Merge pull request #102 from MesquiteProject/development

Development

.classpath

@@ -7,23 +7,22 @@
 	<classpathentry exported="true" kind="lib" path="jars/MRJToolkitStubs.zip"/>
 	<classpathentry exported="true" kind="lib" path="jars/pal.zip"/>
 	<classpathentry exported="true" kind="lib" path="jars/commons-httpclient-3.1.jar"/>
-	<classpathentry exported="true" kind="lib" path="jars/commons-lang-2.3.jar"/>
 	<classpathentry excluding="docs/mesquite/BeanTree/" kind="src" path="Resources"/>
 	<classpathentry kind="src" path="Source"/>
-	<classpathentry exported="true" kind="lib" path="jars/commons-codec-1.6.jar"/>
 	<classpathentry exported="true" kind="lib" path="jars/gson-2.6.2.jar"/>
-	<classpathentry exported="true" kind="lib" path="jars/httpclient-4.3.6.jar"/>
-	<classpathentry exported="true" kind="lib" path="jars/commons-io-2.5.jar"/>
-	<classpathentry exported="true" kind="lib" path="jars/commons-lang3-3.5.jar"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
 		<attributes>
 			<attribute name="module" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry exported="true" kind="lib" path="jars/commons-logging-1.1.3.jar"/>
 	<classpathentry exported="true" kind="lib" path="jars/commons-math3-3.6.1.jar"/>
 	<classpathentry kind="lib" path="jars/byte-buddy-agent-1.7.8.jar"/>
-	<classpathentry exported="true" kind="lib" path="jars/dom4j-2.0.2.jar"/>
 	<classpathentry exported="true" kind="lib" path="jars/jsch-0.1.54.jar"/>
+	<classpathentry kind="lib" path="jars/commons-logging-1.2.jar"/>
+	<classpathentry kind="lib" path="jars/commons-codec-1.11.jar"/>
+	<classpathentry exported="true" kind="lib" path="jars/httpclient-4.5.13.jar"/>
+	<classpathentry exported="true" kind="lib" path="jars/commons-io-2.11.0.jar"/>
+	<classpathentry exported="true" kind="lib" path="jars/commons-lang3-3.12.0.jar"/>
+	<classpathentry exported="true" kind="lib" path="jars/dom4j-2.1.3.jar"/>
 	<classpathentry kind="output" path="Mesquite_Folder"/>
 </classpath>

.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

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

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.
+
+

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
+

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"
+