Merge pull request #26 from wmaddisn/master

Pender Harbour Hackathon Friday

Additional Files/menuSquares.txt

@@ -0,0 +1,2 @@
+◼ ◻  ❑  ⬒  ▣
+◀ ▶ ◢ ◣ ◥ ◤ ◇ ◆ ◈  ◊ 

Source/mesquite/Mesquite.java

@@ -1188,11 +1188,8 @@ private void searchWeb(String queryTerm, MesquiteBoolean addMesquiteToSearch, Me
 	/*New code added April.02.07 oliver*/ //TODO: delete new code comments
 	/*.................................................................................................................*/
 	private void openMesquiteFAQ(){
-		String manualPath = mesquiteDirectoryPath + "docs/mesquite" + MesquiteFile.fileSeparator + "Help/MesquiteFAQ.html" ; 
-		File testing = new File(manualPath);
-		if (testing.exists()) {
+		String manualPath = mesquiteWebSite + "/FAQ" ; 
 			showWebPage(manualPath, false);
-		}
 	}
 	/*End new code added April.02.07 oliver*/
 
@@ -2013,27 +2010,18 @@ else if (checker.compare(this.getClass(), "Shows web page of available commands
 		else if (checker.compare(this.getClass(), "Shows home page of Mesquite", null, commandName, "showHomePage")) {
 			if (MesquiteTrunk.isApplet()) 
 				return null;
-			if (!CommandChecker.documentationComposed) {
-				CommandChecker cchecker = new CommandChecker();
-				cchecker.composeDocumentation();
-			}	
-			String manualPath = "http://mesquiteproject.wikispaces.com" ; 
+
+			String manualPath = mesquiteWebSite; 
 			//File testing = new File(manualPath);
 			showWebPage(manualPath, false);
 
 		}
 		else if (checker.compare(this.getClass(), "Shows Support page of Mesquite manual", null, commandName, "showSupport")) {
 			if (MesquiteTrunk.isApplet()) 
 				return null;
-			if (!CommandChecker.documentationComposed) {
-				CommandChecker cchecker = new CommandChecker();
-				cchecker.composeDocumentation();
-			}	
-			String manualPath = mesquiteDirectoryPath + "docs/mesquite" + MesquiteFile.fileSeparator + "support.html" ; 
-			File testing = new File(manualPath);
-			if (testing.exists()) {
+
+			String manualPath = mesquiteWebSite + "/Getting+Help" ;
 				showWebPage(manualPath, false);
-			}
 		}
 		else if (checker.compare(this.getClass(), "Sets whether the Mesquite window appears automatically when no windows are showing", "[on or off]", commandName, "windowAutoShow")){
 			MesquiteWindow.autoShow = MesquiteBoolean.fromOffOnString(ParseUtil.getFirstToken(arguments, stringPos));

Source/mesquite/align/AlignToDropped/AlignToDropped.java

@@ -142,18 +142,6 @@ private boolean alignTouchedToDropped(int rowToAlign, int recipientRow){
 			long[] newAlignment = Long2DArray.extractRow(aligned,1);
 
 			int[] newGaps = aligner.getGapInsertionArray();
-	/*			if (newGaps!=null) {
-			int total = 0;
-				for (int i=0; i<newGaps.length; i++) {
-					if (newGaps[i]!=0)
-						Debugg.println("      " + i + "   " + newGaps[i]);
-				//	if (newGaps[i]<0)
-				//		newGaps[i]=0;
-					total += newGaps[i];
-				}
-				//Debugg.println("total newGaps: " + total);
-			}
-			*/
 			if (newGaps!=null) 
 				alignUtil.insertNewGaps((MolecularData)data, newGaps, aligner.getPreSequenceTerminalFlaggedGap(), aligner.getPostSequenceTerminalFlaggedGap());
 			Rectangle problem = alignUtil.forceAlignment((MolecularData)data, 0, data.getNumChars()-1, rowToAlign, rowToAlign, 1, aligned);

Source/mesquite/align/MAFFTAlign/MAFFTAlign.java

@@ -51,7 +51,7 @@ public boolean isSubstantive(){
 	}
 	/*.................................................................................................................*/
 	public boolean isPrerelease(){
-		return true;  //put release version
+		return false;  
 	}
 	/*.................................................................................................................*/
 	public String getName() {
@@ -262,7 +262,7 @@ public  String getImportExtension() {
 	 * 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 NEXTRELEASE;  
+		return 300;  
 	}
 
 }

Source/mesquite/align/lib/AlignmentHelper.java

@@ -90,16 +90,6 @@ long[][] ReInsertGaps (int k, int[] followsGapSize, int totalGapChars, boolean s
 			gappedSeq2return[i+usedGaps][1] = inputSequence[i][1] ;
 		}		
 
-/*		if (gapInsertionArray!=null) {
-			int total = 0;
-			for (int m=0; m<gapInsertionArray.length; m++) {
-				if (gapInsertionArray[m]!=0)
-					Debugg.println("|||       " + m + "   " + gapInsertionArray[m]);
-			}
-			Debugg.println("||| total newGaps: " + total);
-		}
-*/
-
 		return gappedSeq2return;	
 	}
 

Source/mesquite/align/lib/PairwiseAligner.java

@@ -471,7 +471,6 @@ public long[][] getAlignment(MolecularData data1, int it1, MolecularData data2,
 	/** This method returns a 2d-long array ([site][taxon]) representing the alignment of the sequences identified by the "taxon" and "site" arguments.
 	 * If object has been told to retain gaps, gaps in taxon1 will remain intact (new ones  may be added)*/
 	public long[][] alignSequences(MCategoricalDistribution data, int taxon1, int taxon2, int firstSite, int lastSite, boolean returnAlignment, MesquiteNumber score) {
-	//	Debugg.println("\n\n****** alignSequences,  taxon1: "+ taxon1 + ", taxon2: "+ taxon2 + ", lastSite: "+ lastSite + ", returnAlignment: "+ returnAlignment);
 		if (lastSite - firstSite+1 <0 || !MesquiteInteger.isCombinable(firstSite) || !MesquiteInteger.isCombinable(lastSite)){
 			firstSite = 0;
 			lastSite = data.getNumChars()-1;
@@ -492,8 +491,6 @@ public long[][] alignSequences(MCategoricalDistribution data, int taxon1, int ta
 		}
 		CategoricalState state=(CategoricalState)(data.getParentData().makeCharacterState());
 
-//		Debugg.println("       firstSite: "+ firstSite + ", lastSite: "+ lastSite);
-
 		long[][] aligned =  alignSequences(extracted1, extracted2, returnAlignment, score);
 
 		return aligned;

Source/mesquite/basic/BasicStringMatcher/BasicStringMatcher.java

@@ -42,5 +42,15 @@ public String getExplanation() {
 	public boolean useDefaultMatching() {
 		return true;
 	}
+	public boolean isPrerelease() {
+		return false;
+	}
+	/*.................................................................................................................*/
+	/** 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 300;  
+	}
 
 }

Source/mesquite/basic/ExamplesNavigator/ExamplesNavigator.java

@@ -130,7 +130,7 @@ else if (checker.compare(this.getClass(), "Jumps to next project recorded", null
 			while (getProject().developing)
 				;
 			String openCommand = "openFile ";
-			if (StringUtil.startsWithIgnoreCase(nextProjectName,"http:") || !getProject().getHomeFile().isLocal())
+			if (StringUtil.startsWithIgnoreCase(nextProjectName,"http") || !getProject().getHomeFile().isLocal())
 				openCommand = "openURL ";
 			String commands = "newThread; getProjectID; Integer.id *It; tell Mesquite; getWindowAutoShow; String.was *It; windowAutoShow off; closeProjectByID *Integer.id; " + openCommand;
 			commands +=  StringUtil.tokenize(MesquiteFile.composePath(getProject().getHomeDirectoryName(), nextProjectName)) + "; ifNotExists It;  showAbout; endIf; windowAutoShow *String.was; endTell;";
@@ -150,7 +150,7 @@ else if (checker.compare(this.getClass(), "Jumps to previous project recorded",
 
 
 			String openCommand = "openFile ";
-			if (StringUtil.startsWithIgnoreCase(prevProjectName,"http:") || !getProject().getHomeFile().isLocal())
+			if (StringUtil.startsWithIgnoreCase(prevProjectName,"http") || !getProject().getHomeFile().isLocal())
 				openCommand = "openURL ";
 
 			String commands = "newThread; getProjectID; Integer.id *It; tell Mesquite; getWindowAutoShow; String.was *It; windowAutoShow off; closeProjectByID *Integer.id; " + openCommand;
@@ -169,7 +169,7 @@ else if (checker.compare(this.getClass(), "Jumps to project", null, commandName,
 			while (getProject().developing)
 				;
 			String openCommand = "openFile ";
-			if (StringUtil.startsWithIgnoreCase(path,"http:") || !getProject().getHomeFile().isLocal())
+			if (StringUtil.startsWithIgnoreCase(path,"http") || !getProject().getHomeFile().isLocal())
 				openCommand = "openURL ";
 			String commands = "newThread; getProjectID; Integer.id *It; tell Mesquite; getWindowAutoShow; String.was *It; windowAutoShow off; closeProjectByID *Integer.id; " + openCommand;
 			commands +=  StringUtil.tokenize(MesquiteFile.composePath(getProject().getHomeDirectoryName(), path)) + "; ifNotExists It;  showAbout; endIf; windowAutoShow *String.was; endTell;";

Source/mesquite/basic/ManageTaxaPartitions/ManageTaxaPartitions.java

@@ -35,6 +35,7 @@ public class ManageTaxaPartitions extends SpecsSetManager {
 	/*.................................................................................................................*/
 	public boolean startJob(String arguments, Object condition, boolean hiredByName) {
 		groups = new TaxaGroupVector();
+		getProject().addFileElement(groups);
 		return true;
 	}
 
@@ -99,8 +100,10 @@ public void notifyOfGroupChange(TaxaGroup e){
 	}
 	public NexusBlock elementAdded(FileElement e){
 		if (e instanceof TaxaGroup){
+
 			if (groups.indexOf(e)<0) {
-				groups.addElement(e, false);
+				groups.addElement(e, true);
+				e.addListener(groups);
 			}
 			e.setManager(this);
 			return null;
@@ -112,7 +115,7 @@ else if (e!=null && e instanceof Taxa){
 	}
 	public void elementDisposed(FileElement e){
 		if (groups !=null)
-			groups.removeElement(e, false);
+			groups.removeElement(e, true);
 	}
 	public void deleteElement(FileElement e){
 		if (e instanceof TaxaGroup){
@@ -141,7 +144,9 @@ public void deleteElement(FileElement e){
 				if (changed)
 					taxa.notifyListeners(this, new Notification(MesquiteListener.PARTS_CHANGED));
 			}
+			getProject().removeFileElement(e);//must remove first, before disposing
 			groups.removeElement(e, true);
+			e.dispose();
 		}
 	}
 	public Class getElementClass(){

Source/mesquite/basic/PrefixTaxonNameWithGroup/PrefixTaxonNameWithGroup.java

@@ -42,9 +42,10 @@ public boolean alterName(Taxa taxa, int it){
 
     	if (taxa!=currentTaxa){
     		currentTaxa=taxa;
-    		if (currentPartition==null)
-    			currentPartition = (TaxaPartition)taxa.getCurrentSpecsSet(TaxaPartition.class);
+    		currentPartition=null;
     	}
+		if (currentPartition==null)
+			currentPartition = (TaxaPartition)taxa.getCurrentSpecsSet(TaxaPartition.class);
 		if (currentPartition!=null){
 			tg = currentPartition.getTaxaGroup(it);
 		}
@@ -84,14 +85,14 @@ public String getExplanation() {
    	 }
  	/*.................................................................................................................*/
  	public boolean isPrerelease(){
- 		return true;  
+ 		return false;  
  	}
  	/*.................................................................................................................*/
  	/** 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 NEXTRELEASE;  
+ 		return 300;  
  	}
 }
 

Source/mesquite/basic/VoucherInfoCoordinator/VoucherInfoCoordinator.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.orgThis 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.basic.VoucherInfoCoordinator; import mesquite.lib.*;public class  VoucherInfoCoordinator extends VoucherInfoCoord {	public void getEmployeeNeeds(){  //This gets called on startup to harvest information; override this and inside, call registerEmployeeNeed		EmployeeNeed e = registerEmployeeNeed(VoucherInfoSource.class, "Voucher information is obtained from a source.",				"This is activated automatically.");	}	/*.................................................................................................................*/	public boolean startJob(String arguments, Object condition, boolean hiredByName) {		hireAllEmployees(VoucherInfoSource.class);		return true;	}			public VoucherInfo getVoucherInfo(String sourceID, String id){		if (sourceID == null || id == null)			return null;		EmployeeVector v = getEmployeeVector();		for (int i = 0; i<v.size(); i++){			if (v.elementAt(i) instanceof VoucherInfoSource){				VoucherInfoSource vis = (VoucherInfoSource)v.elementAt(i);				if (vis.handlesDatabase(sourceID)){					return vis.getVoucherInfo(sourceID, id);				}			}		}		return null;	}	/*.................................................................................................................*/	public String getName() {		return "Coordinator of voucher information";	}	/*.................................................................................................................*/	public boolean isPrerelease(){		return false;  	}	/*.................................................................................................................*/	/** 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 -1;  	}	/*.................................................................................................................*/	/** returns whether this module is requesting to appear as a primary choice */	public boolean requestPrimaryChoice(){		return true;  	}		/*.................................................................................................................*/	/** returns an explanation of what the module does.*/	public String getExplanation() {		return "Finds suppliers of voucher information." ;	}}
+/* 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.orgThis 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.basic.VoucherInfoCoordinator; import mesquite.lib.*;public class  VoucherInfoCoordinator extends OTUIDCodeInfoCoord {	public void getEmployeeNeeds(){  //This gets called on startup to harvest information; override this and inside, call registerEmployeeNeed		EmployeeNeed e = registerEmployeeNeed(OTUIDCodeInfoSource.class, "Voucher information is obtained from a source.",				"This is activated automatically.");	}	/*.................................................................................................................*/	public boolean startJob(String arguments, Object condition, boolean hiredByName) {		hireAllEmployees(OTUIDCodeInfoSource.class);		return true;	}			public VoucherInfoFromOTUIDDB getVoucherInfo(String sourceID, String id){		if (sourceID == null || id == null)			return null;		EmployeeVector v = getEmployeeVector();		for (int i = 0; i<v.size(); i++){			if (v.elementAt(i) instanceof OTUIDCodeInfoSource){				OTUIDCodeInfoSource vis = (OTUIDCodeInfoSource)v.elementAt(i);				if (vis.handlesDatabase(sourceID)){					return vis.getVoucherInfo(sourceID, id);				}			}		}		return null;	}	/*.................................................................................................................*/	public String getName() {		return "Coordinator of voucher information";	}	/*.................................................................................................................*/	public boolean isPrerelease(){		return false;  	}	/*.................................................................................................................*/	/** 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 -1;  	}	/*.................................................................................................................*/	/** returns whether this module is requesting to appear as a primary choice */	public boolean requestPrimaryChoice(){		return true;  	}		/*.................................................................................................................*/	/** returns an explanation of what the module does.*/	public String getExplanation() {		return "Finds suppliers of voucher information." ;	}}