Merge pull request #78 from MesquiteProject/development

Release version 3.40 Build 877

.classpath

@@ -7,14 +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/dom4j-1.6.1.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 kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<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 kind="output" path="Mesquite_Folder"/>
 </classpath>

.gitignore

@@ -1,10 +1,15 @@
 Mesquite_Folder/
+# Workspace files #
+###################
+*.iml
+.project
+.settings/
+
 # Compiled source #
 ###################
 *.com
 *.class
 *.dll
-*.exe
 *.o
 *.so
 
@@ -18,7 +23,6 @@ Mesquite_Folder/
 *.iso
 *.rar
 *.tar
-*.zip
 
 # Logs and databases #
 ######################
@@ -39,3 +43,4 @@ Thumbs.db
 .gitignore
 /.classpath
 /.gitignore
+/target/

Additional Files/classpaths.txt

@@ -0,0 +1 @@
+../../Cartographer/Mesquite_Folder

Additional Files/execsToStartUnderWindows/Mesquite_Start_Script.bat

@@ -0,0 +1 @@
+java -Xmx1000M -Xss4m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar Mesquite.jar

Source/mesquite/align/ClustalAlign/ClustalAlign.java

@@ -76,7 +76,11 @@ public String getExplanation() {
 	public String getProgramName(){
 		 return "ClustalW";
 	 }
-
+	/*.................................................................................................................*/
+	public boolean useDefaultStdOutFileName() {
+		return true;
+	}
+
 	/*.................................................................................................................*/
 	public String getProgramCommand(){
 		if (MesquiteTrunk.isWindows())
@@ -90,13 +94,11 @@ public String getDefaultProgramOptions(){
 	}
 
 	public void appendDefaultOptions(StringBuffer shellScript, String inFilePath, String outFilePath, MolecularData data) {
-		shellScript.append("  -infile=" + StringUtil.protectFilePathForUnix(inFilePath) + " -align -output=pir ");
+		shellScript.append("  -infile=" + StringUtil.protectFilePathForUnix(inFilePath) + " -align -output=pir -outfile="+ StringUtil.protectFilePathForUnix(outFilePath) );
 		if (data instanceof ProteinData)
-			shellScript.append("-type=protein ");
+			shellScript.append(" -type=protein ");
 		else
-			shellScript.append("-type=dna ");
-		if (scriptBased)
-			shellScript.append("-outfile="+StringUtil.protectFilePathForUnix(outFilePath));
+			shellScript.append(" -type=dna ");
 
 	}
 

Source/mesquite/align/ShiftOtherToMatch/ShiftOtherToMatch.java

@@ -73,27 +73,31 @@ public boolean queryOptions(int it, int max) {
 		MesquiteInteger buttonPressed = new MesquiteInteger(1);
 		ExtensibleDialog queryFilesDialog = new ExtensibleDialog(containerOfModule(), "Shift Other To Match",buttonPressed);  //MesquiteTrunk.mesquiteTrunk.containerOfModule()
 		queryFilesDialog.addLabel("Shift Other To Match");
-
+				
 		if (!MesquiteInteger.isCombinable(it1) || !MesquiteInteger.isCombinable(it2) || it1>max || it2>max){
-			if (it>=max) {  
-				it1=1;
-			} else
-				it1 = it+2;  // it+1 to bump it over one, +2 because of the translation to 1-based numbering
-			it2=max;
+			if (it>=max) {  // then it1 has to go back to first taxon
+				it1=0;
+				it2=it-1;
+			} else {
+				it1 = it+1;  // it+1 to bump it over selected one
+				it2=max;  // 
+			}
 		//	if (it2==it)
 		//	it2--;
 		}
-		IntegerField it1Field =  queryFilesDialog.addIntegerField ("First Sequence", it1, 4, 1, max);
-		IntegerField it2Field =  queryFilesDialog.addIntegerField ("Last Sequence", it2, 4, 1, max);
+		if (it2<it1)
+			it2=it1;
+		IntegerField it1Field =  queryFilesDialog.addIntegerField ("First Sequence",(it1+1), 4, 1, max+1);
+		IntegerField it2Field =  queryFilesDialog.addIntegerField ("Last Sequence", (it2+1), 4, 1, max+1);
 		DoubleField matchFractionField = queryFilesDialog.addDoubleField ("Fraction of Match", matchFraction, 6, 0.00001, 1.0);
 
 		Checkbox reverseSequencesCheckBox = queryFilesDialog.addCheckBox("Reverse complement sequences if necessary", reverseComplementIfNecessary);
 
 		queryFilesDialog.completeAndShowDialog(true);
 		if (buttonPressed.getValue()==0)  {
 			matchFraction = matchFractionField.getValue();
-			it1 = it1Field.getValue();
-			it2 = it2Field.getValue();
+			it1 = it1Field.getValue()-1;
+			it2 = it2Field.getValue()-1;
 			reverseComplementIfNecessary = reverseSequencesCheckBox.getState();
 			storePreferences();
 		}
@@ -143,7 +147,7 @@ public boolean alterData(CharacterData data, MesquiteTable table,  UndoReference
 			boolean match=false;
 			int totalAddedToStart = 0;
 			boolean someAdded = false;
-			for (int it = it1-1; it<=it2-1; it++) {  // must subtract 1 off of it1 and it2 as these are 1-based numbers
+			for (int it = it1; it<=it2; it++) {  
 				if (row.getValue()!=it) {
 					match = findMatch(data,table, row.getValue(), firstColumn.getValue(), lastColumn.getValue(), it,matchStart,matchEnd);
 					if (reverseComplementIfNecessary && !match && data instanceof DNAData) {

Source/mesquite/align/lib/ExternalSequenceAligner.java

@@ -70,6 +70,10 @@ else if (externalRunner!=null)
 		return "";
 	}
 	/*.................................................................................................................*/
+	public boolean useDefaultStdOutFileName() {
+		return false;
+	}
+	/*.................................................................................................................*/
 	public String getStdOut() {
 		if (scriptBased){
 			if (scriptRunner!=null)
@@ -384,7 +388,10 @@ else if (!(firstTaxon==0 && lastTaxon==matrix.getNumTaxa())) {  // we are doing
 			arguments=StringUtil.stripBoundingWhitespace(arguments);
 			externalRunner = new ExternalProcessManager(this, rootDir, getProgramPath(), arguments,getName(), outputFilePaths, this, this, true);
 			//ShellScriptUtil.changeDirectory(rootDir, rootDir);
-			externalRunner.setStdOutFileName(outFileName);
+			if (useDefaultStdOutFileName())
+				externalRunner.setStdOutFileName(ShellScriptRunner.stOutFileName);
+			else
+				externalRunner.setStdOutFileName(outFileName);
 			success = externalRunner.executeInShell();
 			if (success)
 				success = externalRunner.monitorAndCleanUpShell(progressIndicator);

Source/mesquite/categ/lib/CategoricalData.java

@@ -19,6 +19,7 @@
 
 import mesquite.lib.*;
 import mesquite.lib.characters.*;
+import mesquite.lib.characters.CharacterData;
 import mesquite.lib.duties.*;
 
 /* ======================================================================== */
@@ -322,6 +323,7 @@ public CategoricalData getDataCopy(){
 		data.resetCellMetadata();
 		return data;
 	}
+
 	/*..........................................  CategoricalData  ..................................................*/
 	/**clone this CharacterData and return new copy.  Does not clone the associated specs sets etc.*/ //TODO: here should use super.setToClone(data) to handle specssets etc.???
 	public CharacterData cloneData(){
@@ -1957,15 +1959,17 @@ public void equalizeCharacter(CharacterData oData, int oic, int ic){
 		//state names
 		if (oData instanceof CategoricalData){
 			CategoricalData cData = (CategoricalData)oData;
-			if (cData.stateNames == null)
-				stateNames = null;
+			if (cData.stateNames == null) {  // incoming stateNames is null
+				if (stateNames!=null)  // this state names is not null, so lets set the values to null
+					for (int is = 0; is<= CategoricalState.maxCategoricalState; is++) 
+							setStateName(ic, is, null);
+			}
 			else {
 				for (int is = 0; is<= CategoricalState.maxCategoricalState; is++) {
-					if (cData.hasStateName(oic, is)){
-						String s = cData.getStateName(oic, is);
-						if (!StringUtil.blank(s))
-							setStateName(ic, is, s);
-					}
+					if (cData.hasStateName(oic, is))
+						setStateName(ic, is, cData.getStateName(oic, is));
+					else 
+						setStateName(ic, is, null);
 				}
 			} 
 			for (int is = 0; is<= CategoricalState.maxCategoricalState; is++) {