + java="jre" + fi + else + java="java" + fi +fi + + +# figure out where I live, then run java w/ my containing dir as classpath +dir=`dirname "$0"` +os=`uname` +if test ${os:0:6} = "CYGWIN" +then + if test ${dir:1:8} = "cygdrive" + then + dir="${dir:10:1}:/${dir:12}" + fi + chmod -R u+w "$dir/com/" + cp -r "$dir/../Resources/com/"* "$dir/com/" >& /dev/null + $java -Djava.library.path=lib -Djri.ignore.ule="yes" -jar Mesquite.jar $* +else + chmod -R u+w "$dir/com/" + cp -r "$dir/../Resources/com/"* "$dir/com/" >& /dev/null + $java -Djava.library.path=lib -Djri.ignore.ule="yes" -jar Mesquite.jar $* +fi + diff --git a/Executables/All OSs - Scripts and Instructions to Users/macOS/Mesquite_Starter-S.command b/Executables/All OSs - Scripts and Instructions to Users/macOS/Mesquite_Starter-S.command new file mode 100755 index 000000000..b731b1198 --- /dev/null +++ b/Executables/All OSs - Scripts and Instructions to Users/macOS/Mesquite_Starter-S.command @@ -0,0 +1,20 @@ +dir=`dirname "$0"` +java -Xmx2000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$dir/Mesquite.jar" + +#================ +#INSTRUCTIONS +#Increase the numbers above to enable more than 2000M total heap and 8M per thread for the stack. The latter enables larger trees, e.g. more than 5000 taxa + +#IF MESQUITE DOESN'T START, TRY THESE: + +#The default command in this file as it is original distributed is as follows (but without the "#"): +#java -Xmx2000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$dir/Mesquite.jar" + +#That uses the default version of Java to run Mesquite. If you need to use another Java, put its full path instead of the word java. For instance, to run Java 1.8 on some macOS versions, use a command like this (but without the "#"). + +#/Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/bin/java -Xmx2000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$dir/Mesquite.jar" + +#On the other hand, if you use a new version of java, you may need to add an "add-export" flag as follows: + +#java --add-exports java.desktop/com.apple.eawt=ALL-UNNAMED -Xmx2000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$dir/Mesquite.jar" + diff --git a/Executables/All OSs - Scripts and Instructions to Users/macOS/Mesquite_Starter_INSTRUCTIONS_macOS.docx b/Executables/All OSs - Scripts and Instructions to Users/macOS/Mesquite_Starter_INSTRUCTIONS_macOS.docx new file mode 100644 index 000000000..37c1a06be Binary files /dev/null and b/Executables/All OSs - Scripts and Instructions to Users/macOS/Mesquite_Starter_INSTRUCTIONS_macOS.docx differ diff --git a/Executables/All OSs - Scripts and Instructions to Users/macOS/Mesquite_Starter_INSTRUCTIONS_macOS.pdf b/Executables/All OSs - Scripts and Instructions to Users/macOS/Mesquite_Starter_INSTRUCTIONS_macOS.pdf new file mode 100644 index 000000000..a223e7873 Binary files /dev/null and b/Executables/All OSs - Scripts and Instructions to Users/macOS/Mesquite_Starter_INSTRUCTIONS_macOS.pdf differ diff --git a/Executables/MacOS via Automator and Script/INSTRUCTIONSForExecutableBuildingByAutomator.txt b/Executables/MacOS via Automator and Script/INSTRUCTIONSForExecutableBuildingByAutomator.txt new file mode 100644 index 000000000..aecc068f3 --- /dev/null +++ b/Executables/MacOS via Automator and Script/INSTRUCTIONSForExecutableBuildingByAutomator.txt @@ -0,0 +1,147 @@ +Here is the procedure used to build the script-based Flex executable (initially made for Catalina and above). +LAST USE AND VERSION August 2021 + +================== BUILDING EXECUTABLE +Building an executable with Automator. + +These are the task that the Automator app completes (see screenshot automatorForMesquiteExecutable.png): + +(1) remembers files dropped on it (seems to get only 1!) +(2) makes Mesquite_Support_Files a new folder (if it doesn't exist) [to hold the file of standard out] +(3) retrieves paths to file dropped on it, and passes into next stage +(4) Applescript figures out where itself is (i.e. the executable), to figure out the path to Mesquite.jar. Also gets path to dropped file. Also reads text files indicating amount of memory to use, path to Java, and any Java flags to add. Composes these together into a string that can be easily parsed by next stage: + +on getPath(this_text, stripLast) + set AppleScript's text item delimiters to the ":" + set the item_list to every text item of this_text + set num to the number of items in item_list + if stripLast then + set lasti to num - 2 + else + set lasti to num + end if + set the item_list to items 2 through lasti of item_list + set AppleScript's text item delimiters to the "/" + set this_text to the item_list as string + set AppleScript's text item delimiters to "" + set this_text to "/" & this_text + return this_text +end getPath + +on run {input, parameters} + set whereAmI to getPath((path to me as text), true) + set javaLocFile to whereAmI & "/RunningOptionsForFlex/Mesquite-JavaToUse.txt" + set javaLoc to "java" + try + set lns to paragraphs of (read POSIX file javaLocFile) + set javaLoc to first item in lns + end try + set memoryFile to whereAmI & "/RunningOptionsForFlex/Mesquite-MemoryToUse.txt" + set memory to 1 + try + set lns to paragraphs of (read POSIX file memoryFile) + set memory to first item in lns + end try + set flagsFile to whereAmI & "/RunningOptionsForFlex/Mesquite-FlagsToUse.txt" + set flags to "" + try + set lns to paragraphs of (read POSIX file flagsFile) + set flags to first item in lns + end try + #display dialog memory as text + set results to whereAmI + try + if input is not equal to {} then + set droppedFiles to getPath(input as text, false) + set results to results & ":" & droppedFiles + end if + end try + set results to javaLoc & ":" & flags & ":" &memory & ":" & results + return results +end run + +(5) Runs a shell script, taking as input the string from part (4): + +read whereAndWhat #where is Mesquite Folder, and what are dropped files +echo $whereAndWhat > Mesquite_Support_Files/Mesquite_Flex_INSTRUCTIONS.txt +IFS=':' read -r -a arr <<< "$whereAndWhat" +JAVALOC=${arr[0]} +FLAGS=${arr[1]} +MEMORY=${arr[2]} +whereAmI=${arr[3]} +if [[ ${#myvar} <1 ]]; #no flags passed in +then + if [[ ${#arr[@]} > 4 ]]; + then + droppedFiles=${arr[4]} #this gets just first file + "${JAVALOC}" --add-exports java.desktop/com.apple.eawt=ALL-UNNAMED -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" "$droppedFiles" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt || "${JAVALOC}" -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" "$droppedFiles" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt + else + "${JAVALOC}" --add-exports java.desktop/com.apple.eawt=ALL-UNNAMED -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt || "${JAVALOC}" -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt + fi +else #flags passed in; use those + if [[ ${#arr[@]} > 4 ]]; + then + droppedFiles=${arr[4]} #this gets just first file + "${JAVALOC}" ${FLAGS} -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" "$droppedFiles" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt + else + "${JAVALOC}" ${FLAGS} -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt + fi +fi + + +================== CUSTOMIZING APP Bundle +In app bundle, Info.plist, change + CFBundleIconFile + AutomatorApplet + +to + CFBundleIconFile + Mesquite.icns + +In the app bundle, Resources, add the file Mesquite.icns + +================== SIGNING EXECUTABLE +Make duplicate of Mesquite app to be signed, and call it Mesquite.app + +Run the signBundle.sh script, i.e.: + +#!/bin/bash +xattr -cr Mesquite.app + +for f in $(find Mesquite.app/Contents); +do + codesign -s "Developer ID Application: Wayne Maddison" $f; +done + +codesign --force --deep --options=runtime -s "Developer ID Application: Wayne Maddison" Mesquite.app +#codesign --force --options=runtime -s "Developer ID Application: Wayne Maddison" Mesquite.app +codesign -d --verbose=4 Mesquite.app +spctl --assess --verbose=4 --type execute Mesquite.app + +================== NOTARIZING EXECUTABLE +==================================================== +NOTARIZING +Zip using + /usr/bin/ditto -c -k --keepParent Mesquite.app Mesquite.zip +Submit for notarization using + xcrun altool --eval-app --primary-bundle-id org.mesquiteproject -u wmaddisn@zoology.ubc.ca -f Mesquite.zip + +Give not Apple-id password, but rather app-specific PASSWORD. (https://support.apple.com/en-us/HT204397) + +For regular Mesquite.app: #### (search for tukk) + +Will respond with a RequestUUID. To check status, enter (replace strange request uu id) + + xcrun altool --eval-info -u wmaddisn@zoology.ubc.ca + +To get more details use the URL given + +Somethow this might help also??? +xcrun altool --notarization-info -u wmaddisn@zoology.ubc.ca + +Once it's approved, run + xcrun stapler staple Mesquite.app + +--------- + xcrun altool --eval-info REPLACEWITHREQUESTUUID -u wmaddisn@zoology.ubc.ca + diff --git a/Executables/MacOS via Automator and Script/Mesquite.icns b/Executables/MacOS via Automator and Script/Mesquite.icns new file mode 100644 index 000000000..280d8334a Binary files /dev/null and b/Executables/MacOS via Automator and Script/Mesquite.icns differ diff --git a/Executables/MacOS via Automator and Script/Mesquite.zip b/Executables/MacOS via Automator and Script/Mesquite.zip new file mode 100644 index 000000000..21d1204e2 Binary files /dev/null and b/Executables/MacOS via Automator and Script/Mesquite.zip differ diff --git a/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-01AutomatorOrig-2021.app/Contents/Info.plist b/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-01AutomatorOrig-2021.app/Contents/Info.plist new file mode 100644 index 000000000..8faf5963c --- /dev/null +++ b/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-01AutomatorOrig-2021.app/Contents/Info.plist @@ -0,0 +1,109 @@ + + + + + AMIsApplet + + AMStayOpen + + BuildMachineOSBuild + 17A405001 + CFBundleAllowMixedLocalizations + + CFBundleDevelopmentRegion + English + CFBundleDocumentTypes + + + CFBundleTypeExtensions + + * + + CFBundleTypeName + Automator workflow file + CFBundleTypeOSTypes + + **** + + CFBundleTypeRole + Viewer + + + CFBundleExecutable + Application Stub + CFBundleIconFile + AutomatorApplet + CFBundleIdentifier + com.apple.automator.Mesquite_Starter_Flex-01AutomatorOrig-2021superFlex + CFBundleInfoDictionaryVersion + 6.0 + CFBundleName + Mesquite_Starter_Flex-01AutomatorOrig-2021superFlex + CFBundlePackageType + APPL + CFBundleShortVersionString + 1.3 + CFBundleSignature + ???? + CFBundleSupportedPlatforms + + MacOSX + + CFBundleURLTypes + + CFBundleVersion + 444.42 + DTCompiler + com.apple.compilers.llvm.clang.1_0 + DTPlatformBuild + 10P70r + DTPlatformName + macosx + DTPlatformVersion + 10.14 + DTSDKBuild + 18F82 + DTSDKName + macosx10.14internal + DTXcode + 1020 + DTXcodeBuild + 10P70r + LSMinimumSystemVersion + 10.6 + LSUIElement + + NSAppleEventsUsageDescription + This workflow needs to control other applications to run. + NSAppleMusicUsageDescription + This workflow needs access to your music to run. + NSAppleScriptEnabled + YES + NSCalendarsUsageDescription + This workflow needs access to your calendars to run. + NSCameraUsageDescription + This workflow needs access to your camera to run. + NSContactsUsageDescription + This workflow needs access to your contacts to run. + NSHomeKitUsageDescription + This workflow needs access to your HomeKit Home to run. + NSMicrophoneUsageDescription 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isViewVisible + + + + action + + AMAccepts + + Container + List + Optional + + Types + + * + + + AMActionVersion + v.1.0.2 + AMApplication + + Automator + + AMParameterProperties + + variableUUID + + isPathPopUp + + selectedVariableUUID + B5724CA0-32E6-41E6-A92D-05F05ECF423A + + + AMProvides + + Container + List + Types + + * + + + AMRequiredResources + + ActionBundlePath + /System/Library/Automator/Get Value of Variable.action + ActionName + Get Value of Variable + ActionParameters + + variableUUID + B5724CA0-32E6-41E6-A92D-05F05ECF423A + + BundleIdentifier + com.apple.Automator.GetValueofVariable + CFBundleVersion + 1.0.2 + CanShowSelectedItemsWhenRun + + CanShowWhenRun + + Category + + AMCategoryUtilities + + Class Name + Get_Value_of_Variable + IgnoresInput + + InputUUID + B3699B55-670C-4E04-8062-7A25776314F6 + Keywords + + variable + binding + input + output + storage + + OutputUUID + 342F6FBC-A8B4-4AB8-8488-094942236BD7 + UUID + 4F14C189-CB3E-41E7-989A-E209FB44368B + UnlocalizedApplications + + Automator + + arguments + + 0 + + default value + + name + variableUUID + required + 0 + type + 0 + uuid + 0 + + + isViewVisible + + location + 619.500000:193.000000 + nibPath + /System/Library/Automator/Get Value of Variable.action/Contents/Resources/Base.lproj/main.nib + + isViewVisible + + + + action + + AMAccepts + + Container + List + Optional + + Types + + com.apple.applescript.object + + + AMActionVersion + 1.0.2 + AMApplication + + Automator + + AMParameterProperties + + source + + + AMProvides + + Container + List + Types + + com.apple.applescript.object + + + ActionBundlePath + /System/Library/Automator/Run AppleScript.action + ActionName + Run AppleScript + ActionParameters + + source + on getPath(this_text, stripLast) set AppleScript's text item delimiters to the ":" set the item_list to every text item of this_text set num to the number of items in item_list if stripLast then set lasti to num - 2 else set lasti to num end if set the item_list to items 2 through lasti of item_list set AppleScript's text item delimiters to the "/" set this_text to the item_list as string set AppleScript's text item delimiters to "" set this_text to "/" & this_text return this_text end getPath on run {input, parameters} set whereAmI to getPath((path to me as text), true) set javaLocFile to whereAmI & "/RunningOptionsForFlex/Mesquite-JavaToUse.txt" set javaLoc to "java" try set lns to paragraphs of (read POSIX file javaLocFile) set javaLoc to first item in lns end try set memoryFile to whereAmI & "/RunningOptionsForFlex/Mesquite-MemoryToUse.txt" set memory to 1 try set lns to paragraphs of (read POSIX file memoryFile) set memory to first item in lns end try set flagsFile to whereAmI & "/RunningOptionsForFlex/Mesquite-FlagsToUse.txt" set flags to "" try set lns to paragraphs of (read POSIX file flagsFile) set flags to first item in lns end try #display dialog memory as text set results to whereAmI try if input is not equal to {} then set droppedFiles to getPath(input as text, false) set results to results & ":" & droppedFiles end if end try set results to javaLoc & ":" & flags & ":" &memory & ":" & results return results end run + + BundleIdentifier + com.apple.Automator.RunScript + CFBundleVersion + 1.0.2 + CanShowSelectedItemsWhenRun + + CanShowWhenRun + + Category + + AMCategoryUtilities + + Class Name + RunScriptAction + InputUUID + 11F3EFA2-BE3D-4DD3-A24A-AFC7373B06F3 + Keywords + + Run + + OutputUUID + F42FD833-E0EE-4550-88BA-39A54F93799B + UUID + 35565B5A-57E2-4F76-B8E4-02CE4A8CD9B2 + UnlocalizedApplications + + Automator + + arguments + + 0 + + default value + on run {input, parameters} + + (* Your script goes here *) + + return input +end run + name + source + required + 0 + type + 0 + uuid + 0 + + + isViewVisible + + location + 619.500000:438.000000 + nibPath + /System/Library/Automator/Run AppleScript.action/Contents/Resources/Base.lproj/main.nib + + isViewVisible + + + + action + + AMAccepts + + Container + List + Optional + + Types + + com.apple.cocoa.string + + + AMActionVersion + 2.0.3 + AMApplication + + Automator + + AMParameterProperties + + COMMAND_STRING + + CheckedForUserDefaultShell + + inputMethod + + shell + + source + + + AMProvides + + Container + List + Types + + com.apple.cocoa.string + + + ActionBundlePath + /System/Library/Automator/Run Shell Script.action + ActionName + Run Shell Script + ActionParameters + + COMMAND_STRING + read whereAndWhat #where is Mesquite Folder, and what are dropped files +echo $whereAndWhat > Mesquite_Support_Files/Mesquite_Flex_INSTRUCTIONS.txt +IFS=':' read -r -a arr <<< "$whereAndWhat" +JAVALOC=${arr[0]} +FLAGS=${arr[1]} +MEMORY=${arr[2]} +whereAmI=${arr[3]} +if [[ ${#myvar} <1 ]]; #no flags passed in +then + if [[ ${#arr[@]} > 4 ]]; + then + droppedFiles=${arr[4]} #this gets just first file + "${JAVALOC}" --add-exports java.desktop/com.apple.eawt=ALL-UNNAMED -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" "$droppedFiles" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt || "${JAVALOC}" -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" "$droppedFiles" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt + else + "${JAVALOC}" --add-exports java.desktop/com.apple.eawt=ALL-UNNAMED -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt || "${JAVALOC}" -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt + fi +else #flags passed in; use those + if [[ ${#arr[@]} > 4 ]]; + then + droppedFiles=${arr[4]} #this gets just first file + "${JAVALOC}" ${FLAGS} -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" "$droppedFiles" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt + else + "${JAVALOC}" ${FLAGS} -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt + fi +fi + CheckedForUserDefaultShell + + inputMethod + 0 + shell + /bin/bash + source + + + BundleIdentifier + com.apple.RunShellScript + CFBundleVersion + 2.0.3 + CanShowSelectedItemsWhenRun + + CanShowWhenRun + + Category + + AMCategoryUtilities + + Class Name + RunShellScriptAction + InputUUID + 7EFF0B18-2D72-45C5-9ED5-1550681238D5 + Keywords + + Shell + Script + Command + Run + Unix + + OutputUUID + B0EFEE58-F461-4027-8168-126B947DC10A + UUID + 59BCA6EA-60BF-47F5-8C7B-221B6D2C77B9 + UnlocalizedApplications + + Automator + + arguments + + 0 + + default value + 0 + name + inputMethod + required + 0 + type + 0 + uuid + 0 + + 1 + + default value + + name + source + required + 0 + type + 0 + uuid + 1 + + 2 + + default value + + name + CheckedForUserDefaultShell + required + 0 + type + 0 + uuid + 2 + + 3 + + default value + + name + COMMAND_STRING + required + 0 + type + 0 + uuid + 3 + + 4 + + default value + /bin/sh + name + shell + required + 0 + type + 0 + uuid + 4 + + + isViewVisible + + location + 619.500000:1122.000000 + nibPath + /System/Library/Automator/Run Shell Script.action/Contents/Resources/Base.lproj/main.nib + + isViewVisible + + + + connectors + + 399C77FB-0C53-4532-9B28-DBA63F886CE7 + + from + 35565B5A-57E2-4F76-B8E4-02CE4A8CD9B2 - 35565B5A-57E2-4F76-B8E4-02CE4A8CD9B2 + to + 59BCA6EA-60BF-47F5-8C7B-221B6D2C77B9 - 59BCA6EA-60BF-47F5-8C7B-221B6D2C77B9 + + 8135E9E8-5924-4DFA-A6FD-BDBC382D5D95 + + from + 2528247D-5A8D-4ADD-9481-A0BC58FA668F - 2528247D-5A8D-4ADD-9481-A0BC58FA668F + to + 4F14C189-CB3E-41E7-989A-E209FB44368B - 4F14C189-CB3E-41E7-989A-E209FB44368B + + E3C6E533-95E6-4726-B169-396BD2EE9AF2 + + from + 4F14C189-CB3E-41E7-989A-E209FB44368B - 4F14C189-CB3E-41E7-989A-E209FB44368B + to + 35565B5A-57E2-4F76-B8E4-02CE4A8CD9B2 - 35565B5A-57E2-4F76-B8E4-02CE4A8CD9B2 + + F8046E3E-C18C-4186-8DD4-A5B45DD64886 + + from + 4B07F06B-F2E4-49D5-8009-9C558FB1CD61 - 4B07F06B-F2E4-49D5-8009-9C558FB1CD61 + to + 2528247D-5A8D-4ADD-9481-A0BC58FA668F - 2528247D-5A8D-4ADD-9481-A0BC58FA668F + + + variables + + + UUID + B5724CA0-32E6-41E6-A92D-05F05ECF423A + identifier + com.apple.Automator.Variable.Text + name + DroppedFiles + value + + + + workflowMetaData + + workflowTypeIdentifier + com.apple.Automator.application + + + diff --git a/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-02Icons.app/Contents/Info.plist b/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-02Icons.app/Contents/Info.plist new file mode 100644 index 000000000..696b8c3c8 --- /dev/null +++ b/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-02Icons.app/Contents/Info.plist @@ -0,0 +1,109 @@ + + + + + AMIsApplet + + AMStayOpen + + BuildMachineOSBuild + 17A405001 + CFBundleAllowMixedLocalizations + + CFBundleDevelopmentRegion + English + CFBundleDocumentTypes + + + CFBundleTypeExtensions + + * + + CFBundleTypeName + Automator workflow file + CFBundleTypeOSTypes + + **** + + CFBundleTypeRole + Viewer + + + CFBundleExecutable + Application Stub + CFBundleIconFile + Mesquite.icns + CFBundleIdentifier + com.apple.automator.Mesquite_Starter_Flex-01AutomatorOrig-2021superFlex + CFBundleInfoDictionaryVersion + 6.0 + CFBundleName + Mesquite_Starter_Flex-01AutomatorOrig-2021superFlex + CFBundlePackageType + APPL + CFBundleShortVersionString + 1.3 + CFBundleSignature + ???? + CFBundleSupportedPlatforms + + MacOSX + + CFBundleURLTypes + + CFBundleVersion + 444.42 + DTCompiler + com.apple.compilers.llvm.clang.1_0 + DTPlatformBuild + 10P70r + DTPlatformName + macosx + DTPlatformVersion + 10.14 + DTSDKBuild + 18F82 + DTSDKName + macosx10.14internal + DTXcode + 1020 + DTXcodeBuild + 10P70r + LSMinimumSystemVersion + 10.6 + LSUIElement + + NSAppleEventsUsageDescription + This workflow needs to control other applications to run. + NSAppleMusicUsageDescription + This workflow needs access to your music to run. + NSAppleScriptEnabled + YES + NSCalendarsUsageDescription + This workflow needs access to your calendars to run. + NSCameraUsageDescription + This workflow needs access to your camera to run. + NSContactsUsageDescription + This workflow needs access to your contacts to run. + NSHomeKitUsageDescription + This workflow needs access to your HomeKit Home to run. + NSMicrophoneUsageDescription + This workflow needs access to your microphone to run. + NSPhotoLibraryUsageDescription + This workflow needs access to your photos to run. + NSPrincipalClass + NSApplication + NSRemindersUsageDescription + This workflow needs access to your reminders to run. + NSServices + + NSSiriUsageDescription + This workflow needs access to Siri to run. + NSSystemAdministrationUsageDescription + This workflow needs access to administer this system in order to run. + UTExportedTypeDeclarations + + UTImportedTypeDeclarations + + + diff --git a/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-02Icons.app/Contents/MacOS/Application Stub b/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-02Icons.app/Contents/MacOS/Application Stub new file mode 100755 index 000000000..cf7a2b4da Binary files /dev/null and b/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-02Icons.app/Contents/MacOS/Application Stub differ diff --git a/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-02Icons.app/Contents/Resources/AutomatorApplet.icns b/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-02Icons.app/Contents/Resources/AutomatorApplet.icns new file mode 100644 index 000000000..1e1593e8a Binary files /dev/null and b/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-02Icons.app/Contents/Resources/AutomatorApplet.icns differ diff --git a/Executables/MacOS via 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hash + + jNwtLiX6ZppLZGBT2AduuHGcdmE= + + hash2 + + t4dWkDY6B0lGC8+jvgpisFfDuDs9xvAvpdF4wP5qDm4= + + optional + + + Resources/vi.lproj/InfoPlist.strings + + hash + + uqOH5qBwvrURhmTjwrj17e/Q/OA= + + hash2 + + 7abgjplfjNbOer9I7gCS+rWphilToacAStN3WsPoMJE= + + optional + + + Resources/zh_CN.lproj/InfoPlist.strings + + hash + + zWQq7Cs/duV+X9oGtocw4eBe0ZI= + + hash2 + + +uJpl8cAmlEG1VKEW8XaXb2WftwpgDQc5RW/PKYMw3g= + + optional + + + Resources/zh_HK.lproj/InfoPlist.strings + + hash + + cHW9oL6O2njSMA6S7/aK7SQAMfw= + + hash2 + + EZzoy3pe9XgRvRPcndIgtLoohQAW0ELmXgnzEn/dr3Q= + + optional + + + Resources/zh_TW.lproj/InfoPlist.strings + + hash + + eFrot6B9EZ+pJlUHTqvldd/g3iQ= + + hash2 + + WI5/PxLUfGiBtRa7ubTCLnCoYZoHGI4TN11epsVlWcw= + + optional + + + document.wflow + + cdhash + + 6NdwFLQ2h7b/LRPgMH7QheNAxao= + + requirement + cdhash H"3f7740de4916a0d7aabb3cfc063a42a4972af4de" or cdhash H"e8d77014b43687b6ff2d13e0307ed085e340c5aa" + + + rules + + ^Resources/ + + ^Resources/.*\.lproj/ + + optional + + weight + 1000 + + ^Resources/.*\.lproj/locversion.plist$ + + omit + + weight + 1100 + + ^Resources/Base\.lproj/ + + weight + 1010 + + ^version.plist$ + + + rules2 + + .*\.dSYM($|/) + + weight + 11 + + ^(.*/)?\.DS_Store$ + + omit + + weight + 2000 + + ^(Frameworks|SharedFrameworks|PlugIns|Plug-ins|XPCServices|Helpers|MacOS|Library/(Automator|Spotlight|LoginItems))/ + + nested + + weight + 10 + + ^.* + + ^Info\.plist$ + + omit + + weight + 20 + + ^PkgInfo$ + + omit + + weight + 20 + + ^Resources/ + + weight + 20 + + ^Resources/.*\.lproj/ + + optional + + weight + 1000 + + ^Resources/.*\.lproj/locversion.plist$ + + omit + + weight + 1100 + + ^Resources/Base\.lproj/ + + weight + 1010 + + ^[^/]+$ + + nested + + weight + 10 + + ^embedded\.provisionprofile$ + + weight + 20 + + ^version\.plist$ + + weight + 20 + + + + diff --git a/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-02Icons.app/Contents/document.wflow b/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-02Icons.app/Contents/document.wflow new file mode 100644 index 000000000..eac06a7de --- /dev/null +++ b/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-02Icons.app/Contents/document.wflow @@ -0,0 +1,706 @@ + + + + + AMApplicationBuild + 444.42 + AMApplicationVersion + 2.9 + AMDocumentVersion + 2 + actions + + + action + + AMAccepts + + Container + List + Optional + + Types + + * + + + AMActionVersion + v.1.0.2 + AMApplication + + Automator + + AMParameterProperties + + variableUUID + + isPathPopUp + + selectedVariableUUID + B5724CA0-32E6-41E6-A92D-05F05ECF423A + + + AMProvides + + Container + List + Types + + * + + + AMRequiredResources + + ActionBundlePath + /System/Library/Automator/Set Value of Variable.action + ActionName + Set Value of Variable + ActionParameters + + variableUUID + B5724CA0-32E6-41E6-A92D-05F05ECF423A + + BundleIdentifier + com.apple.Automator.SetValueofVariable + CFBundleVersion + 1.0.2 + CanShowSelectedItemsWhenRun + + CanShowWhenRun + + Category + + AMCategoryUtilities + + Class Name + Set_Value_of_Variable + InputUUID + 43FB1F79-4EA6-4AA7-A306-B9BCE6E21896 + Keywords + + variable + binding + input + output + storage + + OutputUUID + E791B933-EFA9-43EE-B7B4-F8F6C5EE0E4A + UUID + 4B07F06B-F2E4-49D5-8009-9C558FB1CD61 + UnlocalizedApplications + + Automator + + arguments + + 0 + + default value + + name + variableUUID + required + 0 + type + 0 + uuid + 0 + + + isViewVisible + + location + 619.500000:111.000000 + nibPath + /System/Library/Automator/Set Value of Variable.action/Contents/Resources/Base.lproj/main.nib + + isViewVisible + + + + action + + AMAccepts + + Container + List + Optional + + Types + + com.apple.cocoa.path + + + AMActionVersion + 1.2.2 + AMApplication + + Finder + + AMParameterProperties + + newName + + tokenizedValue + + Mesquite_Support_Files + + + targetLocation + + isPathPopUp + + variableUUIDsInMenu + + + + AMProvides + + Container + List + Types + + public.folder + + + ActionBundlePath + /System/Library/Automator/New Folder.action + ActionName + New Folder + ActionParameters + + newName + Mesquite_Support_Files + targetLocation + ~ + + BundleIdentifier + com.apple.Automator.MakeNewFolder + CFBundleVersion + 1.2.2 + CanShowSelectedItemsWhenRun + + CanShowWhenRun + + Category + + AMCategoryFilesAndFolders + + Class Name + NewFolderAction + IgnoresInput + + InputUUID + 7F253106-A965-4ABC-97FD-1FD2D52366A4 + Keywords + + Folder + Create + Make + New + + OutputUUID + 8EA1A9AF-B3C7-46F2-B605-CDBB38797DA9 + UUID + 2528247D-5A8D-4ADD-9481-A0BC58FA668F + UnlocalizedApplications + + Finder + + arguments + + 0 + + default value + + name + newName + required + 0 + type + 0 + uuid + 0 + + 1 + + default value + ~/Desktop + name + targetLocation + required + 0 + type + 0 + uuid + 1 + + + isViewVisible + + location + 619.500000:152.000000 + nibPath + /System/Library/Automator/New Folder.action/Contents/Resources/Base.lproj/main.nib + + isViewVisible + + + + action + + AMAccepts + + Container + List + Optional + + Types + + * + + + AMActionVersion + v.1.0.2 + AMApplication + + Automator + + AMParameterProperties + + variableUUID + + isPathPopUp + + selectedVariableUUID + B5724CA0-32E6-41E6-A92D-05F05ECF423A + + + AMProvides + + Container + List + Types + + * + + + AMRequiredResources + + ActionBundlePath + /System/Library/Automator/Get Value of Variable.action + ActionName + Get Value of Variable + ActionParameters + + variableUUID + B5724CA0-32E6-41E6-A92D-05F05ECF423A + + BundleIdentifier + com.apple.Automator.GetValueofVariable + CFBundleVersion + 1.0.2 + CanShowSelectedItemsWhenRun + + CanShowWhenRun + + Category + + AMCategoryUtilities + + Class Name + Get_Value_of_Variable + IgnoresInput + + InputUUID + B3699B55-670C-4E04-8062-7A25776314F6 + Keywords + + variable + binding + input + output + storage + + OutputUUID + 342F6FBC-A8B4-4AB8-8488-094942236BD7 + UUID + 4F14C189-CB3E-41E7-989A-E209FB44368B + UnlocalizedApplications + + Automator + + arguments + + 0 + + default value + + name + variableUUID + required + 0 + type + 0 + uuid + 0 + + + isViewVisible + + location + 619.500000:193.000000 + nibPath + /System/Library/Automator/Get Value of Variable.action/Contents/Resources/Base.lproj/main.nib + + isViewVisible + + + + action + + AMAccepts + + Container + List + Optional + + Types + + com.apple.applescript.object + + + AMActionVersion + 1.0.2 + AMApplication + + Automator + + AMParameterProperties + + source + + + AMProvides + + Container + List + Types + + com.apple.applescript.object + + + ActionBundlePath + /System/Library/Automator/Run AppleScript.action + ActionName + Run AppleScript + ActionParameters + + source + on getPath(this_text, stripLast) set AppleScript's text item delimiters to the ":" set the item_list to every text item of this_text set num to the number of items in item_list if stripLast then set lasti to num - 2 else set lasti to num end if set the item_list to items 2 through lasti of item_list set AppleScript's text item delimiters to the "/" set this_text to the item_list as string set AppleScript's text item delimiters to "" set this_text to "/" & this_text return this_text end getPath on run {input, parameters} set whereAmI to getPath((path to me as text), true) set javaLocFile to whereAmI & "/RunningOptionsForFlex/Mesquite-JavaToUse.txt" set javaLoc to "java" try set lns to paragraphs of (read POSIX file javaLocFile) set javaLoc to first item in lns end try set memoryFile to whereAmI & "/RunningOptionsForFlex/Mesquite-MemoryToUse.txt" set memory to 1 try set lns to paragraphs of (read POSIX file memoryFile) set memory to first item in lns end try set flagsFile to whereAmI & "/RunningOptionsForFlex/Mesquite-FlagsToUse.txt" set flags to "" try set lns to paragraphs of (read POSIX file flagsFile) set flags to first item in lns end try #display dialog memory as text set results to whereAmI try if input is not equal to {} then set droppedFiles to getPath(input as text, false) set results to results & ":" & droppedFiles end if end try set results to javaLoc & ":" & flags & ":" &memory & ":" & results return results end run + + BundleIdentifier + com.apple.Automator.RunScript + CFBundleVersion + 1.0.2 + CanShowSelectedItemsWhenRun + + CanShowWhenRun + + Category + + AMCategoryUtilities + + Class Name + RunScriptAction + InputUUID + 11F3EFA2-BE3D-4DD3-A24A-AFC7373B06F3 + Keywords + + Run + + OutputUUID + F42FD833-E0EE-4550-88BA-39A54F93799B + UUID + 35565B5A-57E2-4F76-B8E4-02CE4A8CD9B2 + UnlocalizedApplications + + Automator + + arguments + + 0 + + default value + on run {input, parameters} + + (* Your script goes here *) + + return input +end run + name + source + required + 0 + type + 0 + uuid + 0 + + + isViewVisible + + location + 619.500000:438.000000 + nibPath + /System/Library/Automator/Run AppleScript.action/Contents/Resources/Base.lproj/main.nib + + isViewVisible + + + + action + + AMAccepts + + Container + List + Optional + + Types + + com.apple.cocoa.string + + + AMActionVersion + 2.0.3 + AMApplication + + Automator + + AMParameterProperties + + COMMAND_STRING + + CheckedForUserDefaultShell + + inputMethod + + shell + + source + + + AMProvides + + Container + List + Types + + com.apple.cocoa.string + + + ActionBundlePath + /System/Library/Automator/Run Shell Script.action + ActionName + Run Shell Script + ActionParameters + + COMMAND_STRING + read whereAndWhat #where is Mesquite Folder, and what are dropped files +echo $whereAndWhat > Mesquite_Support_Files/Mesquite_Flex_INSTRUCTIONS.txt +IFS=':' read -r -a arr <<< "$whereAndWhat" +JAVALOC=${arr[0]} +FLAGS=${arr[1]} +MEMORY=${arr[2]} +whereAmI=${arr[3]} +if [[ ${#myvar} <1 ]]; #no flags passed in +then + if [[ ${#arr[@]} > 4 ]]; + then + droppedFiles=${arr[4]} #this gets just first file + "${JAVALOC}" --add-exports java.desktop/com.apple.eawt=ALL-UNNAMED -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" "$droppedFiles" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt || "${JAVALOC}" -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" "$droppedFiles" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt + else + "${JAVALOC}" --add-exports java.desktop/com.apple.eawt=ALL-UNNAMED -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt || "${JAVALOC}" -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt + fi +else #flags passed in; use those + if [[ ${#arr[@]} > 4 ]]; + then + droppedFiles=${arr[4]} #this gets just first file + "${JAVALOC}" ${FLAGS} -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" "$droppedFiles" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt + else + "${JAVALOC}" ${FLAGS} -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt + fi +fi + CheckedForUserDefaultShell + + inputMethod + 0 + shell + /bin/bash + source + + + BundleIdentifier + com.apple.RunShellScript + CFBundleVersion + 2.0.3 + CanShowSelectedItemsWhenRun + + CanShowWhenRun + + Category + + AMCategoryUtilities + + Class Name + RunShellScriptAction + InputUUID + 7EFF0B18-2D72-45C5-9ED5-1550681238D5 + Keywords + + Shell + Script + Command + Run + Unix + + OutputUUID + B0EFEE58-F461-4027-8168-126B947DC10A + UUID + 59BCA6EA-60BF-47F5-8C7B-221B6D2C77B9 + UnlocalizedApplications + + Automator + + arguments + + 0 + + default value + 0 + name + inputMethod + required + 0 + type + 0 + uuid + 0 + + 1 + + default value + + name + source + required + 0 + type + 0 + uuid + 1 + + 2 + + default value + + name + CheckedForUserDefaultShell + required + 0 + type + 0 + uuid + 2 + + 3 + + default value + + name + COMMAND_STRING + required + 0 + type + 0 + uuid + 3 + + 4 + + default value + /bin/sh + name + shell + required + 0 + type + 0 + uuid + 4 + + + isViewVisible + + location + 619.500000:1122.000000 + nibPath + /System/Library/Automator/Run Shell Script.action/Contents/Resources/Base.lproj/main.nib + + isViewVisible + + + + connectors + + 399C77FB-0C53-4532-9B28-DBA63F886CE7 + + from + 35565B5A-57E2-4F76-B8E4-02CE4A8CD9B2 - 35565B5A-57E2-4F76-B8E4-02CE4A8CD9B2 + to + 59BCA6EA-60BF-47F5-8C7B-221B6D2C77B9 - 59BCA6EA-60BF-47F5-8C7B-221B6D2C77B9 + + 8135E9E8-5924-4DFA-A6FD-BDBC382D5D95 + + from + 2528247D-5A8D-4ADD-9481-A0BC58FA668F - 2528247D-5A8D-4ADD-9481-A0BC58FA668F + to + 4F14C189-CB3E-41E7-989A-E209FB44368B - 4F14C189-CB3E-41E7-989A-E209FB44368B + + E3C6E533-95E6-4726-B169-396BD2EE9AF2 + + from + 4F14C189-CB3E-41E7-989A-E209FB44368B - 4F14C189-CB3E-41E7-989A-E209FB44368B + to + 35565B5A-57E2-4F76-B8E4-02CE4A8CD9B2 - 35565B5A-57E2-4F76-B8E4-02CE4A8CD9B2 + + F8046E3E-C18C-4186-8DD4-A5B45DD64886 + + from + 4B07F06B-F2E4-49D5-8009-9C558FB1CD61 - 4B07F06B-F2E4-49D5-8009-9C558FB1CD61 + to + 2528247D-5A8D-4ADD-9481-A0BC58FA668F - 2528247D-5A8D-4ADD-9481-A0BC58FA668F + + + variables + + + UUID + B5724CA0-32E6-41E6-A92D-05F05ECF423A + identifier + com.apple.Automator.Variable.Text + name + DroppedFiles + value + + + + workflowMetaData + + workflowTypeIdentifier + com.apple.Automator.application + + + diff --git a/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-03SignedNotarized.app/Contents/CodeResources b/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-03SignedNotarized.app/Contents/CodeResources new file mode 100755 index 000000000..dd642e059 Binary files /dev/null and b/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-03SignedNotarized.app/Contents/CodeResources differ diff --git a/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-03SignedNotarized.app/Contents/Info.plist b/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-03SignedNotarized.app/Contents/Info.plist new file mode 100755 index 000000000..696b8c3c8 --- /dev/null +++ b/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-03SignedNotarized.app/Contents/Info.plist @@ -0,0 +1,109 @@ + + + + + AMIsApplet + + AMStayOpen + + BuildMachineOSBuild + 17A405001 + CFBundleAllowMixedLocalizations + + CFBundleDevelopmentRegion + English + CFBundleDocumentTypes + + + CFBundleTypeExtensions + + * + + CFBundleTypeName + Automator workflow file + CFBundleTypeOSTypes + + **** + + CFBundleTypeRole + Viewer + + + CFBundleExecutable + Application Stub + CFBundleIconFile + Mesquite.icns + CFBundleIdentifier + com.apple.automator.Mesquite_Starter_Flex-01AutomatorOrig-2021superFlex + CFBundleInfoDictionaryVersion + 6.0 + CFBundleName + Mesquite_Starter_Flex-01AutomatorOrig-2021superFlex + CFBundlePackageType + APPL + CFBundleShortVersionString + 1.3 + CFBundleSignature + ???? + CFBundleSupportedPlatforms + + MacOSX + + CFBundleURLTypes + + CFBundleVersion + 444.42 + DTCompiler + com.apple.compilers.llvm.clang.1_0 + DTPlatformBuild + 10P70r + DTPlatformName + macosx + DTPlatformVersion + 10.14 + DTSDKBuild + 18F82 + DTSDKName + macosx10.14internal + DTXcode + 1020 + DTXcodeBuild + 10P70r + LSMinimumSystemVersion + 10.6 + LSUIElement + + NSAppleEventsUsageDescription + This workflow needs to control other applications to run. + NSAppleMusicUsageDescription + This workflow needs access to your music to run. + NSAppleScriptEnabled + YES + NSCalendarsUsageDescription + This workflow needs access to your calendars to run. + NSCameraUsageDescription + This workflow needs access to your camera to run. + NSContactsUsageDescription + This workflow needs access to your contacts to run. + NSHomeKitUsageDescription + This workflow needs access to your HomeKit Home to run. + NSMicrophoneUsageDescription + This workflow needs access to your microphone to run. + NSPhotoLibraryUsageDescription + This workflow needs access to your photos to run. + NSPrincipalClass + NSApplication + NSRemindersUsageDescription + This workflow needs access to your reminders to run. + NSServices + + NSSiriUsageDescription + This workflow needs access to Siri to run. + NSSystemAdministrationUsageDescription + This workflow needs access to administer this system in order to run. + UTExportedTypeDeclarations + + UTImportedTypeDeclarations + + + diff --git a/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-03SignedNotarized.app/Contents/MacOS/Application Stub b/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-03SignedNotarized.app/Contents/MacOS/Application Stub new file mode 100755 index 000000000..3de3c5e74 Binary files /dev/null and b/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-03SignedNotarized.app/Contents/MacOS/Application Stub differ diff --git a/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-03SignedNotarized.app/Contents/Resources/AutomatorApplet.icns b/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-03SignedNotarized.app/Contents/Resources/AutomatorApplet.icns new file mode 100755 index 000000000..1e1593e8a Binary files /dev/null and b/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-03SignedNotarized.app/Contents/Resources/AutomatorApplet.icns differ diff --git a/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-03SignedNotarized.app/Contents/Resources/Mesquite.icns b/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-03SignedNotarized.app/Contents/Resources/Mesquite.icns new file mode 100755 index 000000000..280d8334a Binary files /dev/null and b/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-03SignedNotarized.app/Contents/Resources/Mesquite.icns differ diff --git a/Executables/MacOS via Automator and 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^Resources/.*\.lproj/locversion.plist$ + + omit + + weight + 1100 + + ^Resources/Base\.lproj/ + + weight + 1010 + + ^version.plist$ + + + rules2 + + .*\.dSYM($|/) + + weight + 11 + + ^(.*/)?\.DS_Store$ + + omit + + weight + 2000 + + ^(Frameworks|SharedFrameworks|PlugIns|Plug-ins|XPCServices|Helpers|MacOS|Library/(Automator|Spotlight|LoginItems))/ + + nested + + weight + 10 + + ^.* + + ^Info\.plist$ + + omit + + weight + 20 + + ^PkgInfo$ + + omit + + weight + 20 + + ^Resources/ + + weight + 20 + + ^Resources/.*\.lproj/ + + optional + + weight + 1000 + + ^Resources/.*\.lproj/locversion.plist$ + + omit + + weight + 1100 + + ^Resources/Base\.lproj/ + + weight + 1010 + + ^[^/]+$ + + nested + + weight + 10 + + ^embedded\.provisionprofile$ + + weight + 20 + + ^version\.plist$ + + weight + 20 + + + + diff --git a/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-03SignedNotarized.app/Contents/document.wflow b/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-03SignedNotarized.app/Contents/document.wflow new file mode 100755 index 000000000..eac06a7de --- /dev/null +++ b/Executables/MacOS via Automator and Script/Mesquite_Starter_Flex-03SignedNotarized.app/Contents/document.wflow @@ -0,0 +1,706 @@ + + + + + AMApplicationBuild + 444.42 + AMApplicationVersion + 2.9 + AMDocumentVersion + 2 + actions + + + action + + AMAccepts + + Container + List + Optional + + Types + + * + + + AMActionVersion + v.1.0.2 + AMApplication + + Automator + + AMParameterProperties + + variableUUID + + isPathPopUp + + selectedVariableUUID + B5724CA0-32E6-41E6-A92D-05F05ECF423A + + + AMProvides + + Container + List + Types + + * + + + AMRequiredResources + + ActionBundlePath + /System/Library/Automator/Set Value of Variable.action + ActionName + Set Value of Variable + ActionParameters + + variableUUID + B5724CA0-32E6-41E6-A92D-05F05ECF423A + + BundleIdentifier + com.apple.Automator.SetValueofVariable + CFBundleVersion + 1.0.2 + CanShowSelectedItemsWhenRun + + CanShowWhenRun + + Category + + AMCategoryUtilities + + Class Name + Set_Value_of_Variable + InputUUID + 43FB1F79-4EA6-4AA7-A306-B9BCE6E21896 + Keywords + + variable + binding + input + output + storage + + OutputUUID + E791B933-EFA9-43EE-B7B4-F8F6C5EE0E4A + UUID + 4B07F06B-F2E4-49D5-8009-9C558FB1CD61 + UnlocalizedApplications + + Automator + + arguments + + 0 + + default value + + name + variableUUID + required + 0 + type + 0 + uuid + 0 + + + isViewVisible + + location + 619.500000:111.000000 + nibPath + /System/Library/Automator/Set Value of Variable.action/Contents/Resources/Base.lproj/main.nib + + isViewVisible + + + + action + + AMAccepts + + Container + List + Optional + + Types + + com.apple.cocoa.path + + + AMActionVersion + 1.2.2 + AMApplication + + Finder + + AMParameterProperties + + newName + + tokenizedValue + + Mesquite_Support_Files + + + targetLocation + + isPathPopUp + + variableUUIDsInMenu + + + + AMProvides + + Container + List + Types + + public.folder + + + ActionBundlePath + /System/Library/Automator/New Folder.action + ActionName + New Folder + ActionParameters + + newName + Mesquite_Support_Files + targetLocation + ~ + + BundleIdentifier + com.apple.Automator.MakeNewFolder + CFBundleVersion + 1.2.2 + CanShowSelectedItemsWhenRun + + CanShowWhenRun + + Category + + AMCategoryFilesAndFolders + + Class Name + NewFolderAction + IgnoresInput + + InputUUID + 7F253106-A965-4ABC-97FD-1FD2D52366A4 + Keywords + + Folder + Create + Make + New + + OutputUUID + 8EA1A9AF-B3C7-46F2-B605-CDBB38797DA9 + UUID + 2528247D-5A8D-4ADD-9481-A0BC58FA668F + UnlocalizedApplications + + Finder + + arguments + + 0 + + default value + + name + newName + required + 0 + type + 0 + uuid + 0 + + 1 + + default value + ~/Desktop + name + targetLocation + required + 0 + type + 0 + uuid + 1 + + + isViewVisible + + location + 619.500000:152.000000 + nibPath + /System/Library/Automator/New Folder.action/Contents/Resources/Base.lproj/main.nib + + isViewVisible + + + + action + + AMAccepts + + Container + List + Optional + + Types + + * + + + AMActionVersion + v.1.0.2 + AMApplication + + Automator + + AMParameterProperties + + variableUUID + + isPathPopUp + + selectedVariableUUID + B5724CA0-32E6-41E6-A92D-05F05ECF423A + + + AMProvides + + Container + List + Types + + * + + + AMRequiredResources + + ActionBundlePath + /System/Library/Automator/Get Value of Variable.action + ActionName + Get Value of Variable + ActionParameters + + variableUUID + B5724CA0-32E6-41E6-A92D-05F05ECF423A + + BundleIdentifier + com.apple.Automator.GetValueofVariable + CFBundleVersion + 1.0.2 + CanShowSelectedItemsWhenRun + + CanShowWhenRun + + Category + + AMCategoryUtilities + + Class Name + Get_Value_of_Variable + IgnoresInput + + InputUUID + B3699B55-670C-4E04-8062-7A25776314F6 + Keywords + + variable + binding + input + output + storage + + OutputUUID + 342F6FBC-A8B4-4AB8-8488-094942236BD7 + UUID + 4F14C189-CB3E-41E7-989A-E209FB44368B + UnlocalizedApplications + + Automator + + arguments + + 0 + + default value + + name + variableUUID + required + 0 + type + 0 + uuid + 0 + + + isViewVisible + + location + 619.500000:193.000000 + nibPath + /System/Library/Automator/Get Value of Variable.action/Contents/Resources/Base.lproj/main.nib + + isViewVisible + + + + action + + AMAccepts + + Container + List + Optional + + Types + + com.apple.applescript.object + + + AMActionVersion + 1.0.2 + AMApplication + + Automator + + AMParameterProperties + + source + + + AMProvides + + Container + List + Types + + com.apple.applescript.object + + + ActionBundlePath + /System/Library/Automator/Run AppleScript.action + ActionName + Run AppleScript + ActionParameters + + source + on getPath(this_text, stripLast) set AppleScript's text item delimiters to the ":" set the item_list to every text item of this_text set num to the number of items in item_list if stripLast then set lasti to num - 2 else set lasti to num end if set the item_list to items 2 through lasti of item_list set AppleScript's text item delimiters to the "/" set this_text to the item_list as string set AppleScript's text item delimiters to "" set this_text to "/" & this_text return this_text end getPath on run {input, parameters} set whereAmI to getPath((path to me as text), true) set javaLocFile to whereAmI & "/RunningOptionsForFlex/Mesquite-JavaToUse.txt" set javaLoc to "java" try set lns to paragraphs of (read POSIX file javaLocFile) set javaLoc to first item in lns end try set memoryFile to whereAmI & "/RunningOptionsForFlex/Mesquite-MemoryToUse.txt" set memory to 1 try set lns to paragraphs of (read POSIX file memoryFile) set memory to first item in lns end try set flagsFile to whereAmI & "/RunningOptionsForFlex/Mesquite-FlagsToUse.txt" set flags to "" try set lns to paragraphs of (read POSIX file flagsFile) set flags to first item in lns end try #display dialog memory as text set results to whereAmI try if input is not equal to {} then set droppedFiles to getPath(input as text, false) set results to results & ":" & droppedFiles end if end try set results to javaLoc & ":" & flags & ":" &memory & ":" & results return results end run + + BundleIdentifier + com.apple.Automator.RunScript + CFBundleVersion + 1.0.2 + CanShowSelectedItemsWhenRun + + CanShowWhenRun + + Category + + AMCategoryUtilities + + Class Name + RunScriptAction + InputUUID + 11F3EFA2-BE3D-4DD3-A24A-AFC7373B06F3 + Keywords + + Run + + OutputUUID + F42FD833-E0EE-4550-88BA-39A54F93799B + UUID + 35565B5A-57E2-4F76-B8E4-02CE4A8CD9B2 + UnlocalizedApplications + + Automator + + arguments + + 0 + + default value + on run {input, parameters} + + (* Your script goes here *) + + return input +end run + name + source + required + 0 + type + 0 + uuid + 0 + + + isViewVisible + + location + 619.500000:438.000000 + nibPath + /System/Library/Automator/Run AppleScript.action/Contents/Resources/Base.lproj/main.nib + + isViewVisible + + + + action + + AMAccepts + + Container + List + Optional + + Types + + com.apple.cocoa.string + + + AMActionVersion + 2.0.3 + AMApplication + + Automator + + AMParameterProperties + + COMMAND_STRING + + CheckedForUserDefaultShell + + inputMethod + + shell + + source + + + AMProvides + + Container + List + Types + + com.apple.cocoa.string + + + ActionBundlePath + /System/Library/Automator/Run Shell Script.action + ActionName + Run Shell Script + ActionParameters + + COMMAND_STRING + read whereAndWhat #where is Mesquite Folder, and what are dropped files +echo $whereAndWhat > Mesquite_Support_Files/Mesquite_Flex_INSTRUCTIONS.txt +IFS=':' read -r -a arr <<< "$whereAndWhat" +JAVALOC=${arr[0]} +FLAGS=${arr[1]} +MEMORY=${arr[2]} +whereAmI=${arr[3]} +if [[ ${#myvar} <1 ]]; #no flags passed in +then + if [[ ${#arr[@]} > 4 ]]; + then + droppedFiles=${arr[4]} #this gets just first file + "${JAVALOC}" --add-exports java.desktop/com.apple.eawt=ALL-UNNAMED -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" "$droppedFiles" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt || "${JAVALOC}" -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" "$droppedFiles" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt + else + "${JAVALOC}" --add-exports java.desktop/com.apple.eawt=ALL-UNNAMED -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt || "${JAVALOC}" -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt + fi +else #flags passed in; use those + if [[ ${#arr[@]} > 4 ]]; + then + droppedFiles=${arr[4]} #this gets just first file + "${JAVALOC}" ${FLAGS} -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" "$droppedFiles" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt + else + "${JAVALOC}" ${FLAGS} -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt + fi +fi + CheckedForUserDefaultShell + + inputMethod + 0 + shell + /bin/bash + source + + + BundleIdentifier + com.apple.RunShellScript + CFBundleVersion + 2.0.3 + CanShowSelectedItemsWhenRun + + CanShowWhenRun + + Category + + AMCategoryUtilities + + Class Name + RunShellScriptAction + InputUUID + 7EFF0B18-2D72-45C5-9ED5-1550681238D5 + Keywords + + Shell + Script + Command + Run + Unix + + OutputUUID + B0EFEE58-F461-4027-8168-126B947DC10A + UUID + 59BCA6EA-60BF-47F5-8C7B-221B6D2C77B9 + UnlocalizedApplications + + Automator + + arguments + + 0 + + default value + 0 + name + inputMethod + required + 0 + type + 0 + uuid + 0 + + 1 + + default value + + name + source + required + 0 + type + 0 + uuid + 1 + + 2 + + default value + + name + CheckedForUserDefaultShell + required + 0 + type + 0 + uuid + 2 + + 3 + + default value + + name + COMMAND_STRING + required + 0 + type + 0 + uuid + 3 + + 4 + + default value + /bin/sh + name + shell + required + 0 + type + 0 + uuid + 4 + + + isViewVisible + + location + 619.500000:1122.000000 + nibPath + /System/Library/Automator/Run Shell Script.action/Contents/Resources/Base.lproj/main.nib + + isViewVisible + + + + connectors + + 399C77FB-0C53-4532-9B28-DBA63F886CE7 + + from + 35565B5A-57E2-4F76-B8E4-02CE4A8CD9B2 - 35565B5A-57E2-4F76-B8E4-02CE4A8CD9B2 + to + 59BCA6EA-60BF-47F5-8C7B-221B6D2C77B9 - 59BCA6EA-60BF-47F5-8C7B-221B6D2C77B9 + + 8135E9E8-5924-4DFA-A6FD-BDBC382D5D95 + + from + 2528247D-5A8D-4ADD-9481-A0BC58FA668F - 2528247D-5A8D-4ADD-9481-A0BC58FA668F + to + 4F14C189-CB3E-41E7-989A-E209FB44368B - 4F14C189-CB3E-41E7-989A-E209FB44368B + + E3C6E533-95E6-4726-B169-396BD2EE9AF2 + + from + 4F14C189-CB3E-41E7-989A-E209FB44368B - 4F14C189-CB3E-41E7-989A-E209FB44368B + to + 35565B5A-57E2-4F76-B8E4-02CE4A8CD9B2 - 35565B5A-57E2-4F76-B8E4-02CE4A8CD9B2 + + F8046E3E-C18C-4186-8DD4-A5B45DD64886 + + from + 4B07F06B-F2E4-49D5-8009-9C558FB1CD61 - 4B07F06B-F2E4-49D5-8009-9C558FB1CD61 + to + 2528247D-5A8D-4ADD-9481-A0BC58FA668F - 2528247D-5A8D-4ADD-9481-A0BC58FA668F + + + variables + + + UUID + B5724CA0-32E6-41E6-A92D-05F05ECF423A + identifier + com.apple.Automator.Variable.Text + name + DroppedFiles + value + + + + workflowMetaData + + workflowTypeIdentifier + com.apple.Automator.application + + + diff --git a/Executables/MacOS via Automator and Script/RunningOptionsForFlex/Mesquite-FlagsToUse.txt b/Executables/MacOS via Automator and Script/RunningOptionsForFlex/Mesquite-FlagsToUse.txt new file mode 100644 index 000000000..8b04e0479 --- /dev/null +++ b/Executables/MacOS via Automator and Script/RunningOptionsForFlex/Mesquite-FlagsToUse.txt @@ -0,0 +1,20 @@ + + + +INSTRUCTIONS +The first line, above, is used as additional information for Mesquite to start by "Mesquite-Starter-Flex.app". These "flags" are important to get Mesquite to work with some version of Java. + +If the line is blank, this means that no flags will be added. + +For Java 1.8 and many others, you can leave the first line blank. + +Below is a suggested alternative: + +Java 16: +--add-exports java.desktop/com.apple.eawt=ALL-UNNAMED + +The above flag is needed for Mesquite to function well under some newer versions of Java (e.g., Java 16). + + +--add-opens java.base/java.net=ALL-UNNAMED +java.lang.reflect.InaccessibleObjectException: Unable to make protected void java.net.URLClassLoader.addURL(java.net.URL) accessible: module java.base does not "opens java.net" to unnamed module @7229724f diff --git a/Executables/MacOS via Automator and Script/RunningOptionsForFlex/Mesquite-JavaToUse.txt b/Executables/MacOS via Automator and Script/RunningOptionsForFlex/Mesquite-JavaToUse.txt new file mode 100644 index 000000000..e84761a75 --- /dev/null +++ b/Executables/MacOS via Automator and Script/RunningOptionsForFlex/Mesquite-JavaToUse.txt @@ -0,0 +1,17 @@ +java + +INSTRUCTIONS +The first line, above, is used as the path to the version of Java to be used by "Mesquite-Starter-Flex.app" + +Below is a library of suggested alternatives: + +DEFAULT: +java + +Place the above line as the first line of this file if you want to use your system's current default version of Java. If it is a very new version, e.g. Java 16, you may need to set a flag (see Mesquite-FlagsForFlex.txt) + +JAVA 1.8: +/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/bin/java + +Place the above line as the first line of this file if you want to use Java 1.8 on some versions of Mesquite. It works for macOS mojave, Catalina and Big Sur, assuming Java 1.8 is installed. You can get Java 1.8 from java.com. + diff --git a/Executables/MacOS via Automator and Script/RunningOptionsForFlex/Mesquite-MemoryToUse.txt b/Executables/MacOS via Automator and Script/RunningOptionsForFlex/Mesquite-MemoryToUse.txt new file mode 100644 index 000000000..a3b4b00fb --- /dev/null +++ b/Executables/MacOS via Automator and Script/RunningOptionsForFlex/Mesquite-MemoryToUse.txt @@ -0,0 +1,4 @@ +2 + +INSTRUCTIONS +On the first line, place the number of gigabytes of active memory (RAM) to reserve for Mesquite when run by "Mesquite-Starter-Flex.app". Use at least 1. Suggested is 2 or 4, or more if you have a very large set of taxa or sequence data. \ No newline at end of file diff --git a/Executables/MacOS via Automator and Script/automatorForMesquiteExecutable.png b/Executables/MacOS via Automator and Script/automatorForMesquiteExecutable.png new file mode 100644 index 000000000..1e5cc2c75 Binary files /dev/null and b/Executables/MacOS via Automator and Script/automatorForMesquiteExecutable.png differ diff --git a/Executables/MacOS via Automator and Script/current executables.zip b/Executables/MacOS via Automator and Script/current executables.zip new file mode 100644 index 000000000..a8bb40464 Binary files /dev/null and b/Executables/MacOS via Automator and Script/current executables.zip differ diff --git a/Executables/MacOS via Automator and Script/current executables/Mesquite_Starter_Flex.app/Contents/CodeResources b/Executables/MacOS via Automator and Script/current executables/Mesquite_Starter_Flex.app/Contents/CodeResources new file mode 100755 index 000000000..dd642e059 Binary files /dev/null and b/Executables/MacOS via Automator and Script/current executables/Mesquite_Starter_Flex.app/Contents/CodeResources differ diff --git a/Executables/MacOS via Automator and Script/current executables/Mesquite_Starter_Flex.app/Contents/Info.plist b/Executables/MacOS via Automator and Script/current executables/Mesquite_Starter_Flex.app/Contents/Info.plist new file mode 100755 index 000000000..696b8c3c8 --- /dev/null +++ b/Executables/MacOS via Automator and Script/current executables/Mesquite_Starter_Flex.app/Contents/Info.plist @@ -0,0 +1,109 @@ + + + + + AMIsApplet + + AMStayOpen + + BuildMachineOSBuild + 17A405001 + CFBundleAllowMixedLocalizations + + CFBundleDevelopmentRegion + English + CFBundleDocumentTypes + + + CFBundleTypeExtensions + + * + + CFBundleTypeName + Automator workflow file + CFBundleTypeOSTypes + + **** + + CFBundleTypeRole + Viewer + + + CFBundleExecutable + Application Stub + CFBundleIconFile + Mesquite.icns + CFBundleIdentifier + com.apple.automator.Mesquite_Starter_Flex-01AutomatorOrig-2021superFlex + CFBundleInfoDictionaryVersion + 6.0 + CFBundleName + Mesquite_Starter_Flex-01AutomatorOrig-2021superFlex + CFBundlePackageType + APPL + CFBundleShortVersionString + 1.3 + CFBundleSignature + ???? + CFBundleSupportedPlatforms + + MacOSX + + CFBundleURLTypes + + CFBundleVersion + 444.42 + DTCompiler + com.apple.compilers.llvm.clang.1_0 + DTPlatformBuild + 10P70r + DTPlatformName + macosx + DTPlatformVersion + 10.14 + DTSDKBuild + 18F82 + DTSDKName + macosx10.14internal + DTXcode + 1020 + DTXcodeBuild + 10P70r + LSMinimumSystemVersion + 10.6 + LSUIElement + + NSAppleEventsUsageDescription + This workflow needs to control other applications to run. + NSAppleMusicUsageDescription + This workflow needs access to your music to run. + NSAppleScriptEnabled + YES + NSCalendarsUsageDescription + This workflow needs access to your calendars to run. + NSCameraUsageDescription + This workflow needs access to your camera to run. + NSContactsUsageDescription + This workflow needs access to your contacts to run. + NSHomeKitUsageDescription + This workflow needs access to your HomeKit Home to run. + NSMicrophoneUsageDescription + This workflow needs access to your microphone to run. + NSPhotoLibraryUsageDescription + This workflow needs access to your photos to run. + NSPrincipalClass + NSApplication + NSRemindersUsageDescription + This workflow needs access to your reminders to run. + NSServices + + NSSiriUsageDescription + This workflow needs access to Siri to run. + NSSystemAdministrationUsageDescription + This workflow needs access to administer this system in order to run. + UTExportedTypeDeclarations + + UTImportedTypeDeclarations + + + diff --git a/Executables/MacOS via Automator and Script/current executables/Mesquite_Starter_Flex.app/Contents/MacOS/Application Stub b/Executables/MacOS via Automator and Script/current 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dqkOqhirv9LBWpRS3Ln9Ls/ErbADeyYmW0UwFzpdrb4= + + optional + + + Resources/sv.lproj/InfoPlist.strings + + hash + + BYdlnFufmWzlpJrheClmCN7Chh8= + + hash2 + + lGH0nxdIuHpjAn5hcBey2jNrEndUjZ35l0dFJCRxeZw= + + optional + + + Resources/th.lproj/InfoPlist.strings + + hash + + WIGfPimaJmK19pVXalyb5HWi1z4= + + hash2 + + 4UuVy5dxfjjz7kWQ6hh4pUP1UVT5/3yqCHTuRRZNvVg= + + optional + + + Resources/tr.lproj/InfoPlist.strings + + hash + + 8awq/XTYFfDJOcYOx3DRl7satYs= + + hash2 + + ZHHJWbfyNzyM3cFSQVravPaezQUP2y/ETgwAwy9YXE4= + + optional + + + Resources/uk.lproj/InfoPlist.strings + + hash + + ZB/a+LXCJydku2nxRhXdFc2jyIU= + + hash2 + + ZZUVLWrSJ9hOa0N8n+/WK7KD9pLekOedwqP2S22wr1k= + + optional + + + Resources/vi.lproj/InfoPlist.strings + + hash + + fBGaXOAYxdQjDvwTk+IeRKLDudQ= + + hash2 + + db2kptf+W9FaSJWqpCb6AYqxPtIkQQJnWO7MPSvb4UQ= + + optional + + + Resources/zh_CN.lproj/InfoPlist.strings + + hash + + GuwX6bfgJVWZ2iL/nf7G2D7m91I= + + hash2 + + Y1Nn88Cu12QEmWMRHQte9A3VlvDUu1kcJBDdS/gy0dI= + + optional + + + Resources/zh_HK.lproj/InfoPlist.strings + + hash + + ztyIfPb4/CLzceG3nbbonph9qRA= + + hash2 + + 6YOzSEI4f/EYeBn6PbSyjKgmrykbnSNRPeBUPsz3IEg= + + optional + + + Resources/zh_TW.lproj/InfoPlist.strings + + hash + + t259jw346xKzUgPwGqw0PCLXjGc= + + hash2 + + YbaT7Ysm60XBG26Mvp8AU2SI9oT85wbUYdGbxQOHxDg= + + optional + + + document.wflow + + cdhash + + SpVgndlS1DB6I2zxWGn+U077PQI= + + requirement + identifier document and anchor apple generic and certificate 1[field.1.2.840.113635.100.6.2.6] /* exists */ and certificate leaf[field.1.2.840.113635.100.6.1.13] /* exists */ and certificate leaf[subject.OU] = "8LT29UFQPL" + + + rules + + ^Resources/ + + ^Resources/.*\.lproj/ + + optional + + weight + 1000 + + ^Resources/.*\.lproj/locversion.plist$ + + omit + + weight + 1100 + + ^Resources/Base\.lproj/ + + weight + 1010 + + ^version.plist$ + + + rules2 + + .*\.dSYM($|/) + + weight + 11 + + ^(.*/)?\.DS_Store$ + + omit + + weight + 2000 + + ^(Frameworks|SharedFrameworks|PlugIns|Plug-ins|XPCServices|Helpers|MacOS|Library/(Automator|Spotlight|LoginItems))/ + + nested + + weight + 10 + + ^.* + + ^Info\.plist$ + + omit + + weight + 20 + + ^PkgInfo$ + + omit + + weight + 20 + + ^Resources/ + + weight + 20 + + ^Resources/.*\.lproj/ + + optional + + weight + 1000 + + ^Resources/.*\.lproj/locversion.plist$ + + omit + + weight + 1100 + + ^Resources/Base\.lproj/ + + weight + 1010 + + ^[^/]+$ + + nested + + weight + 10 + + ^embedded\.provisionprofile$ + + weight + 20 + + ^version\.plist$ + + weight + 20 + + + + diff --git a/Executables/MacOS via Automator and Script/current executables/Mesquite_Starter_Flex.app/Contents/document.wflow b/Executables/MacOS via Automator and Script/current executables/Mesquite_Starter_Flex.app/Contents/document.wflow new file mode 100755 index 000000000..eac06a7de --- /dev/null +++ b/Executables/MacOS via Automator and Script/current executables/Mesquite_Starter_Flex.app/Contents/document.wflow @@ -0,0 +1,706 @@ + + + + + AMApplicationBuild + 444.42 + AMApplicationVersion + 2.9 + AMDocumentVersion + 2 + actions + + + action + + AMAccepts + + Container + List + Optional + + Types + + * + + + AMActionVersion + v.1.0.2 + AMApplication + + Automator + + AMParameterProperties + + variableUUID + + isPathPopUp + + selectedVariableUUID + B5724CA0-32E6-41E6-A92D-05F05ECF423A + + + AMProvides + + Container + List + Types + + * + + + AMRequiredResources + + ActionBundlePath + /System/Library/Automator/Set Value of Variable.action + ActionName + Set Value of Variable + ActionParameters + + variableUUID + B5724CA0-32E6-41E6-A92D-05F05ECF423A + + BundleIdentifier + com.apple.Automator.SetValueofVariable + CFBundleVersion + 1.0.2 + CanShowSelectedItemsWhenRun + + CanShowWhenRun + + Category + + AMCategoryUtilities + + Class Name + Set_Value_of_Variable + InputUUID + 43FB1F79-4EA6-4AA7-A306-B9BCE6E21896 + Keywords + + variable + binding + input + output + storage + + OutputUUID + E791B933-EFA9-43EE-B7B4-F8F6C5EE0E4A + UUID + 4B07F06B-F2E4-49D5-8009-9C558FB1CD61 + UnlocalizedApplications + + Automator + + arguments + + 0 + + default value + + name + variableUUID + required + 0 + type + 0 + uuid + 0 + + + isViewVisible + + location + 619.500000:111.000000 + nibPath + /System/Library/Automator/Set Value of Variable.action/Contents/Resources/Base.lproj/main.nib + + isViewVisible + + + + action + + AMAccepts + + Container + List + Optional + + Types + + com.apple.cocoa.path + + + AMActionVersion + 1.2.2 + AMApplication + + Finder + + AMParameterProperties + + newName + + tokenizedValue + + Mesquite_Support_Files + + + targetLocation + + isPathPopUp + + variableUUIDsInMenu + + + + AMProvides + + Container + List + Types + + public.folder + + + ActionBundlePath + /System/Library/Automator/New Folder.action + ActionName + New Folder + ActionParameters + + newName + Mesquite_Support_Files + targetLocation + ~ + + BundleIdentifier + com.apple.Automator.MakeNewFolder + CFBundleVersion + 1.2.2 + CanShowSelectedItemsWhenRun + + CanShowWhenRun + + Category + + AMCategoryFilesAndFolders + + Class Name + NewFolderAction + IgnoresInput + + InputUUID + 7F253106-A965-4ABC-97FD-1FD2D52366A4 + Keywords + + Folder + Create + Make + New + + OutputUUID + 8EA1A9AF-B3C7-46F2-B605-CDBB38797DA9 + UUID + 2528247D-5A8D-4ADD-9481-A0BC58FA668F + UnlocalizedApplications + + Finder + + arguments + + 0 + + default value + + name + newName + required + 0 + type + 0 + uuid + 0 + + 1 + + default value + ~/Desktop + name + targetLocation + required + 0 + type + 0 + uuid + 1 + + + isViewVisible + + location + 619.500000:152.000000 + nibPath + /System/Library/Automator/New Folder.action/Contents/Resources/Base.lproj/main.nib + + isViewVisible + + + + action + + AMAccepts + + Container + List + Optional + + Types + + * + + + AMActionVersion + v.1.0.2 + AMApplication + + Automator + + AMParameterProperties + + variableUUID + + isPathPopUp + + selectedVariableUUID + B5724CA0-32E6-41E6-A92D-05F05ECF423A + + + AMProvides + + Container + List + Types + + * + + + AMRequiredResources + + ActionBundlePath + /System/Library/Automator/Get Value of Variable.action + ActionName + Get Value of Variable + ActionParameters + + variableUUID + B5724CA0-32E6-41E6-A92D-05F05ECF423A + + BundleIdentifier + com.apple.Automator.GetValueofVariable + CFBundleVersion + 1.0.2 + CanShowSelectedItemsWhenRun + + CanShowWhenRun + + Category + + AMCategoryUtilities + + Class Name + Get_Value_of_Variable + IgnoresInput + + InputUUID + B3699B55-670C-4E04-8062-7A25776314F6 + Keywords + + variable + binding + input + output + storage + + OutputUUID + 342F6FBC-A8B4-4AB8-8488-094942236BD7 + UUID + 4F14C189-CB3E-41E7-989A-E209FB44368B + UnlocalizedApplications + + Automator + + arguments + + 0 + + default value + + name + variableUUID + required + 0 + type + 0 + uuid + 0 + + + isViewVisible + + location + 619.500000:193.000000 + nibPath + /System/Library/Automator/Get Value of Variable.action/Contents/Resources/Base.lproj/main.nib + + isViewVisible + + + + action + + AMAccepts + + Container + List + Optional + + Types + + com.apple.applescript.object + + + AMActionVersion + 1.0.2 + AMApplication + + Automator + + AMParameterProperties + + source + + + AMProvides + + Container + List + Types + + com.apple.applescript.object + + + ActionBundlePath + /System/Library/Automator/Run AppleScript.action + ActionName + Run AppleScript + ActionParameters + + source + on getPath(this_text, stripLast) set AppleScript's text item delimiters to the ":" set the item_list to every text item of this_text set num to the number of items in item_list if stripLast then set lasti to num - 2 else set lasti to num end if set the item_list to items 2 through lasti of item_list set AppleScript's text item delimiters to the "/" set this_text to the item_list as string set AppleScript's text item delimiters to "" set this_text to "/" & this_text return this_text end getPath on run {input, parameters} set whereAmI to getPath((path to me as text), true) set javaLocFile to whereAmI & "/RunningOptionsForFlex/Mesquite-JavaToUse.txt" set javaLoc to "java" try set lns to paragraphs of (read POSIX file javaLocFile) set javaLoc to first item in lns end try set memoryFile to whereAmI & "/RunningOptionsForFlex/Mesquite-MemoryToUse.txt" set memory to 1 try set lns to paragraphs of (read POSIX file memoryFile) set memory to first item in lns end try set flagsFile to whereAmI & "/RunningOptionsForFlex/Mesquite-FlagsToUse.txt" set flags to "" try set lns to paragraphs of (read POSIX file flagsFile) set flags to first item in lns end try #display dialog memory as text set results to whereAmI try if input is not equal to {} then set droppedFiles to getPath(input as text, false) set results to results & ":" & droppedFiles end if end try set results to javaLoc & ":" & flags & ":" &memory & ":" & results return results end run + + BundleIdentifier + com.apple.Automator.RunScript + CFBundleVersion + 1.0.2 + CanShowSelectedItemsWhenRun + + CanShowWhenRun + + Category + + AMCategoryUtilities + + Class Name + RunScriptAction + InputUUID + 11F3EFA2-BE3D-4DD3-A24A-AFC7373B06F3 + Keywords + + Run + + OutputUUID + F42FD833-E0EE-4550-88BA-39A54F93799B + UUID + 35565B5A-57E2-4F76-B8E4-02CE4A8CD9B2 + UnlocalizedApplications + + Automator + + arguments + + 0 + + default value + on run {input, parameters} + + (* Your script goes here *) + + return input +end run + name + source + required + 0 + type + 0 + uuid + 0 + + + isViewVisible + + location + 619.500000:438.000000 + nibPath + /System/Library/Automator/Run AppleScript.action/Contents/Resources/Base.lproj/main.nib + + isViewVisible + + + + action + + AMAccepts + + Container + List + Optional + + Types + + com.apple.cocoa.string + + + AMActionVersion + 2.0.3 + AMApplication + + Automator + + AMParameterProperties + + COMMAND_STRING + + CheckedForUserDefaultShell + + inputMethod + + shell + + source + + + AMProvides + + Container + List + Types + + com.apple.cocoa.string + + + ActionBundlePath + /System/Library/Automator/Run Shell Script.action + ActionName + Run Shell Script + ActionParameters + + COMMAND_STRING + read whereAndWhat #where is Mesquite Folder, and what are dropped files +echo $whereAndWhat > Mesquite_Support_Files/Mesquite_Flex_INSTRUCTIONS.txt +IFS=':' read -r -a arr <<< "$whereAndWhat" +JAVALOC=${arr[0]} +FLAGS=${arr[1]} +MEMORY=${arr[2]} +whereAmI=${arr[3]} +if [[ ${#myvar} <1 ]]; #no flags passed in +then + if [[ ${#arr[@]} > 4 ]]; + then + droppedFiles=${arr[4]} #this gets just first file + "${JAVALOC}" --add-exports java.desktop/com.apple.eawt=ALL-UNNAMED -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" "$droppedFiles" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt || "${JAVALOC}" -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" "$droppedFiles" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt + else + "${JAVALOC}" --add-exports java.desktop/com.apple.eawt=ALL-UNNAMED -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt || "${JAVALOC}" -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt + fi +else #flags passed in; use those + if [[ ${#arr[@]} > 4 ]]; + then + droppedFiles=${arr[4]} #this gets just first file + "${JAVALOC}" ${FLAGS} -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" "$droppedFiles" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt + else + "${JAVALOC}" ${FLAGS} -Xmx${MEMORY}000M -Xss8m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar "$whereAmI/Mesquite.jar" -mqflex > Mesquite_Support_Files/Mesquite_Flex_stdout.txt + fi +fi + CheckedForUserDefaultShell + + inputMethod + 0 + shell + /bin/bash + source + + + BundleIdentifier + com.apple.RunShellScript + CFBundleVersion + 2.0.3 + CanShowSelectedItemsWhenRun + + CanShowWhenRun + + Category + + AMCategoryUtilities + + Class Name + RunShellScriptAction + InputUUID + 7EFF0B18-2D72-45C5-9ED5-1550681238D5 + Keywords + + Shell + Script + Command + Run + Unix + + OutputUUID + B0EFEE58-F461-4027-8168-126B947DC10A + UUID + 59BCA6EA-60BF-47F5-8C7B-221B6D2C77B9 + UnlocalizedApplications + + Automator + + arguments + + 0 + + default value + 0 + name + inputMethod + required + 0 + type + 0 + uuid + 0 + + 1 + + default value + + name + source + required + 0 + type + 0 + uuid + 1 + + 2 + + default value + + name + CheckedForUserDefaultShell + required + 0 + type + 0 + uuid + 2 + + 3 + + default value + + name + COMMAND_STRING + required + 0 + type + 0 + uuid + 3 + + 4 + + default value + /bin/sh + name + shell + required + 0 + type + 0 + uuid + 4 + + + isViewVisible + + location + 619.500000:1122.000000 + nibPath + /System/Library/Automator/Run Shell Script.action/Contents/Resources/Base.lproj/main.nib + + isViewVisible + + + + connectors + + 399C77FB-0C53-4532-9B28-DBA63F886CE7 + + from + 35565B5A-57E2-4F76-B8E4-02CE4A8CD9B2 - 35565B5A-57E2-4F76-B8E4-02CE4A8CD9B2 + to + 59BCA6EA-60BF-47F5-8C7B-221B6D2C77B9 - 59BCA6EA-60BF-47F5-8C7B-221B6D2C77B9 + + 8135E9E8-5924-4DFA-A6FD-BDBC382D5D95 + + from + 2528247D-5A8D-4ADD-9481-A0BC58FA668F - 2528247D-5A8D-4ADD-9481-A0BC58FA668F + to + 4F14C189-CB3E-41E7-989A-E209FB44368B - 4F14C189-CB3E-41E7-989A-E209FB44368B + + E3C6E533-95E6-4726-B169-396BD2EE9AF2 + + from + 4F14C189-CB3E-41E7-989A-E209FB44368B - 4F14C189-CB3E-41E7-989A-E209FB44368B + to + 35565B5A-57E2-4F76-B8E4-02CE4A8CD9B2 - 35565B5A-57E2-4F76-B8E4-02CE4A8CD9B2 + + F8046E3E-C18C-4186-8DD4-A5B45DD64886 + + from + 4B07F06B-F2E4-49D5-8009-9C558FB1CD61 - 4B07F06B-F2E4-49D5-8009-9C558FB1CD61 + to + 2528247D-5A8D-4ADD-9481-A0BC58FA668F - 2528247D-5A8D-4ADD-9481-A0BC58FA668F + + + variables + + + UUID + B5724CA0-32E6-41E6-A92D-05F05ECF423A + identifier + com.apple.Automator.Variable.Text + name + DroppedFiles + value + + + + workflowMetaData + + workflowTypeIdentifier + com.apple.Automator.application + + + diff --git a/Executables/MacOS via Automator and Script/current executables/UnzipThisForMacOS.zip b/Executables/MacOS via Automator and Script/current executables/UnzipThisForMacOS.zip new file mode 100644 index 000000000..29c8b28d3 Binary files /dev/null and b/Executables/MacOS via Automator and Script/current executables/UnzipThisForMacOS.zip differ diff --git a/Executables/MacOS via Automator and Script/signBundle.sh b/Executables/MacOS via Automator and Script/signBundle.sh new file mode 100755 index 000000000..ab6786a58 --- /dev/null +++ b/Executables/MacOS via Automator and Script/signBundle.sh @@ -0,0 +1,12 @@ +#!/bin/bash +xattr -cr Mesquite.app + +for f in $(find Mesquite.app/Contents); +do + codesign -s "Developer ID Application: Wayne Maddison" $f; +done + +codesign --force --deep --options=runtime -s "Developer ID Application: Wayne Maddison" Mesquite.app +#codesign --force --options=runtime -s "Developer ID Application: Wayne Maddison" Mesquite.app +codesign -d --verbose=4 Mesquite.app +spctl --assess --verbose=4 --type execute Mesquite.app diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/INSTRUCTIONS-MesquiteExecutableForOlderMacOS.txt b/Executables/Mesquite.jar & MacOS (pre-Catalina)/INSTRUCTIONS-MesquiteExecutableForOlderMacOS.txt new file mode 100644 index 000000000..e9450dc0b --- /dev/null +++ b/Executables/Mesquite.jar & MacOS (pre-Catalina)/INSTRUCTIONS-MesquiteExecutableForOlderMacOS.txt @@ -0,0 +1,27 @@ +To build the Mesquite executable for older macOSs. +LAST USE AND VERSION Jan 2018 + + +First, build Mesquite.jar that is used as a starter: + +0. Make sure ant is installed. (You can install Homebrew, and then use brew install ant) +0. Make sure you have the appropriate version of ByteBuddy. + If you need a new version, then unpack the jar using + jar xf byte-buddy-agent-1.7.8.jar [this should yield a "net" directory] + +1. get the lastest start.Mesquite.java from the Mesquite Workspace, and use it to replace the one in src/start/ here. + +2. cd into this directory then give this command: + +ant + +3. The Mesquite.jar will be placed in dist/. This can be moved into Mesquite_Folder as a starter, or into the Mesquite application bundle. + +4. to incorporate ByteBuddy: + -move net into dist + - cd into dist + jar uf Mesquite.jar net/bytebuddy/agent/* + -move net out of dist + + +4. The latest unsigned application bundle is also here (Mesquite-appBundle.app). Replace its internal mesquite.jar as needed (note it needs to be lowercase "m"). It was built ca. 2014 by appBundler from Oracle. We have yet to get the javaPackager from Oracle to work. diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/META-INF/MANIFEST.MF b/Executables/Mesquite.jar & MacOS (pre-Catalina)/META-INF/MANIFEST.MF new file mode 100644 index 000000000..6e52f6baa --- /dev/null +++ b/Executables/Mesquite.jar & MacOS (pre-Catalina)/META-INF/MANIFEST.MF @@ -0,0 +1,24 @@ +Manifest-Version: 1.0 +Bundle-Description: The Byte Buddy Java agent allows to access the JVM + 's HotSwap feature. +Automatic-Module-Name: net.bytebuddy.agent +Bundle-License: http://www.apache.org/licenses/LICENSE-2.0.txt +Bundle-SymbolicName: net.bytebuddy.byte-buddy-agent +Built-By: rafael +Agent-Class: net.bytebuddy.agent.Installer +Bnd-LastModified: 1508797941048 +Bundle-ManifestVersion: 2 +Can-Redefine-Classes: true +Import-Package: com.sun.tools.attach;resolution:=optional,com.ibm.tool + s.attach;resolution:=optional +Require-Capability: osgi.ee;filter:="(&(osgi.ee=JavaSE)(version=1.6))" +Can-Set-Native-Method-Prefix: true +Tool: Bnd-3.3.0.201609221906 +Export-Package: net.bytebuddy.agent;version="1.7.8" +Premain-Class: net.bytebuddy.agent.Installer +Bundle-Name: Byte Buddy Java agent +Bundle-Version: 1.7.8 +Can-Retransform-Classes: true +Created-By: Apache Maven Bundle Plugin +Build-Jdk: 1.8.0_151 + diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/META-INF/maven/net.bytebuddy/byte-buddy-agent/pom.properties b/Executables/Mesquite.jar & MacOS (pre-Catalina)/META-INF/maven/net.bytebuddy/byte-buddy-agent/pom.properties new file mode 100644 index 000000000..c90bbce7d --- /dev/null +++ b/Executables/Mesquite.jar & MacOS (pre-Catalina)/META-INF/maven/net.bytebuddy/byte-buddy-agent/pom.properties @@ -0,0 +1,4 @@ +#Created by Apache Maven 3.3.9 +version=1.7.8 +groupId=net.bytebuddy +artifactId=byte-buddy-agent diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/META-INF/maven/net.bytebuddy/byte-buddy-agent/pom.xml b/Executables/Mesquite.jar & MacOS (pre-Catalina)/META-INF/maven/net.bytebuddy/byte-buddy-agent/pom.xml new file mode 100644 index 000000000..8ca39a506 --- /dev/null +++ b/Executables/Mesquite.jar & MacOS (pre-Catalina)/META-INF/maven/net.bytebuddy/byte-buddy-agent/pom.xml @@ -0,0 +1,112 @@ + + + 4.0.0 + + + byte-buddy-parent + net.bytebuddy + 1.7.8 + + + byte-buddy-agent + jar + + + net.bytebuddy.agent.Installer + com.sun.tools.attach + com.ibm.tools.attach + 2.0.4 + + + Byte Buddy Java agent + The Byte Buddy Java agent allows to access the JVM's HotSwap feature. + + + + + + com.kohlschutter.junixsocket + junixsocket-native-common + ${version.unixsocket} + provided + + + junit + junit + ${version.junit} + test + + + org.mockito + mockito-core + ${version.mockito} + test + + + net.bytebuddy + byte-buddy-agent + + + + + + + + extras + + false + + + + + + org.apache.maven.plugins + maven-jar-plugin + ${version.plugin.jar} + + + ${project.build.outputDirectory}/META-INF/MANIFEST.MF + + + + + + org.apache.felix + maven-bundle-plugin + ${version.plugin.bundle} + + + process-classes + + manifest + + + + + + ${bytebuddy.agent} + ${bytebuddy.agent} + true + true + true + + ${attach.package.sun};resolution:="optional", + ${attach.package.ibm};resolution:="optional" + + + net.bytebuddy.agent + + ${project.groupId}.agent + + + + + + + + + diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/Mesquite-appBundle.app/Contents/Info.plist b/Executables/Mesquite.jar & MacOS (pre-Catalina)/Mesquite-appBundle.app/Contents/Info.plist new file mode 100644 index 000000000..6ba6fc8f3 --- /dev/null +++ b/Executables/Mesquite.jar & MacOS (pre-Catalina)/Mesquite-appBundle.app/Contents/Info.plist @@ -0,0 +1,62 @@ + + + + +CFBundleDevelopmentRegion +English +CFBundleExecutable +JavaAppLauncher +CFBundleIconFile +Mesquite.icns +CFBundleIdentifier +start.Mesquite +CFBundleDisplayName +Mesquite +CFBundleDocumentTypes + + + CFBundleTypeExtensions + + nex + + CFBundleTypeName + Mesquite NEXUS file + CFBundleTypeOSTypes + + TEXT + + CFBundleTypeRole + Editor + + +CFBundleInfoDictionaryVersion +6.0 +CFBundleName +Mesquite +CFBundlePackageType +APPL +CFBundleShortVersionString +1.0 +CFBundleSignature +???? +CFBundleVersion +1 +NSHumanReadableCopyright + +JVMMainClassName +start.Mesquite +JVMOptions + +-Djri.ignore.ule="yes" +-Djava.library.path=lib +-Xss4m +-Xmx1000m + +JVMArguments + +-mqex +-nestedStarter + + + + diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/Mesquite-appBundle.app/Contents/Java/mesquite.jar b/Executables/Mesquite.jar & MacOS (pre-Catalina)/Mesquite-appBundle.app/Contents/Java/mesquite.jar new file mode 100644 index 000000000..54c2d0ab8 Binary files /dev/null and b/Executables/Mesquite.jar & MacOS (pre-Catalina)/Mesquite-appBundle.app/Contents/Java/mesquite.jar differ diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/Mesquite-appBundle.app/Contents/MacOS/JavaAppLauncher b/Executables/Mesquite.jar & MacOS (pre-Catalina)/Mesquite-appBundle.app/Contents/MacOS/JavaAppLauncher new file mode 100755 index 000000000..e7ac4129a Binary files /dev/null and b/Executables/Mesquite.jar & MacOS (pre-Catalina)/Mesquite-appBundle.app/Contents/MacOS/JavaAppLauncher differ diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/Mesquite-appBundle.app/Contents/PkgInfo b/Executables/Mesquite.jar & MacOS (pre-Catalina)/Mesquite-appBundle.app/Contents/PkgInfo new file mode 100644 index 000000000..bd04210fb --- /dev/null +++ b/Executables/Mesquite.jar & MacOS (pre-Catalina)/Mesquite-appBundle.app/Contents/PkgInfo @@ -0,0 +1 @@ +APPL???? \ No newline at end of file diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/Mesquite-appBundle.app/Contents/Resources/Mesquite.icns b/Executables/Mesquite.jar & MacOS (pre-Catalina)/Mesquite-appBundle.app/Contents/Resources/Mesquite.icns new file mode 100644 index 000000000..280d8334a Binary files /dev/null and b/Executables/Mesquite.jar & MacOS (pre-Catalina)/Mesquite-appBundle.app/Contents/Resources/Mesquite.icns differ diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/Mesquite-appBundle.app/Contents/Resources/en.lproj/Localizable.strings b/Executables/Mesquite.jar & MacOS (pre-Catalina)/Mesquite-appBundle.app/Contents/Resources/en.lproj/Localizable.strings new file mode 100644 index 000000000..0d306aaaf --- /dev/null +++ b/Executables/Mesquite.jar & MacOS (pre-Catalina)/Mesquite-appBundle.app/Contents/Resources/en.lproj/Localizable.strings @@ -0,0 +1,3 @@ +"JRELoadError" = "Unable to load Java Runtime Environment."; +"MainClassNameRequired" = "Main class name is required."; +"JavaDirectoryNotFound" = "Unable to enumerate Java directory contents."; diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/build.xml b/Executables/Mesquite.jar & MacOS (pre-Catalina)/build.xml new file mode 100644 index 000000000..f517a3a8a --- /dev/null +++ b/Executables/Mesquite.jar & MacOS (pre-Catalina)/build.xml @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/build/depcache/dependencies.txt b/Executables/Mesquite.jar & MacOS (pre-Catalina)/build/depcache/dependencies.txt new file mode 100644 index 000000000..b63eb8eba --- /dev/null +++ b/Executables/Mesquite.jar & MacOS (pre-Catalina)/build/depcache/dependencies.txt @@ -0,0 +1,17 @@ +||:start.Mesquite +java.lang.StringBuilder +java.lang.reflect.Method +java.io.File +java.lang.StringBuffer +java.net.URLClassLoader +java.lang.Class +java.lang.System +java.io.PrintStream +java.lang.Throwable +java.net.URL +start.Mesquite +java.lang.Object +[Ljava.lang.String; +java.lang.ClassLoader +java.lang.String +java.lang.Exception diff --git a/Additional Files/executablesJava17Plus-macOS-June2018.zip b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables.zip similarity index 78% rename from Additional Files/executablesJava17Plus-macOS-June2018.zip rename to Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables.zip index 0d36b6a1f..435e05f94 100644 Binary files a/Additional Files/executablesJava17Plus-macOS-June2018.zip and b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables.zip differ diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E1.app/Contents/Info.plist b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E1.app/Contents/Info.plist new file mode 100644 index 000000000..73421573d --- /dev/null +++ b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E1.app/Contents/Info.plist @@ -0,0 +1,62 @@ + + + + +CFBundleDevelopmentRegion +English +CFBundleExecutable +JavaAppLauncher +CFBundleIconFile +Mesquite.icns +CFBundleIdentifier +start.Mesquite +CFBundleDisplayName +Mesquite +CFBundleDocumentTypes + + + CFBundleTypeExtensions + + nex + + CFBundleTypeName + Mesquite NEXUS file + CFBundleTypeOSTypes + + TEXT + + CFBundleTypeRole + Editor + + +CFBundleInfoDictionaryVersion +6.0 +CFBundleName +Mesquite +CFBundlePackageType +APPL +CFBundleShortVersionString +1.0 +CFBundleSignature +???? +CFBundleVersion +1 +NSHumanReadableCopyright + +JVMMainClassName +start.Mesquite +JVMOptions + +-Djri.ignore.ule="yes" +-Djava.library.path=lib +-Xss4m +-Xmx1000m + +JVMArguments + +-mqex +-mq17 + + + + diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E1.app/Contents/Java/mesquite.jar b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E1.app/Contents/Java/mesquite.jar new file mode 100644 index 000000000..a2a008208 Binary files /dev/null and b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E1.app/Contents/Java/mesquite.jar differ diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E1.app/Contents/MacOS/JavaAppLauncher b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E1.app/Contents/MacOS/JavaAppLauncher new file mode 100755 index 000000000..5e6bd9b6b Binary files /dev/null and b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E1.app/Contents/MacOS/JavaAppLauncher differ diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E1.app/Contents/PkgInfo b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E1.app/Contents/PkgInfo new file mode 100644 index 000000000..bd04210fb --- /dev/null +++ b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E1.app/Contents/PkgInfo @@ -0,0 +1 @@ +APPL???? \ No newline at end of file diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E1.app/Contents/Resources/Mesquite.icns b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E1.app/Contents/Resources/Mesquite.icns new file mode 100644 index 000000000..280d8334a Binary files /dev/null and b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E1.app/Contents/Resources/Mesquite.icns differ diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E1.app/Contents/Resources/en.lproj/Localizable.strings b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E1.app/Contents/Resources/en.lproj/Localizable.strings new file mode 100644 index 000000000..0d306aaaf --- /dev/null +++ b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E1.app/Contents/Resources/en.lproj/Localizable.strings @@ -0,0 +1,3 @@ +"JRELoadError" = "Unable to load Java Runtime Environment."; +"MainClassNameRequired" = "Main class name is required."; +"JavaDirectoryNotFound" = "Unable to enumerate Java directory contents."; diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E1.app/Contents/_CodeSignature/CodeResources b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E1.app/Contents/_CodeSignature/CodeResources new file mode 100644 index 000000000..b198c63f0 --- /dev/null +++ b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E1.app/Contents/_CodeSignature/CodeResources @@ -0,0 +1,165 @@ + + + + + files + + Resources/Mesquite.icns + + mqnGaSRzbpi8l2W1di+4pqXeH9s= + + Resources/en.lproj/Localizable.strings + + hash + + 1x7GcvnGdR/b251TU0nrD14zM/c= + + optional + + + + files2 + + Java/mesquite.jar + + hash + + TOQwMihZO7A8i8OIiIcqaCDCXrQ= + + hash2 + + 6uYEYVmXkQqRUDk8P1UxDWFBJYaerM2FqrGoZJZ+mKo= + + + Resources/Mesquite.icns + + hash + + mqnGaSRzbpi8l2W1di+4pqXeH9s= + + hash2 + + i5EC+dPX7zdVv0gkr98Ez5XSpVYjE3Zym2KoGfXHfAk= + + + Resources/en.lproj/Localizable.strings + + hash + + 1x7GcvnGdR/b251TU0nrD14zM/c= + + hash2 + + +mlNWeuECqXqVd3n2W7JqWMCbbafAJeOxo6lFCIMGvg= + + optional + + + + rules + + ^Resources/ + + ^Resources/.*\.lproj/ + + optional + + weight + 1000 + + ^Resources/.*\.lproj/locversion.plist$ + + omit + + weight + 1100 + + ^Resources/Base\.lproj/ + + weight + 1010 + + ^version.plist$ + + + rules2 + + .*\.dSYM($|/) + + weight + 11 + + ^(.*/)?\.DS_Store$ + + omit + + weight + 2000 + + ^(Frameworks|SharedFrameworks|PlugIns|Plug-ins|XPCServices|Helpers|MacOS|Library/(Automator|Spotlight|LoginItems))/ + + nested + + weight + 10 + + ^.* + + ^Info\.plist$ + + omit + + weight + 20 + + ^PkgInfo$ + + omit + + weight + 20 + + ^Resources/ + + weight + 20 + + ^Resources/.*\.lproj/ + + optional + + weight + 1000 + + ^Resources/.*\.lproj/locversion.plist$ + + omit + + weight + 1100 + + ^Resources/Base\.lproj/ + + weight + 1010 + + ^[^/]+$ + + nested + + weight + 10 + + ^embedded\.provisionprofile$ + + weight + 20 + + ^version\.plist$ + + weight + 20 + + + + diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E2.app/Contents/Info.plist b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E2.app/Contents/Info.plist new file mode 100644 index 000000000..c6f7813cb --- /dev/null +++ b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E2.app/Contents/Info.plist @@ -0,0 +1,61 @@ + + + + +CFBundleDevelopmentRegion +English +CFBundleExecutable +JavaAppLauncher +CFBundleIconFile +Mesquite.icns +CFBundleIdentifier +start.Mesquite +CFBundleDisplayName +Mesquite +CFBundleDocumentTypes + + + CFBundleTypeExtensions + + nex + + CFBundleTypeName + Mesquite NEXUS file + CFBundleTypeOSTypes + + TEXT + + CFBundleTypeRole + Editor + + +CFBundleInfoDictionaryVersion +6.0 +CFBundleName +Mesquite +CFBundlePackageType +APPL +CFBundleShortVersionString +1.0 +CFBundleSignature +???? +CFBundleVersion +1 +NSHumanReadableCopyright + +JVMMainClassName +start.Mesquite +JVMOptions + +-Djri.ignore.ule="yes" +-Djava.library.path=lib +-Xss8m +-Xmx2000m + +JVMArguments + +-mqex + + + + diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E2.app/Contents/Java/mesquite.jar b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E2.app/Contents/Java/mesquite.jar new file mode 100644 index 000000000..a2a008208 Binary files /dev/null and b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E2.app/Contents/Java/mesquite.jar differ diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E2.app/Contents/MacOS/JavaAppLauncher b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E2.app/Contents/MacOS/JavaAppLauncher new file mode 100755 index 000000000..ace847403 Binary files /dev/null and b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E2.app/Contents/MacOS/JavaAppLauncher differ diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E2.app/Contents/PkgInfo b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E2.app/Contents/PkgInfo new file mode 100644 index 000000000..bd04210fb --- /dev/null +++ b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E2.app/Contents/PkgInfo @@ -0,0 +1 @@ +APPL???? \ No newline at end of file diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E2.app/Contents/Resources/Mesquite.icns b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E2.app/Contents/Resources/Mesquite.icns new file mode 100644 index 000000000..280d8334a Binary files /dev/null and b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E2.app/Contents/Resources/Mesquite.icns differ diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E2.app/Contents/Resources/en.lproj/Localizable.strings b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E2.app/Contents/Resources/en.lproj/Localizable.strings new file mode 100644 index 000000000..0d306aaaf --- /dev/null +++ b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E2.app/Contents/Resources/en.lproj/Localizable.strings @@ -0,0 +1,3 @@ +"JRELoadError" = "Unable to load Java Runtime Environment."; +"MainClassNameRequired" = "Main class name is required."; +"JavaDirectoryNotFound" = "Unable to enumerate Java directory contents."; diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E2.app/Contents/_CodeSignature/CodeResources b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E2.app/Contents/_CodeSignature/CodeResources new file mode 100644 index 000000000..b198c63f0 --- /dev/null +++ b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E2.app/Contents/_CodeSignature/CodeResources @@ -0,0 +1,165 @@ + + + + + files + + Resources/Mesquite.icns + + mqnGaSRzbpi8l2W1di+4pqXeH9s= + + Resources/en.lproj/Localizable.strings + + hash + + 1x7GcvnGdR/b251TU0nrD14zM/c= + + optional + + + + files2 + + Java/mesquite.jar + + hash + + TOQwMihZO7A8i8OIiIcqaCDCXrQ= + + hash2 + + 6uYEYVmXkQqRUDk8P1UxDWFBJYaerM2FqrGoZJZ+mKo= + + + Resources/Mesquite.icns + + hash + + mqnGaSRzbpi8l2W1di+4pqXeH9s= + + hash2 + + i5EC+dPX7zdVv0gkr98Ez5XSpVYjE3Zym2KoGfXHfAk= + + + Resources/en.lproj/Localizable.strings + + hash + + 1x7GcvnGdR/b251TU0nrD14zM/c= + + hash2 + + +mlNWeuECqXqVd3n2W7JqWMCbbafAJeOxo6lFCIMGvg= + + optional + + + + rules + + ^Resources/ + + ^Resources/.*\.lproj/ + + optional + + weight + 1000 + + ^Resources/.*\.lproj/locversion.plist$ + + omit + + weight + 1100 + + ^Resources/Base\.lproj/ + + weight + 1010 + + ^version.plist$ + + + rules2 + + .*\.dSYM($|/) + + weight + 11 + + ^(.*/)?\.DS_Store$ + + omit + + weight + 2000 + + ^(Frameworks|SharedFrameworks|PlugIns|Plug-ins|XPCServices|Helpers|MacOS|Library/(Automator|Spotlight|LoginItems))/ + + nested + + weight + 10 + + ^.* + + ^Info\.plist$ + + omit + + weight + 20 + + ^PkgInfo$ + + omit + + weight + 20 + + ^Resources/ + + weight + 20 + + ^Resources/.*\.lproj/ + + optional + + weight + 1000 + + ^Resources/.*\.lproj/locversion.plist$ + + omit + + weight + 1100 + + ^Resources/Base\.lproj/ + + weight + 1010 + + ^[^/]+$ + + nested + + weight + 10 + + ^embedded\.provisionprofile$ + + weight + 20 + + ^version\.plist$ + + weight + 20 + + + + diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E4.app/Contents/Info.plist b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E4.app/Contents/Info.plist new file mode 100644 index 000000000..c1b0122d5 --- /dev/null +++ b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E4.app/Contents/Info.plist @@ -0,0 +1,62 @@ + + + + +CFBundleDevelopmentRegion +English +CFBundleExecutable +JavaAppLauncher +CFBundleIconFile +Mesquite.icns +CFBundleIdentifier +start.Mesquite +CFBundleDisplayName +Mesquite +CFBundleDocumentTypes + + + CFBundleTypeExtensions + + nex + + CFBundleTypeName + Mesquite NEXUS file + CFBundleTypeOSTypes + + TEXT + + CFBundleTypeRole + Editor + + +CFBundleInfoDictionaryVersion +6.0 +CFBundleName +Mesquite +CFBundlePackageType +APPL +CFBundleShortVersionString +1.0 +CFBundleSignature +???? +CFBundleVersion +1 +NSHumanReadableCopyright + +JVMMainClassName +start.Mesquite +JVMOptions + +-Djri.ignore.ule="yes" +-Djava.library.path=lib +-d64 +-Xss16m +-Xmx4000m + +JVMArguments + +-mqex + + + + diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E4.app/Contents/Java/mesquite.jar b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E4.app/Contents/Java/mesquite.jar new file mode 100644 index 000000000..a2a008208 Binary files /dev/null and b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E4.app/Contents/Java/mesquite.jar differ diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E4.app/Contents/MacOS/JavaAppLauncher b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E4.app/Contents/MacOS/JavaAppLauncher new file mode 100755 index 000000000..bbb004f14 Binary files /dev/null and b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E4.app/Contents/MacOS/JavaAppLauncher differ diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E4.app/Contents/PkgInfo b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E4.app/Contents/PkgInfo new file mode 100644 index 000000000..bd04210fb --- /dev/null +++ b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E4.app/Contents/PkgInfo @@ -0,0 +1 @@ +APPL???? \ No newline at end of file diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E4.app/Contents/Resources/Mesquite.icns b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E4.app/Contents/Resources/Mesquite.icns new file mode 100644 index 000000000..280d8334a Binary files /dev/null and b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E4.app/Contents/Resources/Mesquite.icns differ diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E4.app/Contents/Resources/en.lproj/Localizable.strings b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E4.app/Contents/Resources/en.lproj/Localizable.strings new file mode 100644 index 000000000..0d306aaaf --- /dev/null +++ b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E4.app/Contents/Resources/en.lproj/Localizable.strings @@ -0,0 +1,3 @@ +"JRELoadError" = "Unable to load Java Runtime Environment."; +"MainClassNameRequired" = "Main class name is required."; +"JavaDirectoryNotFound" = "Unable to enumerate Java directory contents."; diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E4.app/Contents/_CodeSignature/CodeResources b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E4.app/Contents/_CodeSignature/CodeResources new file mode 100644 index 000000000..b198c63f0 --- /dev/null +++ b/Executables/Mesquite.jar & MacOS (pre-Catalina)/current executables/Mesquite_Starter_E4.app/Contents/_CodeSignature/CodeResources @@ -0,0 +1,165 @@ + + + + + files + + Resources/Mesquite.icns + + mqnGaSRzbpi8l2W1di+4pqXeH9s= + + Resources/en.lproj/Localizable.strings + + hash + + 1x7GcvnGdR/b251TU0nrD14zM/c= + + optional + + + + files2 + + Java/mesquite.jar + + hash + + TOQwMihZO7A8i8OIiIcqaCDCXrQ= + + hash2 + + 6uYEYVmXkQqRUDk8P1UxDWFBJYaerM2FqrGoZJZ+mKo= + + + Resources/Mesquite.icns + + hash + + mqnGaSRzbpi8l2W1di+4pqXeH9s= + + hash2 + + i5EC+dPX7zdVv0gkr98Ez5XSpVYjE3Zym2KoGfXHfAk= + + + Resources/en.lproj/Localizable.strings + + hash + + 1x7GcvnGdR/b251TU0nrD14zM/c= + + hash2 + + +mlNWeuECqXqVd3n2W7JqWMCbbafAJeOxo6lFCIMGvg= + + optional + + + + rules + + ^Resources/ + + ^Resources/.*\.lproj/ + + optional + + weight + 1000 + + ^Resources/.*\.lproj/locversion.plist$ + + omit + + weight + 1100 + + ^Resources/Base\.lproj/ + + weight + 1010 + + ^version.plist$ + + + rules2 + + .*\.dSYM($|/) + + weight + 11 + + ^(.*/)?\.DS_Store$ + + omit + + weight + 2000 + + ^(Frameworks|SharedFrameworks|PlugIns|Plug-ins|XPCServices|Helpers|MacOS|Library/(Automator|Spotlight|LoginItems))/ + + nested + + weight + 10 + + ^.* + + ^Info\.plist$ + + omit + + weight + 20 + + ^PkgInfo$ + + omit + + weight + 20 + + ^Resources/ + + weight + 20 + + ^Resources/.*\.lproj/ + + optional + + weight + 1000 + + ^Resources/.*\.lproj/locversion.plist$ + + omit + + weight + 1100 + + ^Resources/Base\.lproj/ + + weight + 1010 + + ^[^/]+$ + + nested + + weight + 10 + + ^embedded\.provisionprofile$ + + weight + 20 + + ^version\.plist$ + + weight + 20 + + + + diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/manifest.mf b/Executables/Mesquite.jar & MacOS (pre-Catalina)/manifest.mf new file mode 100644 index 000000000..2ea04d173 --- /dev/null +++ b/Executables/Mesquite.jar & MacOS (pre-Catalina)/manifest.mf @@ -0,0 +1,5 @@ +Manifest-Version: 1.0 +X-COMMENT: Main-Class will be added automatically by build +Codebase: *.oracle.com +Permissions: sandbox +Application-Name: Mesquite diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/mesq.html b/Executables/Mesquite.jar & MacOS (pre-Catalina)/mesq.html new file mode 100644 index 000000000..d95dc94c3 --- /dev/null +++ b/Executables/Mesquite.jar & MacOS (pre-Catalina)/mesq.html @@ -0,0 +1,45 @@ + + + + + + + +

Test page for Mesquite

+ Webstart: click to launch this app as webstart

+ + +
+ diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/mesq.jnlp b/Executables/Mesquite.jar & MacOS (pre-Catalina)/mesq.jnlp new file mode 100644 index 000000000..60766afe7 --- /dev/null +++ b/Executables/Mesquite.jar & MacOS (pre-Catalina)/mesq.jnlp @@ -0,0 +1,14 @@ + + + + Mesquite + Mesquite Project Team + Mesquite + + + + + + + + diff --git a/Executables/Mesquite.jar & MacOS (pre-Catalina)/src/start/Mesquite.java b/Executables/Mesquite.jar & MacOS (pre-Catalina)/src/start/Mesquite.java new file mode 100644 index 000000000..f9ca41143 --- /dev/null +++ b/Executables/Mesquite.jar & MacOS (pre-Catalina)/src/start/Mesquite.java @@ -0,0 +1,263 @@ +/* Mesquite source code. Copyright 1997 and onward, W. Maddison and D. Maddison. + + +Disclaimer: The Mesquite source code is lengthy and we are few. There are no doubt inefficiencies and goofs in this code. +The commenting leaves much to be desired. Please approach this source code with the spirit of helping out. +Perhaps with your help we can be more than a few, and make Mesquite better. + +Mesquite is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY. +Mesquite's web site is http://mesquiteproject.org + +This source code and its compiled class files are free and modifiable under the terms of +GNU Lesser General Public License. (http://www.gnu.org/copyleft/lesser.html) + */ + +package start; + +import java.io.File; +import java.io.UnsupportedEncodingException; +import java.lang.reflect.*; +import java.lang.Class; +import java.net.URL; +import java.net.URLClassLoader; +import java.net.URLDecoder; +import java.net.URLEncoder; +import java.util.Vector; +import java.lang.ClassLoader; + +/*This class is used to start Mesquite. It is now the expected way to start Mesquite, whether in executables or not, + * because (as of Java 9) Mesquite needs to use a custom classloader for its modules. + * + * History: In older Javas, application bundles/executables could set their initial classpath to outside the bundle, but in Java 1.7 on MacOS + * that became prohibited. This starter was therefore built to live inside application bundle, and it would manually find mesquite.Mesquite outside the + * application bundle, and start it using the system class loader. This could work because the system classloader was also a URLClassLoader, and therefore + * could have Mesquite's classpath added at runtime by reflection-hacking into addURL. With Java 1.9 that changed, and + * the system ClassLoader was no longer a URLClassLoader and could no longer add classpaths after startup. Thus, this starter had to make its own URLClassLoader, and also find + * and add all the various possible classpaths. + * + * The scenario is this: + * 1. start.Mesquite is instantiated and startMesquite is called + * 2. startMesquite finds the basic Mesquite classpath (i.e. Mesquite_Folder) in order to be able to ask mesquite.Mesquite to supply a class loader with all classpaths added + * 3. makeModuleClassLoader in mesquite.Mesquite adds classpaths for the basic Mesquite_Folder classpath, the directories indicated by classpaths.txt, and supplementary locations (support files/classes, additionalModules) + * Also added are any jars found in jars/ directories. See mesquite.Mesquite.makeModuleClassLoader for details (e.g., when ByteBuddy is used). + * 4. This is all complex because different running conditions generate different configurations: + * —Under Javas before 9.0, the system class loader is a URLClassLoader and so the extra classpaths can be added at runtime. We end up with a single class loader, the system one. + * —Under Java 9, the modules are always loaded by the URLClassLoader created here and filled in by makeModuleClassLoader. + * + * startMesquite then uses the classloader to instantiate mesquite_Mesquite and call its main method. Mesquite then goes on to use the classloader to use modules. + * + * Starting regimes: + * Eclipse: set start.Mesquite as main class + * For all other execution, this class and ByteBuddy classes need to be bundled into a jar file, and that is used to start Mesquite. See Executables folder for instructions. + */ + +public class Mesquite { + URLClassLoader basicLoader; + + public static void main(String args[]) throws Exception{ + Mesquite m = new Mesquite(); + m.startMesquite(args); + } + + Vector startupNotices = new Vector(); + void startMesquite(String args[]){ + ClassLoader cl = start.Mesquite.class.getClassLoader(); + String loc = cl.getResource("start/Mesquite.class").getPath(); + System.out.println("Starting Mesquite with Java: " + System.getProperty("java.version")); + startupNotices.addElement("start.Mesquite: Location of executable start class: " + loc); + + if (loc.startsWith("file:")){ + loc = loc.substring(5, loc.length()); + } + // loc = decodeFromURL(loc); + try { + loc = URLDecoder.decode(loc, "UTF-8"); + } catch (UnsupportedEncodingException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + System.out.println("Location of executable start class: " + loc); + + /*Find Mesquite_Folder by moving upwards until signature folders are found + * Mesquite_Folder must contain "mesquite", "images", and "start"*/ + loc = findMesquite_Folder(loc); + //If started from a jar file within an OS X application bundle, loc is initially within /Contents/Java//start/Mesquite.class + + File mesquiteDirectory = new File(loc); + System.out.println("Mesquite Folder: " + loc + " (exists = " + mesquiteDirectory.exists() + ")"); + startupNotices.addElement("start.Mesquite: Mesquite Folder: " + loc); + + /*First, build a basic class loader that will be used to load mesquite.Mesquite from the Mesquite_Folder + and also passed to Mesquite to use in loading modules. This basic class loader needs to have already + added the URLs to the extra module directories specified in classpaths.txt. + It asks Mesquite to handle much of this.*/ + try { + URL u =null; + URL[] us= null; + u =mesquiteDirectory.toURL(); + URL[] forMF = {u}; + ClassLoader current = ClassLoader.getSystemClassLoader(); + if (current instanceof URLClassLoader){ + basicLoader = (URLClassLoader)current; + Class sysclass = URLClassLoader.class; + + try { + Method method = sysclass.getDeclaredMethod("addURL",new Class[]{URL.class}); + method.setAccessible(true); + method.invoke(basicLoader,new Object[]{ u }); + } + catch (Throwable t) { + } + } + if (basicLoader == null) + basicLoader = new URLClassLoader(forMF, null); + Class mesquiteFileClass = basicLoader.loadClass("mesquite.Mesquite"); + Class[] argTypesMCL = new Class[] {String.class, URLClassLoader.class, Vector.class}; + Method makeClassLoader = mesquiteFileClass.getDeclaredMethod("makeModuleClassLoader", argTypesMCL); + basicLoader = (URLClassLoader)makeClassLoader.invoke(null, new Object[]{loc, basicLoader, startupNotices}); + } + catch (Throwable t) { + t.printStackTrace(); + } + + /*Next, using the basic class loader to start Mesquite, doing it via a special main method that is passed this starter*/ + try { + Class c = basicLoader.loadClass("mesquite.Mesquite"); + Class[] argTypes = new Class[] { String[].class, Object.class}; + Method main = c.getDeclaredMethod("mainViaStarter", argTypes); + main.invoke(null, new Object[]{args, this}); + } + catch (Throwable t) { + System.out.println("There appears to be a problem starting Mesquite."); + t.printStackTrace(); + } + + + } + /*-------------------------*/ + String findMesquite_Folder(String loc){ + while (loc.length() > 0){ + File here = new File(loc); + if (here.exists() && here.isDirectory()){ + String[] list = here.list(); + if (itemFound(list, "mesquite") && itemFound(list, "images") && itemFound(list, "start")) + return loc; + } + loc = stripLast(loc); + } + return null; + } + /*-------------------------*/ + boolean itemFound(String[] list, String item){ + if (list == null || item == null) + return false; + for (int i = 0; i=indexCounter) { + if (to == null) { + newString = newString.substring(0, pos)+newString.substring(pos+from.length(), newString.length()); + indexCounter = pos; + } + else { + newString = newString.substring(0, pos)+to+newString.substring(pos+from.length(), newString.length()); + indexCounter = pos +to.length(); + } + pos = newString.indexOf(from, indexCounter); + } + return newString; + } + + public static String decodeFromURL(String s){ + if (s==null) return null; + boolean done = false; + while (!done){ + done = true; + for (int i = 0; i=0){ + s = replace(s, decodeReplace[i][0], decodeReplace[i][1]); + done = false; + } + } + } + System.out.println("decoded " + s); + StringBuffer buffer = new StringBuffer(s.length()*2); + for (int i=0; i"); + else if (s.charAt(i+1) == '3' && s.charAt(i+2) == 'C') + buffer.append("<"); + else if (s.charAt(i+1) == '2' && s.charAt(i+2) == '2') + buffer.append("\""); + else if (s.charAt(i+1) == '2' && s.charAt(i+2) == '3') + buffer.append("#"); + else if (s.charAt(i+1) == '2' && s.charAt(i+2) == '5') + buffer.append("%"); + else if (s.charAt(i+1) == '7' && s.charAt(i+2) == 'B') + buffer.append("{"); + else if (s.charAt(i+1) == '7' && s.charAt(i+2) == 'D') + buffer.append("}"); + else if (s.charAt(i+1) == '7' && s.charAt(i+2) == 'C') + buffer.append("|"); + else if (s.charAt(i+1) == '5' && s.charAt(i+2) == 'C') + buffer.append("\\"); + else if (s.charAt(i+1) == '5' && s.charAt(i+2) == 'E') + buffer.append("^"); + else if (s.charAt(i+1) == '7' && s.charAt(i+2) == 'E') + buffer.append("E~"); + else if (s.charAt(i+1) == '5' && s.charAt(i+2) == 'B') + buffer.append("["); + else if (s.charAt(i+1) == '5' && s.charAt(i+2) == 'D') + buffer.append("]"); + else if (s.charAt(i+1) == '6' && s.charAt(i+2) == '0') + buffer.append("`"); + i += 2; + } + else + buffer.append(s.charAt(i)); + } + return buffer.toString(); + } + +*/ +} + + + + diff --git a/Executables/Windows via Launch4J /INSTRUCTIONSforBuildingWindowsExecutableForMesquite.txt b/Executables/Windows via Launch4J /INSTRUCTIONSforBuildingWindowsExecutableForMesquite.txt new file mode 100644 index 000000000..82144a57b --- /dev/null +++ b/Executables/Windows via Launch4J /INSTRUCTIONSforBuildingWindowsExecutableForMesquite.txt @@ -0,0 +1,93 @@ +To build Windows executable +LAST USE AND VERSION August 2021 + +Steps 0 ===================================== +Download launch4j. It will generate a launch4j directory with subfolders like this: + bin + build.xml + demo + head + head_jni_BETA + head_src + launch4j + launch4j.jar + launch4j.jfpr + launch4jc + lib + LICENSE.txt + manifest + maven + src + w32api + web + +Move the "mesquiteLaunch4j" directory into the launch4j directory if it's not already there + +Make sure you have the appropriate version of ByteBuddy. + If you need a new version, then unpack the jar using + jar xf byte-buddy-agent-1.7.8.jar [this should yield a "net" directory] + +This does not use launch4j's build.xml, but rather does each piece separately. + +Step 1 ===================================== +Replace mesquiteLaunch4j/mesquite/start/Mesquite.java with latest start.Mesquite.java from Mesquite Workspace + + +Step 2 ===================================== +Make sure l4j/Mesquite.xml has desired memory specs in the VM options, and any other flags/options +e.g., for java higher than 8 use the following. (For Java 8 must change minVersion and delete the add-opens line) + + + gui + ../Mesquite.jar + ../Mesquite.exe + Mesquite + http://java.com/download + . + Mesquite.ico + + start.Mesquite + . + %EXEDIR% + + + 9 + --add-opens java.base/java.net=ALL-UNNAMED + -Xmx8000M + -Xss16m + -Djava.library.path=lib + -Djri.ignore.ule="yes" + + + + +Step 3 ===================================== +Compile necessary Mesquite class file, as follows + +cd into mesquiteLaunch4j/ +Compile mesquite.start.Mesquite using javac. For instance, paste this into terminal (depends on what your java location is!) + +########## +/Library/Java/JavaVirtualMachines/jdk1.8.0_111.jdk/Contents/Home/bin/javac mesquite/start/Mesquite.java +########## + + + +Step 4 ===================================== +Build Jar and run launch4j + +########## +jar cvfm Mesquite.jar manifest.txt mesquite +cd .. +./launch4J mesquiteLaunch4j/l4j/Mesquite.xml +########## + + +Step 5 ===================================== +Then incorporate ByteBuddy: + +########## +cd mesquiteLaunch4j +jar uf Mesquite.jar net/bytebuddy/agent/* +########## + diff --git a/Executables/Windows via Launch4J /current executables/Mesquite_Starter_E1.exe b/Executables/Windows via Launch4J /current executables/Mesquite_Starter_E1.exe new file mode 100755 index 000000000..4d92dba94 Binary files /dev/null and b/Executables/Windows via Launch4J /current executables/Mesquite_Starter_E1.exe differ diff --git a/Executables/Windows via Launch4J /current executables/Mesquite_Starter_E2.exe b/Executables/Windows via Launch4J /current executables/Mesquite_Starter_E2.exe new file mode 100755 index 000000000..0ba56f4a2 Binary files /dev/null and b/Executables/Windows via Launch4J /current executables/Mesquite_Starter_E2.exe differ diff --git a/Executables/Windows via Launch4J /current executables/Mesquite_Starter_E4.exe b/Executables/Windows via Launch4J /current executables/Mesquite_Starter_E4.exe new file mode 100755 index 000000000..c3771f0f7 Binary files /dev/null and b/Executables/Windows via Launch4J /current executables/Mesquite_Starter_E4.exe differ diff --git a/Executables/Windows via Launch4J /current executables/Mesquite_Starter_K1.exe b/Executables/Windows via Launch4J /current executables/Mesquite_Starter_K1.exe new file mode 100755 index 000000000..63c0bbf2c Binary files /dev/null and b/Executables/Windows via Launch4J /current executables/Mesquite_Starter_K1.exe differ diff --git a/Executables/Windows via Launch4J /current executables/Mesquite_Starter_K2.exe b/Executables/Windows via Launch4J /current executables/Mesquite_Starter_K2.exe new file mode 100755 index 000000000..534269960 Binary files /dev/null and b/Executables/Windows via Launch4J /current executables/Mesquite_Starter_K2.exe differ diff --git a/Executables/Windows via Launch4J /current executables/Mesquite_Starter_K4.exe b/Executables/Windows via Launch4J /current executables/Mesquite_Starter_K4.exe new file mode 100755 index 000000000..957e26d07 Binary files /dev/null and b/Executables/Windows via Launch4J /current executables/Mesquite_Starter_K4.exe differ diff --git a/Executables/Windows via Launch4J /current executables/Mesquite_Starter_K8.exe b/Executables/Windows via Launch4J /current executables/Mesquite_Starter_K8.exe new file mode 100755 index 000000000..507936a43 Binary files /dev/null and b/Executables/Windows via Launch4J /current executables/Mesquite_Starter_K8.exe differ diff --git a/Executables/Windows via Launch4J /mesquiteLaunch4J/META-INF/MANIFEST.MF b/Executables/Windows via Launch4J /mesquiteLaunch4J/META-INF/MANIFEST.MF new file mode 100644 index 000000000..6e52f6baa --- /dev/null +++ b/Executables/Windows via Launch4J /mesquiteLaunch4J/META-INF/MANIFEST.MF @@ -0,0 +1,24 @@ +Manifest-Version: 1.0 +Bundle-Description: The Byte Buddy Java agent allows to access the JVM + 's HotSwap feature. +Automatic-Module-Name: net.bytebuddy.agent +Bundle-License: http://www.apache.org/licenses/LICENSE-2.0.txt +Bundle-SymbolicName: net.bytebuddy.byte-buddy-agent +Built-By: rafael +Agent-Class: net.bytebuddy.agent.Installer +Bnd-LastModified: 1508797941048 +Bundle-ManifestVersion: 2 +Can-Redefine-Classes: true +Import-Package: com.sun.tools.attach;resolution:=optional,com.ibm.tool + s.attach;resolution:=optional +Require-Capability: osgi.ee;filter:="(&(osgi.ee=JavaSE)(version=1.6))" +Can-Set-Native-Method-Prefix: true +Tool: Bnd-3.3.0.201609221906 +Export-Package: net.bytebuddy.agent;version="1.7.8" +Premain-Class: net.bytebuddy.agent.Installer +Bundle-Name: Byte Buddy Java agent +Bundle-Version: 1.7.8 +Can-Retransform-Classes: true +Created-By: Apache Maven Bundle Plugin +Build-Jdk: 1.8.0_151 + diff --git a/Executables/Windows via Launch4J /mesquiteLaunch4J/META-INF/maven/net.bytebuddy/byte-buddy-agent/pom.properties b/Executables/Windows via Launch4J /mesquiteLaunch4J/META-INF/maven/net.bytebuddy/byte-buddy-agent/pom.properties new file mode 100644 index 000000000..c90bbce7d --- /dev/null +++ b/Executables/Windows via Launch4J /mesquiteLaunch4J/META-INF/maven/net.bytebuddy/byte-buddy-agent/pom.properties @@ -0,0 +1,4 @@ +#Created by Apache Maven 3.3.9 +version=1.7.8 +groupId=net.bytebuddy +artifactId=byte-buddy-agent diff --git a/Executables/Windows via Launch4J /mesquiteLaunch4J/META-INF/maven/net.bytebuddy/byte-buddy-agent/pom.xml b/Executables/Windows via Launch4J /mesquiteLaunch4J/META-INF/maven/net.bytebuddy/byte-buddy-agent/pom.xml new file mode 100644 index 000000000..8ca39a506 --- /dev/null +++ b/Executables/Windows via Launch4J /mesquiteLaunch4J/META-INF/maven/net.bytebuddy/byte-buddy-agent/pom.xml @@ -0,0 +1,112 @@ + + + 4.0.0 + + + byte-buddy-parent + net.bytebuddy + 1.7.8 + + + byte-buddy-agent + jar + + + net.bytebuddy.agent.Installer + com.sun.tools.attach + com.ibm.tools.attach + 2.0.4 + + + Byte Buddy Java agent + The Byte Buddy Java agent allows to access the JVM's HotSwap feature. + + + + + + com.kohlschutter.junixsocket + junixsocket-native-common + ${version.unixsocket} + provided + + + junit + junit + ${version.junit} + test + + + org.mockito + mockito-core + ${version.mockito} + test + + + net.bytebuddy + byte-buddy-agent + + + + + + + + extras + + false + + + + + + org.apache.maven.plugins + maven-jar-plugin + ${version.plugin.jar} + + + ${project.build.outputDirectory}/META-INF/MANIFEST.MF + + + + + + org.apache.felix + maven-bundle-plugin + ${version.plugin.bundle} + + + process-classes + + manifest + + + + + + ${bytebuddy.agent} + ${bytebuddy.agent} + true + true + true + + ${attach.package.sun};resolution:="optional", + ${attach.package.ibm};resolution:="optional" + + + net.bytebuddy.agent + + ${project.groupId}.agent + + + + + + + + + diff --git a/Executables/Windows via Launch4J /mesquiteLaunch4J/Mesquite.jar b/Executables/Windows via Launch4J /mesquiteLaunch4J/Mesquite.jar new file mode 100644 index 000000000..2ca223c0c Binary files /dev/null and b/Executables/Windows via Launch4J /mesquiteLaunch4J/Mesquite.jar differ diff --git a/Executables/Windows via Launch4J /mesquiteLaunch4J/Mesquite.l4j.ini b/Executables/Windows via Launch4J /mesquiteLaunch4J/Mesquite.l4j.ini new file mode 100644 index 000000000..0fcaa5000 --- /dev/null +++ b/Executables/Windows via Launch4J /mesquiteLaunch4J/Mesquite.l4j.ini @@ -0,0 +1,6 @@ +# Launch4j runtime config +--add-opens java.base/java.net=ALL-UNNAMED +-Xmx1000M +-Xss8m +-Djava.library.path=lib +-Djri.ignore.ule="yes" \ No newline at end of file diff --git a/Executables/Windows via Launch4J /mesquiteLaunch4J/Mesquite.xml b/Executables/Windows via Launch4J /mesquiteLaunch4J/Mesquite.xml new file mode 100644 index 000000000..d74bf1ffd --- /dev/null +++ b/Executables/Windows via Launch4J /mesquiteLaunch4J/Mesquite.xml @@ -0,0 +1,21 @@ + + gui + ../Mesquite.jar + ../Mesquite.exe + Mesquite + http://java.com/download + . + Mesquite.ico + + start.Mesquite + . + %EXEDIR% + + + 9.0.0 + -Xmx1000M + -Xss4m + -Djava.library.path=lib + -Djri.ignore.ule="yes" + + \ No newline at end of file diff --git a/Additional Files/execsToStartUnderWindows/Mesquite.exe b/Executables/Windows via Launch4J /mesquiteLaunch4J/l4j/Mesquite.ico old mode 100755 new mode 100644 similarity index 53% rename from Additional Files/execsToStartUnderWindows/Mesquite.exe rename to Executables/Windows via Launch4J /mesquiteLaunch4J/l4j/Mesquite.ico index 6bfdd286b..2eb4e4441 Binary files a/Additional Files/execsToStartUnderWindows/Mesquite.exe and b/Executables/Windows via Launch4J /mesquiteLaunch4J/l4j/Mesquite.ico differ diff --git a/Executables/Windows via Launch4J /mesquiteLaunch4J/l4j/Mesquite.xml b/Executables/Windows via Launch4J /mesquiteLaunch4J/l4j/Mesquite.xml new file mode 100644 index 000000000..7d580adbf --- /dev/null +++ b/Executables/Windows via Launch4J /mesquiteLaunch4J/l4j/Mesquite.xml @@ -0,0 +1,22 @@ + + gui + ../Mesquite.jar + ../Mesquite.exe + Mesquite + http://java.com/download + . + Mesquite.ico + + start.Mesquite + . + %EXEDIR% + + + 9 + --add-opens java.base/java.net=ALL-UNNAMED + -Xmx8000M + -Xss16m + -Djava.library.path=lib + -Djri.ignore.ule="yes" + + \ No newline at end of file diff --git a/Executables/Windows via Launch4J /mesquiteLaunch4J/lib/readme.txt b/Executables/Windows via Launch4J /mesquiteLaunch4J/lib/readme.txt new file mode 100644 index 000000000..ef44ded3a --- /dev/null +++ b/Executables/Windows via Launch4J /mesquiteLaunch4J/lib/readme.txt @@ -0,0 +1,8 @@ +Put your jar libs here and the build script will include them +in the classpath stored inside the jar manifest. +In order to run your application move the output exe file from +the dist directory to the same level as lib. + +SimpleApp.exe +lib/ +lib/xml.jar diff --git a/Executables/Windows via Launch4J /mesquiteLaunch4J/manifest.txt b/Executables/Windows via Launch4J /mesquiteLaunch4J/manifest.txt new file mode 100644 index 000000000..ee4220df4 --- /dev/null +++ b/Executables/Windows via Launch4J /mesquiteLaunch4J/manifest.txt @@ -0,0 +1 @@ +Main-Class: start.Mesquite diff --git a/Executables/Windows via Launch4J /mesquiteLaunch4J/mesquite/start/Mesquite.java b/Executables/Windows via Launch4J /mesquiteLaunch4J/mesquite/start/Mesquite.java new file mode 100644 index 000000000..98380648e --- /dev/null +++ b/Executables/Windows via Launch4J /mesquiteLaunch4J/mesquite/start/Mesquite.java @@ -0,0 +1,264 @@ +/* Mesquite source code. Copyright 1997 and onward, W. Maddison and D. Maddison. + + +Disclaimer: The Mesquite source code is lengthy and we are few. There are no doubt inefficiencies and goofs in this code. +The commenting leaves much to be desired. Please approach this source code with the spirit of helping out. +Perhaps with your help we can be more than a few, and make Mesquite better. + +Mesquite is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY. +Mesquite's web site is http://mesquiteproject.org + +This source code and its compiled class files are free and modifiable under the terms of +GNU Lesser General Public License. (http://www.gnu.org/copyleft/lesser.html) + */ + +package start; + +import java.io.File; +import java.io.UnsupportedEncodingException; +import java.lang.reflect.*; +import java.lang.Class; +import java.net.URL; +import java.net.URLClassLoader; +import java.net.URLDecoder; +import java.net.URLEncoder; +import java.util.Vector; +import java.lang.ClassLoader; + +/*This class is used to start Mesquite. It is now the expected way to start Mesquite, whether in executables or not, + * because (as of Java 9) Mesquite needs to use a custom classloader for its modules. + * + * History: In older Javas, application bundles/executables could set their initial classpath to outside the bundle, but in Java 1.7 on MacOS + * that became prohibited. This starter was therefore built to live inside application bundle, and it would manually find mesquite.Mesquite outside the + * application bundle, and start it using the system class loader. This could work because the system classloader was also a URLClassLoader, and therefore + * could have Mesquite's classpath added at runtime by reflection-hacking into addURL. With Java 1.9 that changed, and + * the system ClassLoader was no longer a URLClassLoader and could no longer add classpaths after startup. Thus, this starter had to make its own URLClassLoader, and also find + * and add all the various possible classpaths. + * + * The scenario is this: + * 1. start.Mesquite is instantiated and startMesquite is called + * 2. startMesquite finds the basic Mesquite classpath (i.e. Mesquite_Folder) in order to be able to ask mesquite.Mesquite to supply a class loader with all classpaths added + * 3. makeModuleClassLoader in mesquite.Mesquite adds classpaths for the basic Mesquite_Folder classpath, the directories indicated by classpaths.txt, and supplementary locations (support files/classes, additionalModules) + * Also added are any jars found in jars/ directories. See mesquite.Mesquite.makeModuleClassLoader for details (e.g., when ByteBuddy is used). + * 4. This is all complex because different running conditions generate different configurations: + * —Under Javas before 9.0, the system class loader is a URLClassLoader and so the extra classpaths can be added at runtime. We end up with a single class loader, the system one. + * —Under Java 9, the modules are always loaded by the URLClassLoader created here and filled in by makeModuleClassLoader. + * + * startMesquite then uses the classloader to instantiate mesquite_Mesquite and call its main method. Mesquite then goes on to use the classloader to use modules. + * + * Starting regimes: + * Eclipse: set start.Mesquite as main class + * For all other execution, this class and ByteBuddy classes need to be bundled into a jar file, and that is used to start Mesquite. See Executables folder for instructions. + */ + +public class Mesquite { + URLClassLoader basicLoader; + + public static void main(String args[]) throws Exception{ + Mesquite m = new Mesquite(); + m.startMesquite(args); + } + + Vector startupNotices = new Vector(); + void startMesquite(String args[]){ + ClassLoader cl = start.Mesquite.class.getClassLoader(); + String loc = cl.getResource("start/Mesquite.class").getPath(); + System.out.println("Starting Mesquite with Java: " + System.getProperty("java.version")); + + startupNotices.addElement("start.Mesquite: Location of executable start class: " + loc); + + if (loc.startsWith("file:")){ + loc = loc.substring(5, loc.length()); + } + // loc = decodeFromURL(loc); + try { + loc = URLDecoder.decode(loc, "UTF-8"); + } catch (UnsupportedEncodingException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + System.out.println("Location of executable start class: " + loc); + + /*Find Mesquite_Folder by moving upwards until signature folders are found + * Mesquite_Folder must contain "mesquite", "images", and "start"*/ + loc = findMesquite_Folder(loc); + //If started from a jar file within an OS X application bundle, loc is initially within /Contents/Java//start/Mesquite.class + + File mesquiteDirectory = new File(loc); + System.out.println("Mesquite Folder: " + loc + " (exists = " + mesquiteDirectory.exists() + ")"); + startupNotices.addElement("start.Mesquite: Mesquite Folder: " + loc); + + /*First, build a basic class loader that will be used to load mesquite.Mesquite from the Mesquite_Folder + and also passed to Mesquite to use in loading modules. This basic class loader needs to have already + added the URLs to the extra module directories specified in classpaths.txt. + It asks Mesquite to handle much of this.*/ + try { + URL u =null; + URL[] us= null; + u =mesquiteDirectory.toURL(); + URL[] forMF = {u}; + ClassLoader current = ClassLoader.getSystemClassLoader(); + if (current instanceof URLClassLoader){ + basicLoader = (URLClassLoader)current; + Class sysclass = URLClassLoader.class; + + try { + Method method = sysclass.getDeclaredMethod("addURL",new Class[]{URL.class}); + method.setAccessible(true); + method.invoke(basicLoader,new Object[]{ u }); + } + catch (Throwable t) { + } + } + if (basicLoader == null) + basicLoader = new URLClassLoader(forMF, null); + Class mesquiteFileClass = basicLoader.loadClass("mesquite.Mesquite"); + Class[] argTypesMCL = new Class[] {String.class, URLClassLoader.class, Vector.class}; + Method makeClassLoader = mesquiteFileClass.getDeclaredMethod("makeModuleClassLoader", argTypesMCL); + basicLoader = (URLClassLoader)makeClassLoader.invoke(null, new Object[]{loc, basicLoader, startupNotices}); + } + catch (Throwable t) { + t.printStackTrace(); + } + + /*Next, using the basic class loader to start Mesquite, doing it via a special main method that is passed this starter*/ + try { + Class c = basicLoader.loadClass("mesquite.Mesquite"); + Class[] argTypes = new Class[] { String[].class, Object.class}; + Method main = c.getDeclaredMethod("mainViaStarter", argTypes); + main.invoke(null, new Object[]{args, this}); + } + catch (Throwable t) { + System.out.println("There appears to be a problem starting Mesquite."); + t.printStackTrace(); + } + + + } + /*-------------------------*/ + String findMesquite_Folder(String loc){ + while (loc.length() > 0){ + File here = new File(loc); + if (here.exists() && here.isDirectory()){ + String[] list = here.list(); + if (itemFound(list, "mesquite") && itemFound(list, "images") && itemFound(list, "start")) + return loc; + } + loc = stripLast(loc); + } + return null; + } + /*-------------------------*/ + boolean itemFound(String[] list, String item){ + if (list == null || item == null) + return false; + for (int i = 0; i=indexCounter) { + if (to == null) { + newString = newString.substring(0, pos)+newString.substring(pos+from.length(), newString.length()); + indexCounter = pos; + } + else { + newString = newString.substring(0, pos)+to+newString.substring(pos+from.length(), newString.length()); + indexCounter = pos +to.length(); + } + pos = newString.indexOf(from, indexCounter); + } + return newString; + } + + public static String decodeFromURL(String s){ + if (s==null) return null; + boolean done = false; + while (!done){ + done = true; + for (int i = 0; i=0){ + s = replace(s, decodeReplace[i][0], decodeReplace[i][1]); + done = false; + } + } + } + System.out.println("decoded " + s); + StringBuffer buffer = new StringBuffer(s.length()*2); + for (int i=0; i"); + else if (s.charAt(i+1) == '3' && s.charAt(i+2) == 'C') + buffer.append("<"); + else if (s.charAt(i+1) == '2' && s.charAt(i+2) == '2') + buffer.append("\""); + else if (s.charAt(i+1) == '2' && s.charAt(i+2) == '3') + buffer.append("#"); + else if (s.charAt(i+1) == '2' && s.charAt(i+2) == '5') + buffer.append("%"); + else if (s.charAt(i+1) == '7' && s.charAt(i+2) == 'B') + buffer.append("{"); + else if (s.charAt(i+1) == '7' && s.charAt(i+2) == 'D') + buffer.append("}"); + else if (s.charAt(i+1) == '7' && s.charAt(i+2) == 'C') + buffer.append("|"); + else if (s.charAt(i+1) == '5' && s.charAt(i+2) == 'C') + buffer.append("\\"); + else if (s.charAt(i+1) == '5' && s.charAt(i+2) == 'E') + buffer.append("^"); + else if (s.charAt(i+1) == '7' && s.charAt(i+2) == 'E') + buffer.append("E~"); + else if (s.charAt(i+1) == '5' && s.charAt(i+2) == 'B') + buffer.append("["); + else if (s.charAt(i+1) == '5' && s.charAt(i+2) == 'D') + buffer.append("]"); + else if (s.charAt(i+1) == '6' && s.charAt(i+2) == '0') + buffer.append("`"); + i += 2; + } + else + buffer.append(s.charAt(i)); + } + return buffer.toString(); + } + +*/ +} + + + + diff --git a/Source/mesquite/Mesquite.java b/Source/mesquite/Mesquite.java index 42cd234a0..d116119a6 100644 --- a/Source/mesquite/Mesquite.java +++ b/Source/mesquite/Mesquite.java @@ -37,24 +37,24 @@ public class Mesquite extends MesquiteTrunk { /*.................................................................................................................*/ public String getCitation() { - return "Maddison, W.P. & D.R. Maddison. 2019. Mesquite: A modular system for evolutionary analysis. Version 3.61. http://www.mesquiteproject.org"; + return "Maddison, W.P. & D.R. Maddison. 2021. Mesquite: A modular system for evolutionary analysis. Version 3.70. http://www.mesquiteproject.org"; } /*.................................................................................................................*/ public String getVersion() { - return "3.61"; + return "3.70"; } /*.................................................................................................................*/ public int getVersionInt() { - return 361; + return 370; } /*.................................................................................................................*/ public double getMesquiteVersionNumber(){ - return 3.61; + return 3.70; } /*.................................................................................................................*/ public String getDateReleased() { - return "December 2019"; //"April 2007"; + return "August 2020"; //"April 2007"; } /*.................................................................................................................*/ public boolean isPrerelease(){ @@ -380,7 +380,7 @@ else if (prefsFile.exists() || prefsFileXML.exists()) { String logInitString = "Mesquite version " + getMesquiteVersion() + getBuildVersion() + "\n"; if (StringUtil.notEmpty(MesquiteModule.getSpecialVersion())) logInitString +=" " + MesquiteModule.getSpecialVersion()+ "\n"; - logInitString += ("Copyright (c) 1997-2019 W. Maddison and D. Maddison\n"); + logInitString += ("Copyright (c) 1997-2021 W. Maddison and D. Maddison\n"); logInitString += "The basic Mesquite package (class library and basic modules) is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License. " + " Mesquite is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY. For details on license and " + "lack of warranty see the GNU Lesser General Public License by selecting \"Display License\" from the Window menu or at www.gnu.org\n" @@ -443,8 +443,8 @@ else if (prefsFile.exists() || prefsFileXML.exists()) { prepareMesquite(); } if (verboseStartup) System.out.println("main init 18"); - if (isJavaVersionLessThan(1.6)){ - discreetAlert("This version of Mesquite requires Java 1.6 or higher. Please update your version of Java, or use an older version of Mesquite. Please be aware however that earlier versions of Mesquite may have bugs that affect your results. Please check the Mesquite website for information."); + if (isJavaVersionLessThan(1.8)){ + discreetAlert("This version of Mesquite requires Java 1.8 or higher. Please update your version of Java, or use an older version of Mesquite. Please be aware however that earlier versions of Mesquite may have bugs that affect your results. Please check the Mesquite website for information."); exit(true, 0); } @@ -613,7 +613,7 @@ else if (prefsFile.exists() || prefsFileXML.exists()) { } logln(" "); - String ackn = "Mesquite makes use BrowserLauncher by Eric Albert, corejava.Format by Horstmann & Cornell, ByteBuddy (http://bytebuddy.net), and iText by Lowagie & Soares."; + String ackn = "Mesquite uses BrowserLauncher by Eric Albert, corejava.Format by Horstmann & Cornell, ByteBuddy (http://bytebuddy.net), and iText by Lowagie & Soares."; ackn += " Some modules make use of JAMA by The MathWorks and NIST, and JSci by Mark Hale, Jaco van Kooten and others (see Mesquite source code for details)."; ackn += " The PAL library by Drummond and Strimmer is used by the GTR substitution model for DNA sequence simulations."; if (MesquiteTrunk.isWindows()) @@ -678,7 +678,7 @@ else if (prefsFile.exists() || prefsFileXML.exists()) { new MesquiteColorTable(); //initialize default charstate colors resetContainingMenuBar(); - /* hire all inits */ + /* hire all inits */ if (verboseStartup) System.out.println("main init 29"); hireAllEmployees(MesquiteInit.class); @@ -707,6 +707,7 @@ else if (prefsFile.exists() || prefsFileXML.exists()) { addMenuItem(MesquiteTrunk.fileMenu, "Check Now for Notices/Installs...", new MesquiteCommand("checkNotices", this)); if (MesquiteTrunk.phoneHome){ phoneHomeThread = new PhoneHomeThread(); + phoneHomeThread.setContactMessage(earlyWarning); phoneHomeThread.start(); } /**/ @@ -2453,6 +2454,7 @@ public static void prepareMesquite(){ CommandChecker.registerClass(System.class, System.class); } + String earlyWarning = ""; private void registerMacHandlers(){ if (!MesquiteWindow.GUIavailable) return; @@ -2462,8 +2464,19 @@ else if (MesquiteTrunk.isMacOSX()) { ((EAWTHandler)fileHandler).register(); } catch (NoSuchMethodError e) { + String w = "File handling failed to register with macOS (NSME)."; + earlyWarning += w; + System.out.println(w); } catch (NoClassDefFoundError e) { //WAYNECHECK: DAVIDCHECK: need to add alternative macos application event handling methods for post-1.8 Java + String w = "File handling failed to register with macOS (NCME)."; + earlyWarning += w; + System.out.println(w); + } + catch (IllegalAccessError e) { + String w = "File handling failed to register with macOS (IAE)."; + earlyWarning += w; + System.out.println(w); } } } @@ -2494,6 +2507,8 @@ else if (args[i].equals("-nb")) MesquiteTrunk.noBeans = true; else if (args[i].equals("-mqex")) MesquiteTrunk.startedFromExecutable = true; + else if (args[i].equals("-mqcat")) + ; //started from Catalina executable else if (args[i].equals("-mq17")) { MesquiteMessage.warnUser("This executable is not compatible with current Mesquite"); } diff --git a/Source/mesquite/align/ShiftOtherToMatch/ShiftOtherToMatch.java b/Source/mesquite/align/ShiftOtherToMatch/ShiftOtherToMatch.java index 4ce263ea0..73f2ed28b 100644 --- a/Source/mesquite/align/ShiftOtherToMatch/ShiftOtherToMatch.java +++ b/Source/mesquite/align/ShiftOtherToMatch/ShiftOtherToMatch.java @@ -148,7 +148,7 @@ public boolean alterData(CharacterData data, MesquiteTable table, UndoReference int totalAddedToStart = 0; boolean someAdded = false; for (int it = it1; it<=it2; it++) { - if (row.getValue()!=it) { + if (row.getValue()!=it && data.hasDataForTaxon(it)) { // June 2021 added hasDataForTaxon check match = findMatch(data,table, row.getValue(), firstColumn.getValue(), lastColumn.getValue(), it,matchStart,matchEnd); if (reverseComplementIfNecessary && !match && data instanceof DNAData) { MolecularDataUtil.reverseComplementSequencesIfNecessary((DNAData)data, this, data.getTaxa(), it, it, row.getValue(), false, false, false); diff --git a/Source/mesquite/align/lib/AlignUtil.java b/Source/mesquite/align/lib/AlignUtil.java index 0eff6f03a..cc1b92910 100644 --- a/Source/mesquite/align/lib/AlignUtil.java +++ b/Source/mesquite/align/lib/AlignUtil.java @@ -422,7 +422,8 @@ public Rectangle forceAlignment(MolecularData origData, int icOrigStart, int icO if (failed) MesquiteTrunk.mesquiteTrunk.alert("ERROR: alignment incorporation failed to recover states as in aligned matrix. " + failedReportString); else { - MesquiteTrunk.mesquiteTrunk.logln("Checksum passed for incorporating data alignment. "); + if (MesquiteTrunk.debugMode) //DRM 25.June.2021 + MesquiteTrunk.mesquiteTrunk.logln("Checksum passed for incorporating data alignment. "); if (numCharsAligned< icOrigEnd-icOrigStart+1 && numTaxaInOrig == origData.getNumTaxa()) { // the aligned section has fewer characters than the old section int ic = icOrigEnd; //set ic to the end of the piece aligned in the original matrix int numToDelete=0; diff --git a/Source/mesquite/align/lib/ExternalSequenceAligner.java b/Source/mesquite/align/lib/ExternalSequenceAligner.java index 9c416b78f..85894d828 100644 --- a/Source/mesquite/align/lib/ExternalSequenceAligner.java +++ b/Source/mesquite/align/lib/ExternalSequenceAligner.java @@ -45,7 +45,7 @@ public boolean startJob(String arguments, Object condition, boolean hiredByName) rng = new Random(System.currentTimeMillis()); programOptions = getDefaultProgramOptions(); loadPreferences(); - scriptBased = MesquiteTrunk.isJavaVersionLessThan(1.7); + //scriptBased = MesquiteTrunk.isJava VersionLessThan(1.7); return true; } public abstract String getProgramCommand(); diff --git a/Source/mesquite/assoc/ContainedAssociates/ContainedAssociates.java b/Source/mesquite/assoc/ContainedAssociates/ContainedAssociates.java index 8a87bbf81..2dc555358 100644 --- a/Source/mesquite/assoc/ContainedAssociates/ContainedAssociates.java +++ b/Source/mesquite/assoc/ContainedAssociates/ContainedAssociates.java @@ -860,11 +860,11 @@ else if (containingInTree(tree, containing)) { } NameReference migrateRef = NameReference.getNameReference("Migration"); /*....................................................................................................*/ - private void miniTerminals(Graphics g, Tree tree, int node, int[] terminals, double terminalY, int miniSpacing, boolean atTip, Color containedColor) { + private void miniTerminals(Graphics g, Tree tree, int node, int[] terminals, double terminalY, int miniSpacing, boolean atTip, Color containedColor, TaxaPartition partitions) { boolean inA =IntegerArray.inArray(node, terminals); if (tree.nodeIsInternal(node) /*&& !inA*/) { for (int d = tree.firstDaughterOfNode(node); tree.nodeExists(d); d = tree.nextSisterOfNode(d)) { - miniTerminals(g, tree, d, terminals, terminalY, miniSpacing, atTip, containedColor); + miniTerminals(g, tree, d, terminals, terminalY, miniSpacing, atTip, containedColor, partitions); } } if (inA && inTree[node]) { //terminal @@ -1051,10 +1051,10 @@ boolean legalY(double y){ return y>0 && MesquiteDouble.isCombinable(y); // && y1.0){ data.reverseComplement(0, data.getNumChars(), it, false, true); RC=true; - module.logln(" *** Reverse complemented " + taxa.getTaxonName(it)); + if (verbose) + module.logln(" *** Reverse complemented " + taxa.getTaxonName(it)); + else if (it %10 ==0) + module.log("."); } // else // module.logln("Sequence not reverse complemented " + (it+1)); @@ -276,8 +284,10 @@ public static boolean reverseComplementSequencesIfNecessary(DNAData data, Mesqui int stopsRC = getMinimumStops(data, it, modelSet); if (stops<=stopsRC) { data.reverseComplement(0, data.getNumChars(), it, false, true); // then we need to reverse them back. - } else + } else if (verbose) module.logln(" Reverse complemented " + taxa.getTaxonName(it)); + else if (it %10 ==0) + module.log("."); } } } else { @@ -285,16 +295,19 @@ public static boolean reverseComplementSequencesIfNecessary(DNAData data, Mesqui if (taxaToAdjust.isBitOn(it)) { double score = 0; - score = alignmentScoreRatioToRCScore((DNAData)data, module, comparisonTaxon, it, true); + score = alignmentScoreRatioToRCScore((DNAData)data, module, comparisonTaxon, it, MesquiteTrunk.debugMode); if (score>1.0){ data.reverseComplement(0, data.getNumChars(), it, false, true); // then we need to reverse them back. - module.logln(" *** Reverse complemented " + taxa.getTaxonName(it)); + if (verbose) + module.logln(" *** Reverse complemented " + taxa.getTaxonName(it)); RC=true; } // else // module.logln("Sequence not reverse complemented " + (it+1)); + if (it %10 ==0) + module.log("."); } } diff --git a/Source/mesquite/categ/lib/ProteinState.java b/Source/mesquite/categ/lib/ProteinState.java index 78ea57a3e..4e9f64ae4 100644 --- a/Source/mesquite/categ/lib/ProteinState.java +++ b/Source/mesquite/categ/lib/ProteinState.java @@ -155,7 +155,7 @@ else if (s == inapplicable){ if (useSymbols) temp+=ProteinData.symbolsAsStrings[e]; else - temp+=ProteinData.longNamesAsStrings[e]; //added Feb 2019 + temp+=ProteinData.longNamesAsStrings[e]; //added Feb 2 019 first=false; } } diff --git a/Source/mesquite/charMatrices/BasicDataWindowMaker/BasicDataWindowMaker.java b/Source/mesquite/charMatrices/BasicDataWindowMaker/BasicDataWindowMaker.java index 059baf346..59cb82644 100644 --- a/Source/mesquite/charMatrices/BasicDataWindowMaker/BasicDataWindowMaker.java +++ b/Source/mesquite/charMatrices/BasicDataWindowMaker/BasicDataWindowMaker.java @@ -393,6 +393,11 @@ public BasicDataWindow(BasicDataWindowMaker ownerModule, CharacterData data) { editingNotPermitted.setValue(data.isEditInhibited()); ownerModule.addCheckMenuItemToSubmenu(null, cmm,"Editing Not Permitted", ownerModule.makeCommand("toggleEditingNotPermitted", this), editingNotPermitted); + + MesquiteMenuItemSpec mmaa = ownerModule.addMenuItem( "Next Matrix", ownerModule.makeCommand("nextMatrix", this)); + mmaa.setShortcut(KeyEvent.VK_RIGHT); //right + mmaa = ownerModule.addMenuItem( "Previous Matrix", ownerModule.makeCommand("previousMatrix", this)); + mmaa.setShortcut(KeyEvent.VK_LEFT); //left ownerModule.addMenuSeparator(); @@ -421,6 +426,7 @@ public BasicDataWindow(BasicDataWindowMaker ownerModule, CharacterData data) { mCC2.setCompatibilityCheck(data.getStateClass()); textColorerName = new MesquiteString(); mCC2.setSelected(textColorerName); + ownerModule.addCheckMenuItem(ownerModule.displayMenu, "Color only taxon names", MesquiteModule.makeCommand("toggleColorOnlyTaxonNames", this), table.colorOnlyTaxonNames); MesquiteSubmenuSpec mSetColor = ownerModule.addSubmenu(ownerModule.displayMenu, "Assign Color to Selected", MesquiteModule.makeCommand("assignColor", this), ColorDistribution.standardColorNames); @@ -924,6 +930,7 @@ public Snapshot getSnapshot(MesquiteFile file) { if (widthsSet) temp.addLine("setColumnWidth " + columnWidth); temp.addLine("toggleBirdsEye " + table.showBirdsEyeView.toOffOnString()); + temp.addLine("toggleColorOnlyTaxonNames " + table.colorOnlyTaxonNames.toOffOnString()); temp.addLine("toggleShowPaleGrid " + table.showPaleGrid.toOffOnString()); temp.addLine("toggleShowPaleCellColors " + table.showPaleCellColors.toOffOnString()); temp.addLine("toggleShowPaleExcluded " + showPaleExcluded.toOffOnString()); @@ -1368,6 +1375,24 @@ MesquiteModule findCellColorerCharacters(String arguments) { return null; } + public void switchToMatrix(int imNext) { + // ask coordinator to show that window + MesquiteModule bdwC = ownerModule.getEmployer(); + Commandable mb = (Commandable)bdwC.doCommand("showExtraDataWindow", Integer.toString(imNext)); + String cloneCommand = Snapshot.getSnapshotCommands(ownerModule, null, ""); + Puppeteer p = new Puppeteer(ownerModule); + MesquiteInteger pos = new MesquiteInteger(0); + CommandRecord previous = MesquiteThread.getCurrentCommandRecord(); + CommandRecord record = new CommandRecord(true); + MesquiteThread.setCurrentCommandRecord(record); + MesquiteModule.incrementMenuResetSuppression(); + Object obj = p.sendCommands(mb, cloneCommand, pos, "", false, null,CommandChecker.defaultChecker); + MesquiteModule.decrementMenuResetSuppression(); + MesquiteThread.setCurrentCommandRecord(previous); + + // close this one + closeWindow(); + } /* ................................................................................................................. */ MesquiteInteger pos = new MesquiteInteger(0); @@ -1391,6 +1416,35 @@ public Object doCommand(String commandName, String arguments, CommandChecker che else if (checker.compare(this.getClass(), "Returns the matrix info panel", null, commandName, "getInfoPanel")) { return matrixInfoPanel; } + else if (checker.compare(this.getClass(), "Goes to the next matrix", null, commandName, "nextMatrix")) { + // figure out what is next matrix + MesquiteProject proj = data.getProject(); + int im = proj.getMatrixNumber(data); + int imNext = 0; + if (im >= proj.getNumberCharMatrices()-1) + imNext = 0; + else + imNext = im+1; + if (imNext == im) + return null; + switchToMatrix(imNext); + return null; + } + else if (checker.compare(this.getClass(), "Goes to the previous matrix", null, commandName, "previousMatrix")) { + // figure out what is previous matrix + MesquiteProject proj = data.getProject(); + int im = proj.getMatrixNumber(data); + int imPrev = 0; + if (im == 0) + imPrev = proj.getNumberCharMatrices()-1; + else + imPrev = im-1; + + if (imPrev == im) + return null; + switchToMatrix(imPrev); + return null; + } else if (checker.compare(this.getClass(), "Toggles whether the info panel is on", null, commandName, "toggleInfoPanel")) { infoPanelOn.toggleValue(ParseUtil.getFirstToken(arguments, pos)); setMatrixInfoPanel(infoPanelOn.getValue()); @@ -2086,6 +2140,10 @@ else if (checker.compare(this.getClass(), "Sets whether or not birds eye view is resetSequenceLedge(); table.repaintAll(); } + else if (checker.compare(this.getClass(), "Sets whether or not only taxon names are colored", "[on or off]", commandName, "toggleColorOnlyTaxonNames")) { + table.colorOnlyTaxonNames.toggleValue(ParseUtil.getFirstToken(arguments, pos)); + table.repaintAll(); + } else if (checker.compare(this.getClass(), "Sets whether or not the grid is drawn in pale gray", "[on or off]", commandName, "toggleShowPaleGrid")) { table.showPaleGrid.toggleValue(ParseUtil.getFirstToken(arguments, pos)); table.paleGrid = table.showPaleGrid.getValue(); @@ -2455,8 +2513,7 @@ else if (code == MesquiteListener.PARTS_DELETED) { int starting = parameters[0]; int num = parameters[1]; if (data.getNumChars() < table.getNumColumns()) { - for (int i = starting + num - 1; i >= starting; i--) - table.deleteColumn(i); + table.deleteColumns(starting, starting + num - 1); } } else if (table.getNumColumns() != data.getNumChars()) @@ -2957,6 +3014,7 @@ class MatrixTable extends mesquite.lib.table.CMTable implements MesquiteDroppedF MesquiteBoolean reduceCellBorders; MesquiteBoolean showDefaultCharNames; + MesquiteBoolean colorOnlyTaxonNames; MesquiteBoolean autoWithCharNames; @@ -3037,6 +3095,7 @@ public MatrixTable(BasicDataWindowMaker editorModule, BasicDataWindow window, Ch showStates = new MesquiteBoolean(true); reduceCellBorders = new MesquiteBoolean(false); showDefaultCharNames = new MesquiteBoolean(false); + colorOnlyTaxonNames = new MesquiteBoolean(false); autoWithCharNames = new MesquiteBoolean(!(data instanceof MolecularData)); showBirdsEyeView = new MesquiteBoolean(false); showPaleGrid = new MesquiteBoolean(false); @@ -3583,16 +3642,16 @@ public void processFilesDroppedOnPanel(List files) { } fileInterpreter.setImportFileNumber(count); // system.out.println("next file dropped is: " + nextFile); - MesquiteMessage.println("\n\nReading file " + nextFile.getName()); - CommandRecord.tick("\n\nReading file " + nextFile.getName()); + count++; + MesquiteMessage.println("Reading file " + count + " of " + files.size()+": " + nextFile.getName()); + CommandRecord.tick("Reading file " + count + " of " + files.size()+": " + nextFile.getName()); actUponDroppedFileContents(fileInterpreter, nextFile.getAbsolutePath()); - count++; } } if (!abort && fileInterpreter!=null) { if (adjustNewSequences) { - MesquiteMessage.println("Adjusting sequences "); + MesquiteMessage.println("Adjusting sequences... "); if (!data.someApplicableInTaxon(referenceSequence, false)){ MesquiteMessage.println("The reference sequence contains no data; adjustment cancelled."); adjustNewSequences = false; @@ -3605,6 +3664,7 @@ public void processFilesDroppedOnPanel(List files) { MolecularDataUtil.pairwiseAlignMatrix(editorModule, (MolecularData)data, referenceSequence, newTaxa,0, false); data.notifyListeners(this, new Notification(CharacterData.DATA_CHANGED, null, null)); } + MesquiteMessage.println("\nImport completed. "); } fileInterpreter.setMaximumTaxonFilled(-1); fileInterpreter.endRecordingTaxa(taxa); @@ -3888,7 +3948,7 @@ public synchronized void drawMatrixCell(Graphics g, int x, int y, int w, int h, try { Color textColor = null; - if (textColorer != null && !(textColorer instanceof mesquite.charMatrices.NoColor.NoColor)) + if (textColorer != null && !(textColorer instanceof mesquite.charMatrices.NoColor.NoColor) && !colorOnlyTaxonNames.getValue()) textColor = textColorer.getCellColor(column, row); if (textColor == null) { @@ -4068,6 +4128,9 @@ else if (rowNamesColorer != null) { textColor = ColorDistribution.getContrasting(selected, fillColor, hsb, Color.white, Color.black); } g.setColor(textColor); + Font oldFont = g.getFont(); + if (showBoldCellText.getValue()) + g.setFont(GraphicsUtil.getBoldFont(g)); String s = taxa.getAnnotation(row); @@ -4083,7 +4146,7 @@ else if (rowNamesColorer != null) { else g.drawString(t, xgnso, svp); } - + g.setFont(oldFont); g.setColor(oldColor); } @@ -5038,15 +5101,21 @@ public void returnedColumnNameText(int column, String s) { public int getMinColumnWidth() { return 3; } - + boolean turnOffIntegrityWarnings = false; public void repaintAll() { if (MesquiteWindow.checkDoomed(this)) return; displayModifications = checkDisplayModifications(); if (data != null) { String s = data.checkIntegrity(); - if (s != null) - MesquiteTrunk.mesquiteTrunk.alert(s + " (" + data + ")"); + if (s != null) { + if (turnOffIntegrityWarnings) + MesquiteTrunk.mesquiteTrunk.logln(s + " (" + data + ")"); + else + turnOffIntegrityWarnings = !AlertDialog.query(window, "Problem with data", s + " (" + data + ")", "OK", "Don't warn again"); + + // MesquiteTrunk.mesquiteTrunk.alert(s + " (" + data + ")"); + } } MesquiteWindow.uncheckDoomed(this); super.repaintAll(); diff --git a/Source/mesquite/consensus/lib/BipartitionVector.java b/Source/mesquite/consensus/lib/BipartitionVector.java index ea6b3fbc1..51f191bc6 100644 --- a/Source/mesquite/consensus/lib/BipartitionVector.java +++ b/Source/mesquite/consensus/lib/BipartitionVector.java @@ -366,7 +366,7 @@ private void printDiagnostics (Tree tree, int node) { } /*.................................................................................................................*/ - private boolean getPartitions(Tree tree, int node){ + private synchronized boolean getPartitions(Tree tree, int node){ if (node >= nodes.length) { if (((!nodeArraySizeWarningForThisTree && numNodeArraySizeWarnings<10)||node>biggestNode)){ @@ -390,12 +390,14 @@ private boolean getPartitions(Tree tree, int node){ branchLengthArrayWarningForThisTree=true; } - nodes[node].setBit(it); - double length = tree.getBranchLength(node); - if (MesquiteDouble.isCombinable(length)) { - if (!MesquiteDouble.isCombinable(branchLengths[it])) - branchLengths[it] =0.0; - branchLengths[it] += length; + if (it>=0) { + nodes[node].setBit(it); + double length = tree.getBranchLength(node); + if (MesquiteDouble.isCombinable(length)) { + if (!MesquiteDouble.isCombinable(branchLengths[it])) + branchLengths[it] =0.0; + branchLengths[it] += length; + } } return true; } diff --git a/Source/mesquite/cont/lib/ManageContCharsA.java b/Source/mesquite/cont/lib/ManageContCharsA.java index 4d56d4962..7abac63af 100644 --- a/Source/mesquite/cont/lib/ManageContCharsA.java +++ b/Source/mesquite/cont/lib/ManageContCharsA.java @@ -185,7 +185,7 @@ public boolean processCommand(CharacterData data, String commandName, String com } /*.................................................................................................................*/ public String getCharStateLabels(CharacterData data, MesquiteFile file) { - if (file.writeCharLabels){ + if (file.writeCharStateLabelsSeparately){ String csl = "CHARLABELS " + StringUtil.lineEnding(); boolean found = false; for (int i = 0; iPlease choose."; id.appendToHelpString(helpString); - RadioButtons radio = id.addRadioButtons(new String[] {"Don't Add", "Replace Data","Replace If Empty, Otherwise Add","Replace If Empty, Otherwise Ignore","Add As New Taxa"},treatmentOfIncomingDuplicates); + RadioButtons radio = id.addRadioButtons(new String[] {"Ignore", "Replace Data","Replace If Empty, Otherwise Add","Replace If Empty, Otherwise Ignore","Add As New Taxa"},treatmentOfIncomingDuplicates); id.completeAndShowDialog(true); @@ -261,6 +261,7 @@ else if (replaceDataOfTaxonWithSameNameInt==REPLACEIFEMPTYOTHERWISEIGNORE) { for (int ic=0; ic-1 && getMultiFileImport()) { @@ -291,13 +292,13 @@ else if (replaceDataOfTaxonWithSameNameInt==REPLACEIFEMPTYOTHERWISEIGNORE) { taxa.notifyListeners(this, new Notification(MesquiteListener.PARTS_ADDED), CharacterData.class, true); } } + processFileName(fileName, data, taxa, taxonNumber); } Taxon t = null; if (taxonNumber>=0) t = taxa.getTaxon(taxonNumber); - processFileName(fileName, data, taxa, taxonNumber); if (t!=null) { recordAsNewlyAddedTaxon(taxa,taxonNumber); @@ -348,7 +349,7 @@ else if (replaceDataOfTaxonWithSameNameInt==REPLACEIFEMPTYOTHERWISEIGNORE) { } - } + } } if (added) lastTaxonNumber++; diff --git a/Source/mesquite/io/lib/InterpretHennig86Base.java b/Source/mesquite/io/lib/InterpretHennig86Base.java index 5d2879e96..fc02d688d 100644 --- a/Source/mesquite/io/lib/InterpretHennig86Base.java +++ b/Source/mesquite/io/lib/InterpretHennig86Base.java @@ -463,7 +463,7 @@ public StringBuffer getDataAsFileText(MesquiteFile file, CharacterData data) { writeTaxaWithAllMissing = file.writeTaxaWithAllMissing; writeExcludedCharacters = file.writeExcludedCharacters; fractionApplicable = file.fractionApplicable; - writeCharLabels = file.writeCharLabels; + writeCharLabels = file.writeCharLabelInfo; } diff --git a/Source/mesquite/io/xExportSimpleNexus/xExportSimpleNexus.java b/Source/mesquite/io/xExportSimpleNexus/xExportSimpleNexus.java index 125b536a4..c0ea6e03c 100644 --- a/Source/mesquite/io/xExportSimpleNexus/xExportSimpleNexus.java +++ b/Source/mesquite/io/xExportSimpleNexus/xExportSimpleNexus.java @@ -153,7 +153,7 @@ public boolean exportFile(MesquiteFile file, String arguments) { //if file is nu f.useDataBlocks = useData; f.ambiguityToMissing = convertAmbiguities; f.interleaveAllowed = interleaveAllowed; - f.writeCharLabels = writeCharLabels; + f.writeCharStateLabelsSeparately = writeCharLabels; // writeOnlySelectedData ; // writeOnlyIncludedData ; f.writeOnlySelectedTaxa = writeOnlySelectedTaxa ; diff --git a/Source/mesquite/lib/ExtensibleDialog.java b/Source/mesquite/lib/ExtensibleDialog.java index 692471f76..fc2f3af06 100644 --- a/Source/mesquite/lib/ExtensibleDialog.java +++ b/Source/mesquite/lib/ExtensibleDialog.java @@ -1809,7 +1809,7 @@ public Checkbox[][] addCheckboxMatrix(int numColumns, int numRows, String[] colu /*.................................................................................................................*/ public TextArea addTextArea (String initialString, int numRows, Font font) { - return addTextArea(initialString, numRows, 40, font); + return addTextArea(initialString, numRows, 80, font); } /*.................................................................................................................*/ public TextArea addTextArea (String initialString, int numRows, int numColumns, Font font, int scrollbars, boolean textAreaFullDialogWidth) { @@ -2038,10 +2038,10 @@ public void mouseReleased(MouseEvent e){ } /*.................................................................................................................*/ public void mousePressed(MouseEvent e){ - if (MesquiteTrunk.isMacOSXYosemiteOrLater() && MesquiteTrunk.isJavaVersionLessThan(1.7)) // workaround because of bug in Yosemite Java 1.6 - checkForButtonHit(e); + // if (MesquiteTrunk.isMacOSXYosemiteOrLater() && MesquiteTrunk.isJava VersionLessThan(1.7)) // workaround because of bug in Yosemite Java 1.6 + // checkForButtonHit(e); } - + public void selectButton(String label){ //for use by scripting & console buttonHit(label, null); if (autoDispose) diff --git a/Source/mesquite/lib/ExternalProcessManager.java b/Source/mesquite/lib/ExternalProcessManager.java index 94b330986..10769c334 100644 --- a/Source/mesquite/lib/ExternalProcessManager.java +++ b/Source/mesquite/lib/ExternalProcessManager.java @@ -245,8 +245,6 @@ public static String[] getStringArrayWithSplitting(String string1, String string /** executes a shell script at "scriptPath". If runningFilePath is not blank and not null, then Mesquite will create a file there that will * serve as a flag to Mesquite that the script is running. */ public boolean executeInShell(){ - if (MesquiteTrunk.isJavaVersionLessThan(1.7)) - return false; proc = null; externalProcess = new MesquiteExternalProcess(); externalProcess.start(directoryPath, stdOutFilePath, stdErrFilePath, getStringArrayWithSplitting(programCommand, programOptions)); diff --git a/Source/mesquite/lib/GraphicsUtil.java b/Source/mesquite/lib/GraphicsUtil.java index a36daa8f1..431ae0901 100644 --- a/Source/mesquite/lib/GraphicsUtil.java +++ b/Source/mesquite/lib/GraphicsUtil.java @@ -37,6 +37,14 @@ public static void drawString(Graphics g, String s, double x, double y) { public static void drawString(Graphics2D g2, String s, double x, double y) { g2.drawString(s, (float)x, (float)y); } + + + public static Font getBoldFont(Graphics g) { + Font oldFont = g.getFont(); + FontMetrics fm = g.getFontMetrics(g.getFont()); + Font boldFont = new Font(oldFont.getName(), Font.BOLD, oldFont.getSize()); + return boldFont; + } /*_________________________________________________*/ public static void drawLine(Graphics2D g2, double fromX, double fromY, double toX, double toY) { Line2D line = new Line2D.Double(fromX, fromY, toX, toY); diff --git a/Source/mesquite/lib/ListDialog.java b/Source/mesquite/lib/ListDialog.java index 910901661..e419d2592 100644 --- a/Source/mesquite/lib/ListDialog.java +++ b/Source/mesquite/lib/ListDialog.java @@ -89,7 +89,7 @@ else if (names instanceof String[]) hideSecondaryCheckbox = addCheckBox(hideSecString, false); hideSecondaryCheckbox.setState(hideSecondary); hideSecondaryCheckbox.addItemListener(this); - requiresResetWorkaround = MesquiteTrunk.isMacOSX() && !MesquiteTrunk.isJavaVersionLessThan(1.5); + requiresResetWorkaround = MesquiteTrunk.isMacOSX(); if (requiresResetWorkaround) thread = new WorkaroundThread(this); resetShowSecondary(hideSecondary); diff --git a/Source/mesquite/lib/MesquiteDialog.java b/Source/mesquite/lib/MesquiteDialog.java index ebd1309d6..ee8958495 100644 --- a/Source/mesquite/lib/MesquiteDialog.java +++ b/Source/mesquite/lib/MesquiteDialog.java @@ -83,7 +83,7 @@ else if (parent instanceof MesquiteWindow){ } } if (f == MesquiteWindow.dialogAnchor && (MesquiteTrunk.debugMode)) - MesquiteMessage.printStackTrace("@@@@@@@@@@@DIALOG ANCHOR USED FOR " + title); //Debugg.println + MesquiteMessage.printStackTrace("@@@@@@@@@@@DIALOG ANCHOR USED FOR " + title); parentDialog = new MesquiteDialogParent(f, title, !usingWizard); //parentDialog = new MesquiteDialogParent(MesquiteWindow.dialogAnchor, title, !usingWizard); @@ -884,10 +884,11 @@ public void mouseExited(MouseEvent e) { } public void mousePressed(MouseEvent e) { - if (MesquiteTrunk.isMacOSXYosemite() && MesquiteTrunk.isJavaVersionLessThan(1.7) && e.getComponent() instanceof Button) { + /* if (MesquiteTrunk.isMacOSXYosemite() && MesquiteTrunk.isJava VersionLessThan(1.7) && e.getComponent() instanceof Button) { buttonHit(((Button) e.getComponent()).getLabel(), (Button) e.getComponent()); dispose(); } + */ } public void mouseReleased(MouseEvent e) { diff --git a/Source/mesquite/lib/MesquiteDouble.java b/Source/mesquite/lib/MesquiteDouble.java index 7f3e27205..6f8c57a40 100644 --- a/Source/mesquite/lib/MesquiteDouble.java +++ b/Source/mesquite/lib/MesquiteDouble.java @@ -840,6 +840,8 @@ else if (d == 0.0){ sFromDouble = myFormatter.format(d); if (digits==0) sFromDouble = StringUtil.removeLastCharacterIfMatch(sFromDouble, '.'); + else if (sFromDouble.indexOf(".")<0 && sFromDouble.indexOf("E")<0) //no decimal; add it if it doesn't have an exponent + sFromDouble = sFromDouble + ".0"; sb.append(sFromDouble); return sb.toString(); diff --git a/Source/mesquite/lib/MesquiteFile.java b/Source/mesquite/lib/MesquiteFile.java index 3dbb3a219..237174689 100644 --- a/Source/mesquite/lib/MesquiteFile.java +++ b/Source/mesquite/lib/MesquiteFile.java @@ -70,7 +70,8 @@ public class MesquiteFile extends Listened implements HNode, Commandable, Listab public boolean interleaveAllowed = true; //todo: this is temporary until general format options system built public boolean simplifyNames = false; //todo: this is temporary until general format options system built public boolean ambiguityToMissing = false; //todo: this is temporary until general format options system built - public boolean writeCharLabels = false; //todo: this is temporary until general format options system built + public boolean writeCharLabelInfo = true; //todo: this is temporary until general format options system built + public boolean writeCharStateLabelsSeparately = false; //todo: this is temporary until general format options system built public boolean writeExcludedCharacters=true; public boolean writeTaxaWithAllMissing = true; public boolean writeOnlySelectedTaxa = false; @@ -793,7 +794,7 @@ public static String chooseDirectory(String message, String suggestedDir) { MainThread.incrementSuppressWaitWindow(); String tempFileName=null; String tempDirectoryName=null; - if (!MesquiteWindow.GUIavailable || MesquiteWindow.suppressAllWindows || (MesquiteTrunk.isMacOS() && MesquiteTrunk.isJavaVersionLessThan(1.4))) { + if (!MesquiteWindow.GUIavailable || MesquiteWindow.suppressAllWindows) { MesquiteFileDialog fdlg= new MesquiteFileDialog(MesquiteTrunk.mesquiteTrunk.containerOfModule(), message, 3); fdlg.setResizable(true); if (suggestedDir != null) diff --git a/Source/mesquite/lib/MesquiteFileDialog.java b/Source/mesquite/lib/MesquiteFileDialog.java index fe3b9cd4a..b40c8f33d 100644 --- a/Source/mesquite/lib/MesquiteFileDialog.java +++ b/Source/mesquite/lib/MesquiteFileDialog.java @@ -37,7 +37,7 @@ public class MesquiteFileDialog extends FileDialog implements Commandable, Lista public static MesquiteFileDialog currentFileDialog = null; public MesquiteFileDialog (MesquiteWindow f, String message, int type) { super(getFrame(f), message, type); - if (type == FileDialog.LOAD && (MesquiteTrunk.isMacOS() || MesquiteTrunk.isMacOSX()) && MesquiteTrunk.getOSXVersion()>10){ + if (!StringUtil.blank(message) && (type == FileDialog.LOAD || type == FileDialog.SAVE) && (MesquiteTrunk.isMacOS() || MesquiteTrunk.isMacOSX()) && MesquiteTrunk.getOSXVersion()>10){ titleWindow = new JWindow(); titleWindow.setSize(twWidth,twHeight); titleWindowLabel = new Label(); diff --git a/Source/mesquite/lib/MesquiteFrame.java b/Source/mesquite/lib/MesquiteFrame.java index 7d18a623a..1ff0563ba 100644 --- a/Source/mesquite/lib/MesquiteFrame.java +++ b/Source/mesquite/lib/MesquiteFrame.java @@ -621,10 +621,14 @@ public void popIn(MesquiteWindow w){ if (windows == null || (!w.popAsTile && windows.indexOf(w)>=0)) //POPOUTBUGS: If window is popped out in separate window, then this doesn't work, in part as windows.indexOf(w)=0 but there is only one window. return; if (w.popAsTile){ - setVisible(w, false); //remove from resources w.poppedOut = false; + w.popAsTile= false; + setVisible(w, false); //remove from resources addPage(w, MAIN); + w.poppedOut = false; + w.popAsTile= false; setVisible(w, true); + w.resetMenus(); } else { MesquiteFrame parentFrame = w.getParentFrame(); @@ -889,7 +893,8 @@ int countMenus(){ public void diagnose(){ System.out.println(" FRAME ~~~~~~~~~ visible = " + isVisible() + " size " + getBounds().width + " " + getBounds().height + " this =" + id); System.out.println(" layout = " + mainLayout); - for (int i = 0; i\" in output in log file) " + path); @@ -4437,6 +4437,17 @@ public synchronized boolean deleteClade(int node, boolean notify) { } return false; } + /** Excise node and clade above it from tree, zeroing information at each node in clade.*/ + public synchronized static void pruneTaxaNotInCommon(MesquiteTree tree1, MesquiteTree tree2, boolean notify) { + if (tree1.getTaxa() != tree2.getTaxa()) + return; + for (int it=0; it=0 || System.getProperty("os.version").indexOf("10.11")>=0 || System.getProperty("os.version").indexOf("10.12")>=0|| System.getProperty("os.version").indexOf("10.13")>=0); } /*.................................................................................................................*/ + public static boolean isMacOSXCatalinaOrLater(){ + return System.getProperty("os.name").startsWith("Mac OS X") && (getOSXVersion()>=15); + } + /*.................................................................................................................*/ public static boolean isMacOSXJaguar(){ String mrj = System.getProperty("mrj.version"); if (mrj == null) diff --git a/Source/mesquite/lib/MesquiteWindow.java b/Source/mesquite/lib/MesquiteWindow.java index 5d02d0f1b..1554e44b0 100644 --- a/Source/mesquite/lib/MesquiteWindow.java +++ b/Source/mesquite/lib/MesquiteWindow.java @@ -1807,9 +1807,13 @@ public void resetContentsSize(){ //the size returned may not be that requested! */ if (MesquiteWindow.checkDoomed(this)) return; + try { if (windowFinishedBuilding) outerContents.validate(); windowResized(); + } + catch (StackOverflowError e) { + } MesquiteWindow.uncheckDoomed(this); } public void pack(){ diff --git a/Source/mesquite/lib/MiniScrollButton.java b/Source/mesquite/lib/MiniScrollButton.java index b12e86655..cf9a659f7 100644 --- a/Source/mesquite/lib/MiniScrollButton.java +++ b/Source/mesquite/lib/MiniScrollButton.java @@ -62,7 +62,7 @@ public MiniScrollButton (MiniScroll miniScroll, int orientation, String itemName int hlf = 6; int pg = 4; int cg = 4; - if (orientation==LEFT) { //made more inclusive Dec 2019 + if (orientation==LEFT) { //made more inclusive Dec 2 019 arrowPoly.npoints=0; arrowPoly.addPoint(0, hlf); arrowPoly.addPoint(wid-cg, 0); diff --git a/Source/mesquite/lib/ShellScriptRunner.java b/Source/mesquite/lib/ShellScriptRunner.java index 7fc8ff577..b6912a3eb 100644 --- a/Source/mesquite/lib/ShellScriptRunner.java +++ b/Source/mesquite/lib/ShellScriptRunner.java @@ -80,6 +80,10 @@ public void setOutErrFilePaths(){ public static boolean localScriptRunsCanDisplayTerminalWindow(){ return !MesquiteTrunk.isLinux(); } + /*.................................................................................................................*/ + public void deleteRunningFile(){ + MesquiteFile.deleteFile(runningFilePath); + } /*.................................................................................................................*/ public Snapshot getSnapshot(MesquiteFile file) { diff --git a/Source/mesquite/lib/ShellScriptUtil.java b/Source/mesquite/lib/ShellScriptUtil.java index 3b8fbbf54..80ee91729 100644 --- a/Source/mesquite/lib/ShellScriptUtil.java +++ b/Source/mesquite/lib/ShellScriptUtil.java @@ -191,6 +191,7 @@ public static Process executeScript(String scriptPath, boolean visibleTerminal){ else { scriptPath = scriptPath.replaceAll("//", "/"); pathArray = new String[] {scriptPath}; + // pathArray = new String[] {scriptPath, "&"}; } /*ProcessBuilder processBuilder =new ProcessBuilder(scriptPath,""); processBuilder.directory(new File(MesquiteFile.getDirectoryPathFromFilePath(scriptPath))); diff --git a/Source/mesquite/lib/characters/CharactersBlock.java b/Source/mesquite/lib/characters/CharactersBlock.java index 8a622d300..2c0cedb6b 100644 --- a/Source/mesquite/lib/characters/CharactersBlock.java +++ b/Source/mesquite/lib/characters/CharactersBlock.java @@ -37,9 +37,11 @@ public boolean mustBeAfter(NexusBlock block){ if (block==null) return false; if (data!=null && block instanceof TaxaBlock) { - return data.getTaxa() == ((TaxaBlock)block).getTaxa(); + boolean isMatchingTaxa = data.getTaxa() == ((TaxaBlock)block).getTaxa(); + return isMatchingTaxa; } - return (block.getBlockName().equalsIgnoreCase("TAXA")); + boolean isTaxa = (block.getBlockName().equalsIgnoreCase("TAXA")); + return isTaxa; } public void dispose(){ diff --git a/Source/mesquite/lib/duties/TreeInferer.java b/Source/mesquite/lib/duties/TreeInferer.java index c9378f704..85d091c11 100644 --- a/Source/mesquite/lib/duties/TreeInferer.java +++ b/Source/mesquite/lib/duties/TreeInferer.java @@ -45,6 +45,18 @@ public String getLogText() { return ""; } + /*.................................................................................................................*/ + public String getTitleOfTextCommandLink() { + return ""; + } + /*.................................................................................................................*/ + public String getCommandOfTextCommandLink() { + return ""; + } + /*.................................................................................................................*/ + public void processUserClickingOnTextCommandLink(String command) { + } + public void setOutputTextListener(OutputTextListener textListener){ } @@ -187,8 +199,8 @@ public void showIntermediatesWindow(){ if (tWindowMaker == null) { tWindowMaker = (TWindowMaker)hireNamedEmployee(TWindowMaker.class, "#ObedientTreeWindow"); String commands = getExtraTreeWindowCommands(false, MesquiteLong.unassigned); + commands += " showWindowForce;"; MesquiteWindow w = tWindowMaker.getModuleWindow(); - if (w != null){ if (w instanceof SimpleTreeWindow) ((SimpleTreeWindow)w).setWindowTitle("Most Recent Tree"); @@ -196,9 +208,6 @@ public void showIntermediatesWindow(){ p.execute(w, commands, new MesquiteInteger(0), "end;", false); } } - if (tWindowMaker != null){ - tWindowMaker.setWindowVisible(true); - } } diff --git a/Source/mesquite/lib/duties/TreeSearcher.java b/Source/mesquite/lib/duties/TreeSearcher.java index 36c09f51e..b84fbfcab 100644 --- a/Source/mesquite/lib/duties/TreeSearcher.java +++ b/Source/mesquite/lib/duties/TreeSearcher.java @@ -39,6 +39,17 @@ public String getMessageIfUserAbortRequested () { public void setOutputTextListener(OutputTextListener textListener){ + } + /*.................................................................................................................*/ + public String getTitleOfTextCommandLink() { + return ""; + } + /*.................................................................................................................*/ + public String getCommandOfTextCommandLink() { + return ""; + } + /*.................................................................................................................*/ + public void processUserClickingOnTextCommandLink(String command) { } diff --git a/Source/mesquite/lib/table/EditorTextField.java b/Source/mesquite/lib/table/EditorTextField.java index 0b7587cfe..a6ecbd42f 100644 --- a/Source/mesquite/lib/table/EditorTextField.java +++ b/Source/mesquite/lib/table/EditorTextField.java @@ -10,7 +10,7 @@ This source code and its compiled class files are free and modifiable under the terms of GNU Lesser General Public License. (http://www.gnu.org/copyleft/lesser.html) -*/ + */ package mesquite.lib.table; import java.awt.*; @@ -39,7 +39,7 @@ public class EditorTextField extends TextField { Undoer originalUndoer = null; Listened listened = new Listened(); boolean somethingTyped = false; - + public EditorTextField (EditorPanel panel, int column, int row) { super(); try { @@ -54,12 +54,12 @@ public EditorTextField (EditorPanel panel, int column, int row) { textReturnedCommand = MesquiteModule.makeCommand("returnText", panel); textReturnedCommand.setSuppressLogging(true); setBackground(ColorDistribution.veryLightGray); - // setBackground(ColorDistribution.cyan); + // setBackground(ColorDistribution.cyan); kListener = new KListener(panel.getMesquiteWindow(), this); addKeyListener(kListener); addFocusListener(new FListener()); } - + public Listened getListened() { return listened; } @@ -81,9 +81,9 @@ public void setFont(Font f){ fontMetrics = g.getFontMetrics(getFont()); g.dispose(); } - -private int ccc = 0; + + private int ccc = 0; public void setText(String s){ if (s == null) super.setText(""); @@ -93,7 +93,7 @@ public void setText(String s){ } allowReturn = true; } - + public String getOriginalText(){ return originalText; } @@ -124,7 +124,7 @@ public void resetLocation(){ panel.getWindow().setUndoer(new UndoInstructions(UndoInstructions.SINGLEDATACELL, column, row, new MesquiteString(getOriginalText()),new MesquiteString(getText()), (mesquite.lib.characters.CharacterData)panel.getTable().getColumnAssociable(), panel.getTable())); else panel.getWindow().setUndoer((Undoer)null); - + } somethingTyped = false; //setUndoer @@ -139,8 +139,8 @@ public void setColumnRow (int column, int row) { this.row = row; } public void paint(Graphics g){ //^^^ - if (MesquiteWindow.checkDoomed(this)) - return; + if (MesquiteWindow.checkDoomed(this)) + return; super.paint(g); if (fontMetrics==null) { fontMetrics = g.getFontMetrics(getFont()); @@ -148,8 +148,8 @@ public void paint(Graphics g){ //^^^ } MesquiteWindow.uncheckDoomed(this); } - - + + public int getColumn() { return column; } @@ -200,7 +200,7 @@ public void recordEdit() { } class FListener extends FocusAdapter { public void focusLost(FocusEvent e){ - + if (editing && !suppressFocusLost) { wasEditingListener = editing; selStart = getSelectionStart(); @@ -245,37 +245,39 @@ public void setWindow(MesquiteWindow window) { } public void keyPressed(KeyEvent e){ //Event queue - if (e.getKeyCode()== KeyEvent.VK_ENTER) { + if (e.getKeyCode()== KeyEvent.VK_ENTER) { panel.enterPressed(e); } else if (e.getKeyCode()== KeyEvent.VK_TAB) { panel.tabPressed(e); } - else if (e.getKeyCode()== KeyEvent.VK_RIGHT){ - if (getSelectionStart()==0 && getSelectionEnd()== getText().length()) - panel.rightArrowPressed(e); - } - else if (e.getKeyCode()== KeyEvent.VK_LEFT) { - if (getSelectionStart()==0 && getSelectionEnd()== getText().length()) - panel.leftArrowPressed(e); + else if (!MesquiteEvent.commandOrControlKeyDown(MesquiteEvent.getModifiers(e))) { + if (e.getKeyCode()== KeyEvent.VK_RIGHT){ + if (getSelectionStart()==0 && getSelectionEnd()== getText().length()) + panel.rightArrowPressed(e); + } + else if (e.getKeyCode()== KeyEvent.VK_LEFT) { + if (getSelectionStart()==0 && getSelectionEnd()== getText().length()) + panel.leftArrowPressed(e); + } + else if (e.getKeyCode()== KeyEvent.VK_UP) + panel.upArrowPressed(e); + else if (e.getKeyCode()== KeyEvent.VK_DOWN) + panel.downArrowPressed(e); + else { //not commandORControl down + somethingTyped=true; + if (window!=null) + if (textField.getOriginalText()!=null) { + originalUndoer = new UndoInstructions(UndoInstructions.EDITTEXTFIELD, new MesquiteString(textField.getOriginalText()),new MesquiteString(""), textField); + window.setUndoer(originalUndoer); + } + } } - else if (e.getKeyCode()== KeyEvent.VK_UP) - panel.upArrowPressed(e); - else if (e.getKeyCode()== KeyEvent.VK_DOWN) - panel.downArrowPressed(e); - else if (MesquiteEvent.commandOrControlKeyDown(MesquiteEvent.getModifiers(e))) { + else { if (window!=null & somethingTyped) { window.setNewUndoState(new MesquiteString(textField.getText())); } } - else { //not commandORControl down - somethingTyped=true; - if (window!=null) - if (textField.getOriginalText()!=null) { - originalUndoer = new UndoInstructions(UndoInstructions.EDITTEXTFIELD, new MesquiteString(textField.getOriginalText()),new MesquiteString(""), textField); - window.setUndoer(originalUndoer); - } - } } } diff --git a/Source/mesquite/lib/table/MesquiteTable.java b/Source/mesquite/lib/table/MesquiteTable.java index 0f440b342..095a8f6ee 100644 --- a/Source/mesquite/lib/table/MesquiteTable.java +++ b/Source/mesquite/lib/table/MesquiteTable.java @@ -1,6 +1,6 @@ /* Mesquite source code. Copyright 1997 and onward, W. Maddison and D. Maddison. - + Disclaimer: The Mesquite source code is lengthy and we are few. There are no doubt inefficiencies and goofs in this code. The commenting leaves much to be desired. Please approach this source code with the spirit of helping out. Perhaps with your help we can be more than a few, and make Mesquite better. @@ -787,27 +787,27 @@ protected void OLDpasteIt(String s) { protected void pasteIt(String s) { int count = 0; MesquiteInteger pos = new MesquiteInteger(0); - for (int i = 0; i < numColumnsTotal; i++) { - if (isColumnNameSelected(i) || isColumnSelected(i)) { - String t = StringUtil.getNextTabbedToken(s, pos); - if (t != null && columnNamesEditable && columnNamesCopyPaste) - returnedColumnNameText(i, t); - count++; - } + for (int i = 0; i < numColumnsTotal; i++) { + if (isColumnNameSelected(i) || isColumnSelected(i)) { + String t = StringUtil.getNextTabbedToken(s, pos); + if (t != null && columnNamesEditable && columnNamesCopyPaste) + returnedColumnNameText(i, t); + count++; } - + } + for (int j = 0; j < numRowsTotal; j++) { if (isRowNameSelected(j) || isRowSelected(j)) { - String t = StringUtil.getNextTabbedToken(s, pos); - if (t != null && rowNamesEditable && rowNamesCopyPaste) - returnedRowNameText(j, t); + String t = StringUtil.getNextTabbedToken(s, pos); + if (t != null && rowNamesEditable && rowNamesCopyPaste) + returnedRowNameText(j, t); count++; } for (int i = 0; i < numColumnsTotal; i++) { if (isCellSelected(i, j) || isRowSelected(j) || isColumnSelected(i)) { - String t = StringUtil.getNextTabbedToken(s, pos); - if (t != null && isCellEditable(i, j)) - returnedMatrixText(i, j, t); + String t = StringUtil.getNextTabbedToken(s, pos); + if (t != null && isCellEditable(i, j)) + returnedMatrixText(i, j, t); count++; } } @@ -1122,25 +1122,27 @@ else if (e.getKeyCode() == KeyEvent.VK_TAB){ key.setSuppressLogging(true); key.doItMainThread(arguments, null, this); } - else if (e.getKeyCode() == KeyEvent.VK_RIGHT){ - MesquiteCommand key = new MesquiteCommand("rightArrowPressed", arguments, this); - key.setSuppressLogging(true); - key.doItMainThread(arguments, null, this); - } - else if (e.getKeyCode() == KeyEvent.VK_LEFT) { - MesquiteCommand key = new MesquiteCommand("leftArrowPressed", arguments, this); - key.setSuppressLogging(true); - key.doItMainThread(arguments, null, this); - } - else if (e.getKeyCode() == KeyEvent.VK_UP){ - MesquiteCommand key = new MesquiteCommand("upArrowPressed", arguments, this); - key.setSuppressLogging(true); - key.doItMainThread(arguments, null, this); - } - else if (e.getKeyCode() == KeyEvent.VK_DOWN){ - MesquiteCommand key = new MesquiteCommand("downArrowPressed", arguments, this); - key.setSuppressLogging(true); - key.doItMainThread(arguments, null, this); + else if (!MesquiteEvent.commandOrControlKeyDown(e.getModifiers())) { + if (e.getKeyCode() == KeyEvent.VK_RIGHT){ + MesquiteCommand key = new MesquiteCommand("rightArrowPressed", arguments, this); + key.setSuppressLogging(true); + key.doItMainThread(arguments, null, this); + } + else if (e.getKeyCode() == KeyEvent.VK_LEFT) { + MesquiteCommand key = new MesquiteCommand("leftArrowPressed", arguments, this); + key.setSuppressLogging(true); + key.doItMainThread(arguments, null, this); + } + else if (e.getKeyCode() == KeyEvent.VK_UP){ + MesquiteCommand key = new MesquiteCommand("upArrowPressed", arguments, this); + key.setSuppressLogging(true); + key.doItMainThread(arguments, null, this); + } + else if (e.getKeyCode() == KeyEvent.VK_DOWN){ + MesquiteCommand key = new MesquiteCommand("downArrowPressed", arguments, this); + key.setSuppressLogging(true); + key.doItMainThread(arguments, null, this); + } } } @@ -2214,15 +2216,46 @@ public void resetComponentSizes() { resetNumRowsVisible(); } + /* ............................................................................................................... */ + /** Deletes the given column (but doesn't call for repaint) */ + public void deleteColumns(int firstColumn, int lastColumn) { + if (!columnLegal(firstColumn) || !columnLegal(lastColumn)) + return; + + if (lastColumn < numColumnsTotal && firstColumn >= 0) { + int numToDelete = lastColumn-firstColumn+1; + int[] newColumnWidths = new int[numColumnsTotal - numToDelete]; + for (int c = 0; c < numColumnsTotal - numToDelete; c++) + if (c >= firstColumn) + newColumnWidths[c] = columnWidths[c + numToDelete]; + else + newColumnWidths[c] = columnWidths[c]; + + columnWidths = newColumnWidths; + + numColumnsTotal = numColumnsTotal - numToDelete; + for (int i = 0; i < numSelectTypes; i++) { + columnsSelected[i] = new Bits(numColumnsTotal); + cellsSelected[i] = new Bits((numRowsTotal) * (numColumnsTotal)); + columnNamesSelected[i] = new Bits(numColumnsTotal); + } + if (firstColumnVisible >= numColumnsTotal || firstColumnVisible < 0) + firstColumnVisible = 0; + if (horizScroll != null) { + horizScroll.setValue(firstColumnVisible); + horizScroll.setMaximum(numColumnsTotal); + } + } + } /* ............................................................................................................... */ /** Deletes the given column (but doesn't call for repaint) */ public void deleteColumn(int column) { if (!columnLegal(column)) return; - if (column < numColumnsTotal && column >= 0) { + if (column < numColumnsTotal && column >= 0) { int[] newColumnWidths = new int[numColumnsTotal - 1]; for (int c = 0; c < numColumnsTotal - 1; c++) - if (c > column) + if (c >= column) newColumnWidths[c] = columnWidths[c + 1]; else newColumnWidths[c] = columnWidths[c]; @@ -2230,7 +2263,7 @@ public void deleteColumn(int column) { columnWidths = newColumnWidths; numColumnsTotal = numColumnsTotal - 1; - for (int i = 0; i < numSelectTypes; i++) { + for (int i = 0; i < numSelectTypes; i++) { columnsSelected[i] = new Bits(numColumnsTotal); cellsSelected[i] = new Bits((numRowsTotal) * (numColumnsTotal)); columnNamesSelected[i] = new Bits(numColumnsTotal); @@ -2420,7 +2453,7 @@ public void resetNumRowsVisible() { if (numRowsPossiblyVisible>verticalScrollPageIncrement) verticalScrollPageIncrement = numRowsPossiblyVisible; } - + //vertScroll.setBlockIncrement(getNumRows()-1); if (numRowsTotal < 2) vertScroll.setBlockIncrement(1); @@ -4448,7 +4481,7 @@ public boolean nextSingleRowBlockSelected(MesquiteInteger row, MesquiteInteger f if (!row.isCombinable()) { incomingRow = 0; } - + int incomingLastColumn = lastColumn.getValue(); if (!lastColumn.isCombinable()){ // can only happen on first time through incomingLastColumn = -1; @@ -4459,13 +4492,13 @@ else if (incomingLastColumn >= numColumnsTotal - 1) { // end of previous row, ne } else incomingLastColumn++; - + if (nextRow) incomingRow++; - + if (incomingRow >= numRowsTotal) //incomingRow is 0-based but numRowsTotal is 1-based return false; - + for (int i = incomingRow; i < numRowsTotal; i++) { // go through the rows if (wholeRowSelectedAnyWay(i)) { row.setValue(i); diff --git a/Source/mesquite/lists/TaxonListVoucherDB/TaxonListVoucherDB.java b/Source/mesquite/lists/TaxonListVoucherDB/TaxonListVoucherDB.java index 5739eddca..2359ffe48 100644 --- a/Source/mesquite/lists/TaxonListVoucherDB/TaxonListVoucherDB.java +++ b/Source/mesquite/lists/TaxonListVoucherDB/TaxonListVoucherDB.java @@ -1 +1 @@ -/* Mesquite source code. Copyright 2005 and onward, David Maddison and Wayne Maddison. Disclaimer: The Mesquite source code is lengthy and we are few. There are no doubt inefficiencies and goofs in this code. The commenting leaves much to be desired. Please approach this source code with the spirit of helping out. Perhaps with your help we can be more than a few, and make Mesquite better. Mesquite is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY. Mesquite's web site is http://mesquiteproject.org This source code and its compiled class files are free and modifiable under the terms of GNU Lesser General Public License. (http://www.gnu.org/copyleft/lesser.html) */ package mesquite.lists.TaxonListVoucherDB; /*~~ */ import mesquite.lists.lib.*; import mesquite.lib.*; import mesquite.lib.table.*; /* ======================================================================== */ public class TaxonListVoucherDB extends TaxonListAssistant { Taxa taxa; MesquiteTable table=null; MesquiteMenuItemSpec msbrowseDB; MesquiteMenuItemSpec msSetDB; /*.................................................................................................................*/ public boolean startJob(String arguments, Object condition, boolean hiredByName) { return true; } /*.................................................................................................................*/ public void setTableAndTaxa(MesquiteTable table, Taxa taxa){ if (this.taxa != null) this.taxa.removeListener(this); this.taxa = taxa; if (this.taxa != null) this.taxa.addListener(this); this.table = table; deleteMenuItem(msbrowseDB); msbrowseDB = addMenuItem("Browse for OTU ID code database...", makeCommand("browseDB", this)); deleteMenuItem(msSetDB); msSetDB = addMenuItem("Set OTU ID code database...", makeCommand("setDB", this)); } /*.................................................................................................................*/ public void dispose() { super.dispose(); if (taxa!=null) taxa.removeListener(this); } /*.................................................................................................................*/ private void setDBURL(String arguments){ if (table !=null && taxa!=null) { boolean changed=false; String path = arguments; //parser.getFirstToken(arguments); if (StringUtil.blank(path)) return; if (employer!=null && employer instanceof ListModule) { int c = ((ListModule)employer).getMyColumn(this); for (int i=0; i=0){ - int height = index; + int neededHeight = index; //make sure block is in OK place for (int i = index-1; i>=0; i--) { //now look to all higher to see if nb should jump above them NexusBlock nR = (NexusBlock)blocks.elementAt(i); if (!nb.mustBeAfter(nR) && (nb.getFile()==nR.getFile())) { //nb needs to jump above nR - height = i; //remember height of nR + if (i=0; i--) { if (bs[i] instanceof TaxaBlock){ blocks.removeElement((NexusBlock)bs[i], false); blocks.insertElementAt((NexusBlock)bs[i], 0, false); } } - } /** Asks if block is sorted relative to other blocks in its file and before its file in file read order. NOT USED as of 3. 02 */ diff --git a/Source/mesquite/molec/TaxaListHasData/TaxaListHasData.java b/Source/mesquite/molec/TaxaListHasData/TaxaListHasData.java index ac0e5c976..0a7cb94a5 100644 --- a/Source/mesquite/molec/TaxaListHasData/TaxaListHasData.java +++ b/Source/mesquite/molec/TaxaListHasData/TaxaListHasData.java @@ -22,6 +22,7 @@ import java.awt.Color; import java.awt.Container; import java.awt.Graphics; +import java.awt.Label; import java.awt.Toolkit; import java.awt.datatransfer.Clipboard; import java.awt.datatransfer.DataFlavor; @@ -69,10 +70,13 @@ public boolean startJob(String arguments, Object condition, boolean hiredByName) // addMenuItem("Delete *", makeCommand("deleteStar", this)); // for Wayne!!!!!! addMenuItem("Delete Data For Selected Taxa", makeCommand("deleteData", this)); addMenuSeparator(); + addMenuItem("(Right click cell for more options)", null); addMenuItem("Sort Taxa by Presence of Data", makeCommand("sortByPresence", this)); addMenuItem("Prepend Sequence Length", makeCommand("prependLength", this)); addMenuItem("Prepend Number of Non-missing Sites", makeCommand("prependNumSites", this)); addMenuItem("Delete Stored Annotation", makeCommand("deleteAnnotation", this)); + addMenuItem("Delete Stored Genbank Reference", makeCommand("deleteGenbankAnnotation", this)); + addMenuItem("Delete Stored Publication Reference", makeCommand("deletePublicationAnnotation", this)); return true; } @@ -146,9 +150,15 @@ public boolean clipBoardHasString() { /*.................................................................................................................*/ public boolean arrowTouchInRow(Graphics g, int ic, int x, int y, boolean doubleClick, int modifiers){ - if (MesquiteEvent.rightClick(modifiers)) { + if (MesquiteEvent.commandOrControlKeyDown(modifiers) || MesquiteEvent.rightClick(modifiers)) { + MesquitePopup popup = new MesquitePopup(table.getMatrixPanel()); - + + MesquiteCommand mcEditCell = makeCommand("editCell", this); + mcEditCell.setDefaultArguments(""+ic); + MesquiteMenuItem mEditCellItem = new MesquiteMenuItem("Edit Cell...", this, mcEditCell, null); + popup.add(mEditCellItem); + String copyMenuText = "Copy "; if (observedStates != null) { CharacterData data = observedStates.getParentData(); @@ -160,7 +170,7 @@ public boolean arrowTouchInRow(Graphics g, int ic, int x, int y, boolean doubleC } MesquiteCommand mcCopy = makeCommand("copyData", this); mcCopy.setDefaultArguments(""+ic); - MesquiteCheckMenuItem mCopyItem = new MesquiteCheckMenuItem(copyMenuText, this, mcCopy, null, null); + MesquiteMenuItem mCopyItem = new MesquiteMenuItem(copyMenuText, this, mcCopy, null); popup.add(mCopyItem); String pasteMenuText = "Paste "; @@ -172,13 +182,13 @@ public boolean arrowTouchInRow(Graphics g, int ic, int x, int y, boolean doubleC } MesquiteCommand mcPaste = makeCommand("pasteData", this); //only if something in clipboard mcPaste.setDefaultArguments(""+ic); - MesquiteCheckMenuItem mPasteItem = new MesquiteCheckMenuItem(pasteMenuText, this, mcPaste, null, null); + MesquiteMenuItem mPasteItem = new MesquiteMenuItem(pasteMenuText, this, mcPaste, null); mPasteItem.setEnabled(StringUtil.notEmpty(localCopyDataClipboard)); popup.add(mPasteItem); MesquiteCommand mcDelete = makeCommand("deleteDataTouched", this); mcDelete.setDefaultArguments(""+ic); - MesquiteCheckMenuItem mDeleteItem = new MesquiteCheckMenuItem("Delete Data...", this, mcDelete, null, null); + MesquiteMenuItem mDeleteItem = new MesquiteMenuItem("Delete Data...", this, mcDelete, null); popup.add(mDeleteItem); popup.showPopup(x,y+18); @@ -394,6 +404,36 @@ else if (checker.compare(this.getClass(), "Prepends to the note the number of no parametersChanged(); return null; } + else if (checker.compare(this.getClass(), "Edits the touched cell", null, commandName, "editCell")) { + int it = MesquiteInteger.fromString(parser.getFirstToken(arguments)); + + String noteTM = getNote(it,CharacterData.taxonMatrixNotesRef); + String noteGB = getNote(it,MolecularData.genBankNumberRef); + String notePC = getNote(it,CharacterData.publicationCodeNameRef); + MesquiteInteger button = new MesquiteInteger(); + ExtensibleDialog dialog = new ExtensibleDialog(containerOfModule(), "Edit notes", button); + + dialog.addLabel("Note: ", Label.LEFT); + SingleLineTextField noteTMField = dialog.addTextField(noteTM); + dialog.addLabel("Genbank: ", Label.LEFT); + SingleLineTextField noteGBField = dialog.addTextField(noteGB); + dialog.addLabel("Publication Code: ", Label.LEFT); + SingleLineTextField notePCField = dialog.addTextField(notePC); + + noteTMField.requestFocus(); + dialog.completeAndShowDialog(true,null); + boolean ok = (dialog.query()==0); + if (ok) { + setNote(it, noteTMField.getText(), CharacterData.taxonMatrixNotesRef); + setNote(it, noteGBField.getText(), MolecularData.genBankNumberRef); + setNote(it, notePCField.getText(), CharacterData.publicationCodeNameRef); + } + dialog.dispose(); + + outputInvalid(); + parametersChanged(); + return null; + } else if (checker.compare(this.getClass(), "Deletes the notes for the selected taxa", null, commandName, "deleteAnnotation")) { if (observedStates == null || taxa == null) return null; @@ -414,13 +454,53 @@ else if (checker.compare(this.getClass(), "Deletes the notes for the selected ta parametersChanged(); return null; } + else if (checker.compare(this.getClass(), "Deletes the genbank notes for the selected taxa", null, commandName, "deleteGenbankAnnotation")) { + if (observedStates == null || taxa == null) + return null; + boolean anySelected = taxa.anySelected(); + int myColumn = -1; + if (getEmployer() instanceof ListModule){ + + myColumn = ((ListModule)getEmployer()).getMyColumn(this); + if (table != null) + anySelected = anySelected || table.anyCellSelectedInColumnAnyWay(myColumn); + } + for (int it = 0; it0) { // need to reset all of tree display extras!!!!! - for (int itree = 0; itree0) { // need to reset all of tree display extras!!!!! - for (int itree = 0; itree0) { + String n = choices.nameOfElementAt(0); + valueName.setName(n); + valueName.setValue(n); + } + } + + /** Called to provoke any necessary initialization. This helps prevent the module's intialization queries to the user from + happening at inopportune times (e.g., while a long chart calculation is in mid-progress)*/ + public void initialize(Tree tree){ + if (tree == null) + return; + taxa = tree.getTaxa(); + rememberChoices(tree); + } + + /*.................................................................................................................*/ + public String getParameters(){ + return "Values: " + valueName.getValue() ; + } + /*.................................................................................................................*/ + public String getNameAndParameters(){ + return valueName.getValue(); + } + /*.................................................................................................................*/ + /** returns the version number at which this module was first released. If 0, then no version number is claimed. If a POSITIVE integer + * then the number refers to the Mesquite version. This should be used only by modules part of the core release of Mesquite. + * If a NEGATIVE integer, then the number refers to the local version of the package, e.g. a third party package*/ + public int getVersionOfFirstRelease(){ + return 370; + } + /*.................................................................................................................*/ + public boolean isPrerelease(){ + return false; + } + + /*.................................................................................................................*/ + /*.................................................................................................................*/ + /** returns whether this module is requesting to appear as a primary choice */ + public boolean requestPrimaryChoice(){ + return false; + } + +} + diff --git a/Source/mesquite/trees/TerminalBranchLength/TerminalBranchLength.java b/Source/mesquite/trees/TerminalBranchLength/TerminalBranchLength.java new file mode 100644 index 000000000..42e507d2b --- /dev/null +++ b/Source/mesquite/trees/TerminalBranchLength/TerminalBranchLength.java @@ -0,0 +1,84 @@ +/* Mesquite source code, Treefarm package. Copyright 1997 and onward, W. Maddison, D. Maddison and P. Midford. + + +Disclaimer: The Mesquite source code is lengthy and we are few. There are no doubt inefficiencies and goofs in this code. +The commenting leaves much to be desired. Please approach this source code with the spirit of helping out. +Perhaps with your help we can be more than a few, and make Mesquite better. + +Mesquite is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY. +Mesquite's web site is http://mesquiteproject.org + +This source code and its compiled class files are free and modifiable under the terms of +GNU Lesser General Public License. (http://www.gnu.org/copyleft/lesser.html) + */ +package mesquite.trees.TerminalBranchLength; +/*~~ */ + + +import mesquite.lib.*; +import mesquite.lib.duties.*; +import mesquite.treefarm.lib.*; + +/** ======================================================================== */ +public class TerminalBranchLength extends NForTaxonWithTree { + /*.................................................................................................................*/ + public boolean startJob(String arguments, Object condition, boolean hiredByName) { + return true; + } + /*.................................................................................................................*/ + /** returns whether this module is requesting to appear as a primary choice */ + public boolean requestPrimaryChoice(){ + return false; + } + /*.................................................................................................................*/ + public void calculateNumbers(Taxa taxa, Tree tree, NumberArray results, MesquiteString resultsString){ + if (tree == null) + return; + clearResultAndLastResult(results); + results.zeroArray(); + for (int it=0; it2)) { // have to add in other branch + double otherLength = tree.getBranchLength(tree.nextSisterOfNode(node)); + if (MesquiteDouble.isCombinable(otherLength)) + terminalBranchLength+= otherLength; + } + results.setValue(it, terminalBranchLength); + } + } + saveLastResult(results); + saveLastResultString(resultsString); + } + /*.................................................................................................................*/ + /** returns the version number at which this module was first released. If 0, then no version number is claimed. If a POSITIVE integer + * then the number refers to the Mesquite version. This should be used only by modules part of the core release of Mesquite. + * If a NEGATIVE integer, then the number refers to the local version of the package, e.g. a third party package*/ + public int getVersionOfFirstRelease(){ + return 370; + } + /*.................................................................................................................*/ + public String getVeryShortName() { + return "Terminal Branch Length"; + } + /*.................................................................................................................*/ + public String getName() { + return "Terminal Branch Length"; + } + /*.................................................................................................................*/ + public String getVersion() { + return null; + } + /*.................................................................................................................*/ + public boolean isPrerelease() { + return false; + } + /*.................................................................................................................*/ + /** returns an explanation of what the module does.*/ + public String getExplanation() { + return "For each taxon, calculates the length of the terminal branch on the tree, if present. If a taxon is a descendant of a dichotomous root in a tree with more than 2 taxa, then the length of the other descendant is also added in. ."; + } + +} + diff --git a/Source/mesquite/trees/lib/ManyTreesFromFileLib.java b/Source/mesquite/trees/lib/ManyTreesFromFileLib.java index f9be703e9..1ec4626fc 100644 --- a/Source/mesquite/trees/lib/ManyTreesFromFileLib.java +++ b/Source/mesquite/trees/lib/ManyTreesFromFileLib.java @@ -210,7 +210,7 @@ private int findTreeNumber(int treeNum) { } return treeNum; } - boolean fileReady = false; + protected boolean fileReady = false; /*.................................................................................................................*/ private boolean obtainFile(String arguments){ fileReady = false; @@ -267,7 +267,7 @@ private boolean getFileFromPath(String pathName){ } return (file != null); } - private boolean processFile(){ + protected boolean processFile(){ if (!goToTreeBlock(file)) return false; if (!processTreeBlock()) diff --git a/Source/mesquite/trunk/AboutPanel.java b/Source/mesquite/trunk/AboutPanel.java index 531e374e7..c523cf23a 100644 --- a/Source/mesquite/trunk/AboutPanel.java +++ b/Source/mesquite/trunk/AboutPanel.java @@ -53,7 +53,7 @@ public void paint(Graphics g) { g.drawImage(InfoBar.prereleaseImage,3,3,(ImageObserver)this); } g.drawString("http://www.mesquiteproject.org", 5,210); - g.drawString("Copyright (c) 1997-2019 W. & D. Maddison.", 5,225); + g.drawString("Copyright (c) 1997-2021 W. & D. Maddison.", 5,225); MesquiteWindow.uncheckDoomed(this); } diff --git a/Source/mesquite/trunk/PhoneHomeThread.java b/Source/mesquite/trunk/PhoneHomeThread.java index 85a0d27f6..17bf939b0 100644 --- a/Source/mesquite/trunk/PhoneHomeThread.java +++ b/Source/mesquite/trunk/PhoneHomeThread.java @@ -46,6 +46,12 @@ public void run() { } } } + + String contactMessage = ""; + public void setContactMessage(String contactMessage) { + this.contactMessage = contactMessage; + } + public void postBean(NameValuePair[] pairs){ beans.addElement(pairs); } @@ -59,6 +65,8 @@ public void checkForMessagesFromAllHomes(){ String buildNum = Integer.toString(MesquiteTrunk.getBuildNumber()); if (MesquiteTrunk.mesquiteTrunk.isPrerelease()) buildNum = "PreRelease-" + buildNum; + if (contactMessage != null) + buildNum += "&" + contactMessage; BaseHttpRequestMaker.contactServer(buildNum, MesquiteModule.versionReportURL, response); String r = response.toString(); //if mq3rs is included in response, then this is real response diff --git a/Source/start/Mesquite.java b/Source/start/Mesquite.java index f9ca41143..98380648e 100644 --- a/Source/start/Mesquite.java +++ b/Source/start/Mesquite.java @@ -64,6 +64,7 @@ void startMesquite(String args[]){ ClassLoader cl = start.Mesquite.class.getClassLoader(); String loc = cl.getResource("start/Mesquite.class").getPath(); System.out.println("Starting Mesquite with Java: " + System.getProperty("java.version")); + startupNotices.addElement("start.Mesquite: Location of executable start class: " + loc); if (loc.startsWith("file:")){ diff --git a/docs/Acknowledgements.html b/docs/Acknowledgements.html index 3c9c061e5..ea6a56fd8 100644 --- a/docs/Acknowledgements.html +++ b/docs/Acknowledgements.html @@ -41,8 +41,8 @@ Mesquite
Acknowledgements
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -235,7 +235,7 @@

Acknowledgements


diff --git a/docs/Additional Mesquite Packages.html b/docs/Additional Mesquite Packages.html index 498e60bad..f1826451d 100644 --- a/docs/Additional Mesquite Packages.html +++ b/docs/Additional Mesquite Packages.html @@ -41,8 +41,8 @@ Mesquite
Additional Packages
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -290,7 +290,7 @@

diff --git a/docs/Align.html b/docs/Align.html index 25688ea1d..47d4e173a 100644 --- a/docs/Align.html +++ b/docs/Align.html @@ -41,8 +41,8 @@ Mesquite
Sequence Alignment
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -327,7 +327,7 @@

Citation


diff --git a/docs/Analyzing Continuous Characters.html b/docs/Analyzing Continuous Characters.html index 5e5098ebe..0245a49b5 100644 --- a/docs/Analyzing Continuous Characters.html +++ b/docs/Analyzing Continuous Characters.html @@ -41,8 +41,8 @@ Mesquite
Continuous characters
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -227,7 +227,7 @@


diff --git a/docs/Analyzing Molecular Data.html b/docs/Analyzing Molecular Data.html index f7333722f..9b8c74ede 100644 --- a/docs/Analyzing Molecular Data.html +++ b/docs/Analyzing Molecular Data.html @@ -41,8 +41,8 @@ Mesquite
Molecular Data
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -263,7 +263,7 @@

diff --git a/docs/Ancestral States.html b/docs/Ancestral States.html index db36c211f..0f71da2ad 100644 --- a/docs/Ancestral States.html +++ b/docs/Ancestral States.html @@ -41,8 +41,8 @@ Mesquite
Ancestral States
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -327,7 +327,7 @@


diff --git a/docs/Are strepsipterans related to flies.html b/docs/Are strepsipterans related to flies.html index 0001f76a5..c9939b205 100644 --- a/docs/Are strepsipterans related to flies.html +++ b/docs/Are strepsipterans related to flies.html @@ -41,8 +41,8 @@ Mesquite
Hypothesis testing
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -285,7 +285,7 @@

diff --git a/docs/Beginning Mesquite.html b/docs/Beginning Mesquite.html index 8f9afa6e2..42ef85ea0 100644 --- a/docs/Beginning Mesquite.html +++ b/docs/Beginning Mesquite.html @@ -41,8 +41,8 @@ Mesquite
Beginning Mesquite
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -212,7 +212,7 @@

Beginning Mesquite


diff --git a/docs/Bugs and Troubleshooting.html b/docs/Bugs and Troubleshooting.html index 888118108..1b289792f 100644 --- a/docs/Bugs and Troubleshooting.html +++ b/docs/Bugs and Troubleshooting.html @@ -41,8 +41,8 @@ Mesquite
Bugs and Troubleshooting
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -205,14 +205,11 @@

Bugs and Troubleshooting

Small text in Mesquite on Windows

There is a bug in some versions of Java which causes applications like Mesquite to show text (including that for Windows) in font that is extremely small. If you have this problem, do the following: -

Right-click on the Mesquite.exe icon, and choose Properties. The following instructions are for Windows 10; you will need to find the equivalent for other Windows versions. In the Properties dialog box, go to the Compatibility tab. Touch the "Change high DPI settings" button. In the dialog box that appears, check "Override high DPI scaling behavior.", and in the popup menu under "Scaling performed by:" choose "System". Press OK on this dialog, and then OK on the other dialog box.
-
-

-

Mesquite under MacOS X 10.12 (Sierra)

- Under MacOS X Sierra, starting up versions of Mesquite prior to 3.2 may result in nothing more than the icon bouncing in the Dock a few times, then disappearing. That is, it won't start up. If you see this behaviour, try downloading the latest version of Mesquite, which should work. If it does not, please contact us.
+

Right-click on the Mesquite.exe icon, and choose Properties. The following instructions are for Windows 10; you will need to find the equivalent for other Windows versions. In the Properties dialog box, go to the Compatibility tab. Touch the "Change high DPI settings" button. In the dialog box that appears, check "Override high DPI scaling behavior.", and in the popup menu under "Scaling performed by:" choose "System". Press OK on this dialog, and then OK on the other dialog box


-

Why does <insert feature> not seem to work properly?

+

+

Why does <insert feature> not seem to work properly?

It could be that the feature in question is one whose operation you don't fully understand, or it could be that you have found a bug. Some bugs you may encounter will be bugs not in Mesquite but in the operating system or Java virtual machine (for example, see the list, below).

thassus.jpg

@@ -257,7 +254,7 @@

diff --git a/docs/Character Evolution.html b/docs/Character Evolution.html index 1ecf1abf9..cda37e898 100644 --- a/docs/Character Evolution.html +++ b/docs/Character Evolution.html @@ -41,8 +41,8 @@ Mesquite
Character Evolution
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -208,7 +208,7 @@

Character Evolution


diff --git a/docs/Characters & Matrices.html b/docs/Characters & Matrices.html index 09acee7ed..e6277a699 100644 --- a/docs/Characters & Matrices.html +++ b/docs/Characters & Matrices.html @@ -41,8 +41,8 @@ Mesquite
Characters & Matrices
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -402,7 +402,7 @@

How Characte
diff --git a/docs/Charts.html b/docs/Charts.html index d322b21fc..34aca9ffc 100644 --- a/docs/Charts.html +++ b/docs/Charts.html @@ -41,8 +41,8 @@ Mesquite
Charts
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -255,7 +255,7 @@

diff --git a/docs/Contact Us.html b/docs/Contact Us.html index a80cd0478..2cbc58d45 100644 --- a/docs/Contact Us.html +++ b/docs/Contact Us.html @@ -41,8 +41,8 @@ Mesquite
Contact Us
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -208,7 +208,7 @@

Contact Us


diff --git a/docs/Developers Documentation.html b/docs/Developers Documentation.html index 2d3824c66..7cb640b5b 100644 --- a/docs/Developers Documentation.html +++ b/docs/Developers Documentation.html @@ -41,8 +41,8 @@ Mesquite
Developer's Documentation
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -209,7 +209,7 @@

Developer's documentation<
diff --git a/docs/Developers Reference.html b/docs/Developers Reference.html index 049717230..a4a4c4868 100644 --- a/docs/Developers Reference.html +++ b/docs/Developers Reference.html @@ -41,8 +41,8 @@ Mesquite
Developer's Reference
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -208,7 +208,7 @@

Developer's Reference


diff --git a/docs/Development Team.html b/docs/Development Team.html index d2b6e5c23..715129632 100644 --- a/docs/Development Team.html +++ b/docs/Development Team.html @@ -41,8 +41,8 @@ Mesquite
Development Team
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -220,7 +220,7 @@

The Development Team


diff --git a/docs/Diversification.html b/docs/Diversification.html index 44141c1e3..9635924c4 100644 --- a/docs/Diversification.html +++ b/docs/Diversification.html @@ -41,8 +41,8 @@ Mesquite
Diversification
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -241,7 +241,7 @@


diff --git a/docs/Documenting Your Work.html b/docs/Documenting Your Work.html index f77d92553..a8fb5b0c1 100644 --- a/docs/Documenting Your Work.html +++ b/docs/Documenting Your Work.html @@ -41,8 +41,8 @@ Mesquite
Documenting Your Work
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -219,7 +219,7 @@

diff --git a/docs/Example Files.html b/docs/Example Files.html index 6a2dd26ce..15293fe56 100644 --- a/docs/Example Files.html +++ b/docs/Example Files.html @@ -41,8 +41,8 @@ Mesquite
Example Files
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -214,7 +214,7 @@

Example Files


diff --git a/docs/FAQ.html b/docs/FAQ.html index 67bba4377..5845d97ad 100644 --- a/docs/FAQ.html +++ b/docs/FAQ.html @@ -41,8 +41,8 @@ Mesquite
FAQ
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -224,7 +224,7 @@

diff --git a/docs/Files.html b/docs/Files.html index 77b27f631..4c689c21b 100644 --- a/docs/Files.html +++ b/docs/Files.html @@ -41,8 +41,8 @@ Mesquite
Files
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -249,7 +249,7 @@

diff --git a/docs/Gene Trees.html b/docs/Gene Trees.html index c0c6fc913..92411f18b 100644 --- a/docs/Gene Trees.html +++ b/docs/Gene Trees.html @@ -41,8 +41,8 @@ Mesquite
Gene Trees
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -320,7 +320,7 @@

diff --git a/docs/Getting Help.html b/docs/Getting Help.html index 09f34d12d..ddfe5fb2d 100644 --- a/docs/Getting Help.html +++ b/docs/Getting Help.html @@ -41,8 +41,8 @@ Mesquite
Getting Help
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -211,7 +211,7 @@

Getting Help


diff --git a/docs/Glossary.html b/docs/Glossary.html index ceeb828f5..bdc040d01 100644 --- a/docs/Glossary.html +++ b/docs/Glossary.html @@ -41,8 +41,8 @@ Mesquite
Glossary
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -213,7 +213,7 @@

diff --git a/docs/History of Mesquite.html b/docs/History of Mesquite.html index 09678edca..4e5fbcb1d 100644 --- a/docs/History of Mesquite.html +++ b/docs/History of Mesquite.html @@ -41,8 +41,8 @@ Mesquite
History of Mesquite
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -216,7 +216,7 @@

History of Mesquite


diff --git a/docs/History of New Features.html b/docs/History of New Features.html index f01d6b012..8cc752416 100644 --- a/docs/History of New Features.html +++ b/docs/History of New Features.html @@ -41,8 +41,8 @@ Mesquite
History of New Features
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -207,16 +207,28 @@

Features to come in the next release version of Mesquite are listed on this web page. These new features and bug fixes are already contained in latest source code in the development branch of the MesquiteProject/MesquiteCore repository on GitHub.

 

-
-

Next Version

+
+ +

Version 3.70

New Features

    -
  • None yet
    • +
  • You can now scroll from matrix to matrix in the Character Matrix Editor using the Next Matrix and Previous Matrix menu items. This is especially useful for genomic datasets with separate alignments, to scroll from locus to locus.
    • +
  • Option to only consider taxon in common when using the Tree Congruent with Specified Tree Topology feature.
    • +
  • Added Terminal Branch Length as a number for taxa. 

Bug Fixes and Workarounds

    -
  • None yet
    • +
  • New systems for starting Mesquite on various newer operating systems and newer versions of Java created. 
    • +
  •  Export for MrBayes no longer generates two competing "currentPartition" partitions that would cause MrBayes to stop execution.
    • +
  • The OTU ID Code database code now correctly processes the path to the database. A bug was introduced into 3.61 that prevented proper processing in many cases, which led to failure to export correct FASTA files for use with tbl2asn for GenBank submission using Chromaseq.
    • +
  • NEXUS with protein data sometimes were sometimes written incorrectly.
    • +
  • TNT files did not have the character and state label information written.
    • +
  • Miscellaneous small bugs fixed.
+

Known bugs

+
    +
  • A bug in Oracle Java for Linux versions 11-16 causes a StackOverflowError at startup. Until we find a workaround, please use Java 8 on Linux.
    • +

Version 3.61

New Features

@@ -504,7 +516,7 @@

diff --git a/docs/How Mesquite Works.html b/docs/How Mesquite Works.html index 3d4322623..72ff88e37 100644 --- a/docs/How Mesquite Works.html +++ b/docs/How Mesquite Works.html @@ -41,8 +41,8 @@ Mesquite
How Mesquite Works
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -218,7 +218,7 @@

diff --git a/docs/How to Cite Mesquite.html b/docs/How to Cite Mesquite.html index 102633d9c..64b842c9f 100644 --- a/docs/How to Cite Mesquite.html +++ b/docs/How to Cite Mesquite.html @@ -41,8 +41,8 @@ Mesquite
How to Cite Mesquite
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -213,8 +213,8 @@

Maddison, W. P. and D.R. Maddison. 2019. Mesquite: a modular system for - evolutionary analysis. Version 3.61 http://www.mesquiteproject.org +
Maddison, W. P. and D.R. Maddison. 2021. Mesquite: a modular system for
+     evolutionary analysis.  Version 3.70  http://www.mesquiteproject.org
(The version number listed above might not be up to date. Check the Mesquite Startup window or the Project and Files window when Mesquite is running to find the version you have.)

@@ -234,7 +234,7 @@

Citing --> -
The Mesquite Project Team. 2019. Documentation for Mesquite: a modular system for
+
The Mesquite Project Team. 2021. Documentation for Mesquite: a modular system for
      evolutionary analysis.  http://www.mesquiteproject.org

 
 

@@ -259,8 +259,8 @@ 
<
 
Doe, J. 2012. SNIDIND: a Mesquite module for calculating the Snidely Index,
      version 3.5.
  
-Maddison, W. P. and D.R. Maddison. 2018. Mesquite: a modular system for
-     evolutionary analysis.  Version 3.61 http://www.mesquiteproject.org.
+Maddison, W. P. and D.R. Maddison. 2021. Mesquite: a modular system for
+     evolutionary analysis.  Version 3.70. http://www.mesquiteproject.org.
  
 Za, T. 2014. SimSpeciation: a package of modules to simulate evolutionary
      trees. Version 3.14159.

@@ -280,7 +280,7 @@ 
Wh
     
 	

   
 
 
diff --git a/docs/Installation on Linux.html b/docs/Installation on Linux.html
index 2146d7941..b0664a8df 100644
--- a/docs/Installation on Linux.html	
+++ b/docs/Installation on Linux.html	
@@ -41,8 +41,8 @@
     Mesquite
     
Installation on Linux

      
-    Version 3.61

-      26 December 2019

+    Version 3.70

+      August 2021

   
 
 
@@ -199,11 +199,14 @@ 
 

     
     
 
Mesquite installation for UNIX/LINUX

- Requirements: JRE or JDK 1.6 or better (java.com/download). (It is best to get the Sun-Oracle Java VM; Mesquite does not run on some third-party virtual machines.)

-

+	  Requirements: JRE or JDK 1.8 (java.com/download). (It is best to get the Sun-Oracle Java VM; Mesquite does not run on some third-party virtual machines.)  At the moment, Mesquite does not run on Linux with Oracle Java version 11 and above. This is due to a bug in Oracle Java that causes Mesquite to crash during startup with a StackOverflowError. The only workaround we know is to use Java version 8 (i.e. 1.8) which is available from java.com. You may need to make adjustments so that your system knows to use Java 8 (e.g., see instructions here http://www.ormbunkar.se/aliview/#java8install).

+	   

 Instructions:

 
  1. If you have an older version of Mesquite, you may want to delete it (by deleting Mesquite_Folder), so as to avoid getting confused as to what version of Mesquite is starting up. First, however, you may want to take from Mesquite_Folder/mesquite any third party packages (e.g., PDAP, TreeSetViz) before deleting the directory.
  2. Download the latest version of Mesquite from the Mesquite Github repository. For Linux, use the file ending in .tgz.
  3. Extract all of the files from the tgz. You will see a Mesquite_Folder. Place this Mesquite_Folder where you want on your hard drive, though if it is in a folder that requires a password for you to modify, you may have problems updating in the future. The contents of Mesquite_Folder should be approximately as follows:


-
    • Mesquite_Folder
      • com/
      • corejava
      • documentation.html
      • edu/
      • examples/
      • images/
      • jars/
      • lesser.txt
      • lib/
      • mesquite/
      • org/
      • mesquite.sh
      • settings/
      • README-Starting Mesquite on Linux.txt


+
    • Mesquite_Folder
      • com/
      • corejava
      • documentation.html
      • edu/
      • examples/
      • images/
      • jars/
      • lesser.txt
      • lib/
      • mesquite/
        • 
+  
      • Mesquite.jar
        • 
+  
      • mesquite.sh
        • 
+  
      • org/
      • settings/
      • README-Starting Mesquite on Linux.txt


 To start Mesquite, execute the mesquite.sh script from the command line:

 
 
java -cp /home/myuser/Mesquite_Folder mesquite.Mesquite

+
+
java -cp /home/myuser/Mesquite_Folder -jar Mesquite.jar
 
-where /home/myuser/Mesquite_Folder could be replaced by whatever is the path to the Mesquite_Folder. On some systems the java virtual machine is started by "jre" instead of "java", and thus the command would be:

+This is the minimal way to start Mesquite; a better call would be:
+

 
-
jre -cp /home/myuser/Mesquite_Folder mesquite.Mesquite

+  
+

+
jre -cp /home/myuser/Mesquite_Folder -jar Mesquite.jar

 
 Depending on your configuration, you may need to give the explicit path to the java virtual machine, as in:

 
@@ -263,7 +276,7 @@ 
/usr/java/jre1.6.0/bin/java -cp /usr/local/Mesquite_Folder mesquite.Mesquite
+
/usr/java/jre1.8.0/bin/java -cp /usr/local/Mesquite_Folder  -jar Mesquite.jar
If you've changed the name of Mesquite_Folder to, for instance, "Mesquite2", you may need to use a command like:
@@ -277,16 +290,18 @@

/usr/java/jre1.6.0/bin/java -cp /usr/local/Mesquite2 mesquite.Mesquite +
/usr/java/jre1.8.0/bin/java -cp /usr/local/Mesquite2  -jar Mesquite.jar
If you've had to do all this because the shell script isn't working, please let us know what happened, and what you did to make Mesquite work. That way, we can make it easier for the next person.

Window Managers

Mesquite attempts to place windows in particular places on the screen for ease of use, using standard Java calls. Some window managers override this, resulting in haphazard placement of windows. You may need to change your window manager if this sort of thing is happening.
-

Virtual Machines & Ubuntu

- If you are running Ubuntu 8.10 (other versions have not been tested but may have the same issue), your default JVM may be Open Java, which has some problems with font rendering/spacing. It is recommended that you use Sun's virtual machine. Java 6 can be installed with the Synaptic Package Manager (sun-java6-jre for running Mesquite, sun-java6-jdk if you are programming in Mesquite) or via the command line "apt-get install" process.
-If you have multiple JVMs installed, you may need to edit the run_mesquite.sh file to instruct Mesquite where to look for the virtual machine. To do this, open run_mesquite.sh in a text editor and find the line:
- -
java="java"
+ +

+ 
java="java"
-Replace it (or comment it out, as below, using "#" and append it) with the absolute path to Sun's JVM (which may be different than the path listed below):
+Replace it (or comment it out, as below, using "#" and append it) with the absolute path to Oracle's JVM (which may be different than the path listed below):
java="/usr/lib/jvm/java-6-sun-1.6.0.10/bin/java"
+ +
java="PATHTOJAVA/bin/java"
making sure to pay attention to spacing; the script may have problems if there is extra whitespace between "java" & "=". Alternatively, if you don't use the script, but would like to run Mesquite from the Terminal command line, just use the absolute path to the Java VM you prefer when starting Mesquite, as above:
@@ -337,7 +355,7 @@

/usr/lib/jvm/java-6-sun-1.6.0.10/bin/java -cp /home/myuser/Mesquite_Folder mesquite.Mesquite +
     PATHTOJAVA/bin/java -cp /home/myuser/Mesquite_Folder  -jar Mesquite.jar
More details of issues of using Mesquite under Linux/UNIX are described in the Bugs and Troubleshooting page.

@@ -349,7 +367,7 @@

diff --git a/docs/Installation on MacOS X.html b/docs/Installation on MacOS X.html index 402c326b6..39cb4807b 100644 --- a/docs/Installation on MacOS X.html +++ b/docs/Installation on MacOS X.html @@ -41,8 +41,8 @@ Mesquite
Installation on MacOS X
  - Version 3.61
- 26 December 2019
+ Version 3.70
+ August 2021
@@ -200,13 +200,27 @@

 

Mesquite installation for MacOS X


-System requirements: Mac OS X 10.6 or higher, with Java 1.6 to Java 10. Mesquite 3.6 will probably not function under Java 11. (MacOS X 10.10 or higher with Java 1.8 recommended.)
+System requirements: Mac OS X 10.10 or higher, with Java 1.8 or higher required. (Java 1.8 is also called Java 8.) Mesquite may or may not run on older systems.

Instructions:
  1. If you have an older version of Mesquite, you may want to delete it (by deleting Mesquite_Folder), so as to avoid getting confused as to what version of Mesquite is starting up. First, however, you may want to take from Mesquite_Folder/mesquite any third party packages (e.g., PDAP, TreeSetViz) before deleting the directory.
    2. -
  2. Download the latest version of Mesquite from the Mesquite Github repository. For Mac OS X, use the files ending in .dmg. There are two alternatives, one for Java 1.6 (recommended for OS X 10.9, Mavericks, and lower), the other for Java 1.7 and above (recommended for OS X 10.10, Yosemite, and higher).
    3. -
  3. For MacOS X 10.10 (Yosemite) and later versions of the MacOS, we recommend using Java 1.8 and the version of Mesquite for Java 1.7 and above.
    4. -
  4. If the downloaded file doesn't mount into a disk image automatically, double click it to mount. You will see a Mesquite_Folder. Drag this Mesquite_Folder to your hard drive (e.g., your Applications folder). Its contents should be approximately as follows:
    • Mesquite_Folder
      • com/
      • corejava
      • documentation.html
      • edu/
      • examples/
      • images/
      • jars/
      • lesser.txt
      • lib/
      • mesquite/
      • Mesquite.app
      • org/
      • OtherWaysToStartMesquite
      • settings/
      • README-Starting Mesquite on Mac OS X.txt
  5. Double click the Mesquite icon to start Mesquite. If you don't have Java installed, you will be asked to install it.
  6. There are other executables to start Mesquite, within the folder OtherWaysToStartMesquite. They give you different options, for example, for amount of memory used. See the file "README-Starting Mesquite on Mac OS X.txt" for instructions.
  7. On Mac OS X 10.9 or below, Mesquite runs best with Java 1.6. On Mac OS X 10.0 or higher, Mesquite runs best on Java 1.7 or higher. To install Java 1.7 or higher, get it from http://java.com.

+
  • Download the latest version of Mesquite from the Mesquite Github repository.
    +
    +
    • +
  • If the downloaded file doesn't mount into a disk image automatically, double click it to mount. You will see a Mesquite_Folder. Drag this Mesquite_Folder to your hard drive (e.g., your Applications folder). Its contents should be approximately as follows:
    • + +
      +
      • Mesquite_Folder
        • com/
        • corejava
        • documentation.html
        • edu/
        • examples/
        • images/
        • jars/
        • lesser.txt
        • lib/
        • mesquite/
          • +
        • Mesquite_Starter.app [There will be several different versions of this, with slightly different names]
        • Mesquite_Starter_INSTRUCTIONS-macOS.txt
          • +
        • mesquite.jar
          • +
        • org/
          • +
        • RunningOptionsForFlex/
        • settings/
          • +
        • start/
      +
    1. Double click one of the Mesquite_Starter icons to start Mesquite. If you don't have Java installed, you may be asked to install it.
      2. +
    2. Which Mesquite_Starter should you use? We offer several different versions because the diversity of macOS versions and Java versions make it too challenging to provide you a single solution. The different versions of Starters also provide different amounts of memory. Try them, and see what works.
      3. +
    3. For more complete instructions about starting Mesquite and what can go wrong, see the file Mesquite_Starter_INSTRUCTIONS-macOS.txt.
      4. +
    +

    More details of issues of using Mesquite under Mac OS X are described in the Support page.
    (Please email us (info {at} mesquiteproject.org) with questions or comments about downloading Mesquite). @@ -217,7 +231,7 @@

    Mesquite installat
    diff --git a/docs/Installation on Windows.html b/docs/Installation on Windows.html index 7d2b49cb5..429c8fed4 100644 --- a/docs/Installation on Windows.html +++ b/docs/Installation on Windows.html @@ -41,8 +41,8 @@ Mesquite
    Installation on Windows
      - Version 3.61
    - 26 December 2019
    + Version 3.70
    + August 2021
    @@ -200,18 +200,25 @@

     

    Mesquite installation for Windows


    -System Requirements: Java 1.6 or higher.
    +System Requirements: Java 1.8 or higher.

    Instructions:
    1. If you have an older version of Mesquite, you may want to delete it (by deleting Mesquite_Folder), so as to avoid getting confused as to what version of Mesquite is starting up. First, however, you may want to take from Mesquite_Folder/mesquite any third party packages (e.g., PDAP, TreeSetViz) before deleting the directory.
    2. Mesquite requires Java to be installed. If you don't have it installed, Mesquite should ask you to install it the first time it runs. In case that doesn't happen, you can download Java from http://java.com/download.
    3. Download the latest version of Mesquite from the Mesquite Github repository. For Windows, use the file ending in .zip.
    4. Extract all of the files from the zip. You will see a Mesquite_Folder. Place this Mesquite_Folder where you want on your hard drive, though if it is in a folder that requires a password for you to modify, you may have problems updating in the future. The contents of Mesquite_Folder should be approximately as follows:
      -
      • Mesquite_Folder
        • com/
        • corejava
        • documentation.html
        • edu/
        • examples/
        • images/
        • jars/
        • lesser.txt
        • lib/
        • mesquite/
        • Mesquite.exe
        • OtherWaysToStartMesquite/
        • settings/
        • README-Starting Mesquite on Windows.txt
    +
    • Mesquite_Folder
      • com/
        • +
      • corejava/
      • documentation.html
      • edu/
      • examples/
      • images/
      • jars/
      • lesser.txt
      • lib/
      • mesquite/
        • +
      • mesquite.jar
        • +
      • Mesquite_Starter.exe [There will be several different versions of this, with slightly different names]
        • +
      • Mesquite_Starter_INSTRUCTIONS-Windows.txt
        • +
      • org/
        • +
      • settings/
        • +
      • start/
      -
    1. Right-click on the Mesquite.exe icon, and choose Properties. The following instructions are for Windows 10; you will need to find the equivalent for other Windows versions. In the Properties dialog box, go to the Compatibility tab. Touch the "Change high DPI settings" button. In the dialog box that appears, check "Override high DPI scaling behavior.", and in the popup menu under "Scaling performed by:" choose "System". Press OK on this dialog, and then OK on the other dialog box.
      2. -
    2. Double click Mesquite.exe to start Mesquite. If you don't have Java installed, you will be asked to install it.
      3. -
    3. Within the folder OtherWaysToStartMesquite are other executable files to start Mesquite, giving you different options for memory used. For instructions, see the file README-Starting Mesquite on Windows.txt
    4. The executable icons use the latest version of Java you have.

    - Requirements: Tested on Windows XP through Windows 10. Java 1.6 or later required.
    +
  • Double click one of the Mesquite_Starter icons to start Mesquite. If you don't have Java installed, you may be asked to install it.
    • +
  • Which Mesquite_Starter should you use? We offer several different versions because the diversity of Java versions make it too challenging to provide you a single solution. The different versions of Starters also provide different amounts of memory. Try them, and see what works. For more complete instructions about starting Mesquite, and what can go wrong, see the file Mesquite_Starter_INSTRUCTIONS-Windows.txt.
    • +
  • If the text in Mesquite is too small, you may need to adjust the properties of your Starter executable. To do this, Right-click on the Mesquite_Starter icon that you want to use, and choose Properties. The following instructions are for Windows 10; you will need to find the equivalent for other Windows versions. In the Properties dialog box, go to the Compatibility tab. Touch the "Change high DPI settings" button. In the dialog box that appears, check "Override high DPI scaling behavior.", and in the popup menu under "Scaling performed by:" choose "System". Press OK on this dialog, and then OK on the other dialog box.

    • + Requirements: Tested on Windows XP through Windows 10. Java 1.8 or later required.

    More details of issues of using Mesquite under Windows are described in the Support page.
    (Please email us (info {at} mesquiteproject.org) with questions or comments about downloading Mesquite). @@ -222,7 +229,7 @@

    Mesquite installat
    diff --git a/docs/Installation.html b/docs/Installation.html index 3a83212ca..7debf714d 100644 --- a/docs/Installation.html +++ b/docs/Installation.html @@ -41,8 +41,8 @@ Mesquite
    Installation
      - Version 3.61
    - 26 December 2019
    + Version 3.70
    + August 2021
    @@ -200,7 +200,7 @@

     

    Download and Installation

    Instructions are here given for downloading and installing Mesquite on the following operating systems:
    -
    +
    To download older versions of Mesquite, go to the History page. @@ -209,7 +209,7 @@

    Download and Installation<
    diff --git a/docs/Installing Mesquite Packages.html b/docs/Installing Mesquite Packages.html index 758eab4b0..297156b36 100644 --- a/docs/Installing Mesquite Packages.html +++ b/docs/Installing Mesquite Packages.html @@ -41,8 +41,8 @@ Mesquite
    Installing Mesquite Packages
      - Version 3.61
    - 26 December 2019
    + Version 3.70
    + August 2021
    @@ -205,7 +205,7 @@

     


    diff --git a/docs/Interactions with Other Programs.html b/docs/Interactions with Other Programs.html index 5f9151d30..93db8816e 100644 --- a/docs/Interactions with Other Programs.html +++ b/docs/Interactions with Other Programs.html @@ -41,8 +41,8 @@ Mesquite
    Interactions with Other Programs
      - Version 3.61
    - 26 December 2019
    + Version 3.70
    + August 2021
    @@ -226,7 +226,7 @@

    <
    diff --git a/docs/Learning how to use Mesquite.html b/docs/Learning how to use Mesquite.html index 6501c96b7..b632b0bcf 100644 --- a/docs/Learning how to use Mesquite.html +++ b/docs/Learning how to use Mesquite.html @@ -41,8 +41,8 @@ Mesquite
    Learning Mesquite
      - Version 3.61
    - 26 December 2019
    + Version 3.70
    + August 2021
    @@ -246,7 +246,7 @@

    diff --git a/docs/Managing Continuous Data.html b/docs/Managing Continuous Data.html index 4d40939f8..6dca602c1 100644 --- a/docs/Managing Continuous Data.html +++ b/docs/Managing Continuous Data.html @@ -41,8 +41,8 @@ Mesquite
    Managing Continuous Data
      - Version 3.61
    - 26 December 2019
    + Version 3.70
    + August 2021
    @@ -211,7 +211,7 @@

    Man
    diff --git a/docs/Managing Molecular Data.html b/docs/Managing Molecular Data.html index a80032314..dfeadcaa8 100644 --- a/docs/Managing Molecular Data.html +++ b/docs/Managing Molecular Data.html @@ -41,8 +41,8 @@ Mesquite
    Managing Molecular Data
      - Version 3.61
    - 26 December 2019
    + Version 3.70
    + August 2021
    @@ -347,7 +347,7 @@

    diff --git a/docs/Menus.html b/docs/Menus.html index c3cf4769b..33f75ea58 100644 --- a/docs/Menus.html +++ b/docs/Menus.html @@ -41,8 +41,8 @@ Mesquite
    Menus
      - Version 3.61
    - 26 December 2019
    + Version 3.70
    + August 2021
    @@ -232,7 +232,7 @@

    Where to
    diff --git a/docs/MesquiteLogSupport.html b/docs/MesquiteLogSupport.html index 3ceb8b462..a379f93be 100644 --- a/docs/MesquiteLogSupport.html +++ b/docs/MesquiteLogSupport.html @@ -41,8 +41,8 @@ Mesquite
    Log & Support Files
      - Version 3.61
    - 26 December 2019
    + Version 3.70
    + August 2021
    @@ -209,7 +209,7 @@

    Log & Support Files


    diff --git a/docs/Mesquites Features.html b/docs/Mesquites Features.html index b10a75426..4ce299769 100644 --- a/docs/Mesquites Features.html +++ b/docs/Mesquites Features.html @@ -41,8 +41,8 @@ Mesquite
    Mesquite's Features
      - Version 3.61
    - 26 December 2019
    + Version 3.70
    + August 2021
    @@ -216,7 +216,7 @@

    List of Features


    diff --git a/docs/Module Index.html b/docs/Module Index.html index 5cd733040..d8c54d215 100644 --- a/docs/Module Index.html +++ b/docs/Module Index.html @@ -41,8 +41,8 @@ Mesquite
    Module Index
      - Version 3.61
    - 26 December 2019
    + Version 3.70
    + August 2021
    @@ -208,7 +208,7 @@

    diff --git a/docs/Modules.html b/docs/Modules.html index 875a6dcd9..0ce29aadc 100644 --- a/docs/Modules.html +++ b/docs/Modules.html @@ -41,8 +41,8 @@ Mesquite
    Modules
      - Version 3.61
    - 26 December 2019
    + Version 3.70
    + August 2021
    @@ -237,7 +237,7 @@


    diff --git a/docs/Pagel Correlation Method.html b/docs/Pagel Correlation Method.html index 4f6eaec2b..26502bbad 100644 --- a/docs/Pagel Correlation Method.html +++ b/docs/Pagel Correlation Method.html @@ -41,8 +41,8 @@ Mesquite
    Pagel Correlation Method
      - Version 3.61
    - 26 December 2019
    + Version 3.70
    + August 2021
    @@ -242,7 +242,7 @@

    <
    diff --git a/docs/Processes of Character Evolution.html b/docs/Processes of Character Evolution.html index 1eeb50e13..57cfefa67 100644 --- a/docs/Processes of Character Evolution.html +++ b/docs/Processes of Character Evolution.html @@ -41,8 +41,8 @@ Mesquite
    Processes of Character Evolution
      - Version 3.61
    - 26 December 2019
    + Version 3.70
    + August 2021
    @@ -252,7 +252,7 @@


    diff --git a/docs/Publication Quality Trees.html b/docs/Publication Quality Trees.html index 4bae4cdf2..0e6d5a8b5 100644 --- a/docs/Publication Quality Trees.html +++ b/docs/Publication Quality Trees.html @@ -41,8 +41,8 @@ Mesquite
    Publication Quality Trees
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    + August 2021
    @@ -259,7 +259,7 @@


    diff --git a/docs/Publishing Results.html b/docs/Publishing Results.html index d38342463..3a9540307 100644 --- a/docs/Publishing Results.html +++ b/docs/Publishing Results.html @@ -41,8 +41,8 @@ Mesquite
    Publishing Results
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    + Version 3.70
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    @@ -213,7 +213,7 @@

    Disclaim
    diff --git a/docs/Release Dates.html b/docs/Release Dates.html index 71da41444..344c5b9ff 100644 --- a/docs/Release Dates.html +++ b/docs/Release Dates.html @@ -41,8 +41,8 @@ Mesquite
    Release Dates
      - Version 3.6
    - 27 December 2018
    + Version 3.70
    + August 2021
    @@ -217,6 +217,18 @@

    diff --git a/docs/Scripts & Macros.html b/docs/Scripts & Macros.html index 64438813c..d165ca023 100644 --- a/docs/Scripts & Macros.html +++ b/docs/Scripts & Macros.html @@ -41,8 +41,8 @@ Mesquite
    Scripts & Macros
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    @@ -429,7 +429,7 @@

    Technical De
    diff --git a/docs/Selection.html b/docs/Selection.html index 7185ba1b2..ff3500643 100644 --- a/docs/Selection.html +++ b/docs/Selection.html @@ -41,8 +41,8 @@ Mesquite
    Selection
      - Version 3.6
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    @@ -213,7 +213,7 @@

    Selection


    diff --git a/docs/Simplifying the Interface.html b/docs/Simplifying the Interface.html index 8e65e0ea4..17fae3bc1 100644 --- a/docs/Simplifying the Interface.html +++ b/docs/Simplifying the Interface.html @@ -41,8 +41,8 @@ Mesquite
    Simplifying the Interface
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    diff --git a/docs/Simulating Characters.html b/docs/Simulating Characters.html index 9e124c651..629bbea9b 100644 --- a/docs/Simulating Characters.html +++ b/docs/Simulating Characters.html @@ -41,8 +41,8 @@ Mesquite
    Simulating Characters
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    @@ -224,7 +224,7 @@

    diff --git a/docs/Simulating DNA Evolution.html b/docs/Simulating DNA Evolution.html index 96228580e..9ed60a73c 100644 --- a/docs/Simulating DNA Evolution.html +++ b/docs/Simulating DNA Evolution.html @@ -41,8 +41,8 @@ Mesquite
    Simulating DNA Evolution
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    @@ -401,7 +401,7 @@

    diff --git a/docs/Simulations & Randomizations.html b/docs/Simulations & Randomizations.html index b1e163749..c9b38af1c 100644 --- a/docs/Simulations & Randomizations.html +++ b/docs/Simulations & Randomizations.html @@ -41,8 +41,8 @@ Mesquite
    Simulations & Randomizations
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    diff --git a/docs/Slatkin and Maddison.html b/docs/Slatkin and Maddison.html index 65ecc29ff..3771f0718 100644 --- a/docs/Slatkin and Maddison.html +++ b/docs/Slatkin and Maddison.html @@ -41,8 +41,8 @@ Mesquite
    Slatkin and Maddison
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    @@ -292,7 +292,7 @@

    diff --git a/docs/Source Code.html b/docs/Source Code.html index d48974339..ad7a76707 100644 --- a/docs/Source Code.html +++ b/docs/Source Code.html @@ -41,8 +41,8 @@ Mesquite
    Source Code
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    @@ -404,7 +404,7 @@

    diff --git a/docs/Studies of Tree Topology.html b/docs/Studies of Tree Topology.html index 83911a0a8..02b3cd0fc 100644 --- a/docs/Studies of Tree Topology.html +++ b/docs/Studies of Tree Topology.html @@ -41,8 +41,8 @@ Mesquite
    Studies of Tree Topology
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    Studies of Tree Topology
    diff --git a/docs/Suggesting New Features.html b/docs/Suggesting New Features.html index 5cdd51c2e..1c02fb848 100644 --- a/docs/Suggesting New Features.html +++ b/docs/Suggesting New Features.html @@ -41,8 +41,8 @@ Mesquite
    Suggesting New Features
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    @@ -212,7 +212,7 @@


    diff --git a/docs/Taxa.html b/docs/Taxa.html index d62d2ffbe..dba77e218 100644 --- a/docs/Taxa.html +++ b/docs/Taxa.html @@ -41,8 +41,8 @@ Mesquite
    Taxa
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    @@ -265,7 +265,7 @@

    diff --git a/docs/Templates/MesquiteTemplate.dwt b/docs/Templates/MesquiteTemplate.dwt index 75a4e7404..ece49d106 100644 --- a/docs/Templates/MesquiteTemplate.dwt +++ b/docs/Templates/MesquiteTemplate.dwt @@ -41,8 +41,8 @@ Mesquite
    subtitle
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    @@ -205,7 +205,7 @@
    diff --git a/docs/Testing monophyly of a group of beetles.html b/docs/Testing monophyly of a group of beetles.html index 6d3cb2310..0b2aa951a 100644 --- a/docs/Testing monophyly of a group of beetles.html +++ b/docs/Testing monophyly of a group of beetles.html @@ -41,8 +41,8 @@ Mesquite
    Example: Testing monophyly
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    @@ -302,7 +302,7 @@

    diff --git a/docs/Tree Simulations.html b/docs/Tree Simulations.html index 6bdaf73f0..0ac22a186 100644 --- a/docs/Tree Simulations.html +++ b/docs/Tree Simulations.html @@ -41,8 +41,8 @@ Mesquite
    Tree Simulations
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    @@ -221,7 +221,7 @@

    diff --git a/docs/Trees.html b/docs/Trees.html index d762864b0..07f905ee0 100644 --- a/docs/Trees.html +++ b/docs/Trees.html @@ -41,8 +41,8 @@ Mesquite
    Trees
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    @@ -549,7 +549,7 @@

    diff --git a/docs/What Mesquite does.html b/docs/What Mesquite does.html index f484d7b44..2ff3f5116 100644 --- a/docs/What Mesquite does.html +++ b/docs/What Mesquite does.html @@ -41,8 +41,8 @@ Mesquite
    Introduction to Mesquite
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    @@ -295,7 +295,7 @@

    Extending Mesq
    diff --git a/docs/Windows.html b/docs/Windows.html index 24899bf63..56b303960 100644 --- a/docs/Windows.html +++ b/docs/Windows.html @@ -41,8 +41,8 @@ Mesquite
    Windows
      - Version 3.61
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    @@ -305,7 +305,7 @@

    diff --git a/docs/home.html b/docs/home.html index 11477f991..0c34e9b07 100644 --- a/docs/home.html +++ b/docs/home.html @@ -41,8 +41,8 @@ Mesquite
      - Version 3.61
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    @@ -198,7 +198,7 @@

     



    Mesquite: A modular system for evolutionary analysis

    -

    Version: 3.61

    +

    Version: 3.70


    Mesquite is modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses available depend on the modules installed.

    @@ -236,7 +236,7 @@


    diff --git a/docs/index.html b/docs/index.html index 9cba99e2b..3430d22ec 100644 --- a/docs/index.html +++ b/docs/index.html @@ -41,8 +41,8 @@ Mesquite
    Home
      - Version 3.61
    - 26 December 2019
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    + August 2021
    @@ -201,12 +201,12 @@

     

    If you're looking for Mesquite Software, Inc. or its CSIM toolkit for building simulation models, go here

    Mesquite: A modular system for evolutionary analysis

    -

    Current release version: 3.61 [download]

    +

    Current release version: 3.70 [download]

    If you have a previous version, please update because of bug fixes and new features.

    Mesquite is modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses available depend on the modules installed.

    Note: if you are running on Windows, and the text of menus and other elements is too small, then see the Bugs and Troubleshooting page for information about a fix.

    -

    Note: if you are running on macOS, Mesquite will probably not function under Java 11. We suggest you stay with Java 8.

    +

    Note: The problems with starting Mesquite under MacOS X 10.15 (Catalina) have been fixed (see the Installation) page. In addition, the problems opening up the MacOS X .dmg file under older versions of the MacOS have also been fixed.

    Use the menus at left to explore. Some good starting points are:

    • Introduction to Mesquite
      • @@ -224,7 +224,7 @@


      diff --git a/docs/space.menu.html b/docs/space.menu.html index 284050eff..d9d16ba75 100644 --- a/docs/space.menu.html +++ b/docs/space.menu.html @@ -41,8 +41,8 @@ Mesquite
        - Version 3.61
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      @@ -217,7 +217,7 @@

      Overview of Mesquite


      diff --git a/docs/whyMesquite.html b/docs/whyMesquite.html index dc0e1cf07..d1ca5f831 100644 --- a/docs/whyMesquite.html +++ b/docs/whyMesquite.html @@ -41,8 +41,8 @@ Mesquite
      Why Mesquite?
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      @@ -249,7 +249,7 @@

      References


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