Merge pull request #27 from wmaddisn/master

Pender Harbour Mesquite hackathon Saturday
MesquiteProject · Aug 23, 2014 · f6d8f61 · f6d8f61
2 parents 8b37c8d + b0a7433
commit f6d8f61
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Showing 49 changed files with 644 additions and 239 deletions.
diff --git a/Source/mesquite/Mesquite.java b/Source/mesquite/Mesquite.java
@@ -350,7 +350,7 @@ else if (prefsFile.exists() || prefsFileXML.exists()) {
 		try {
 			equiv = ImageIO.read(new File(MesquiteModule.getRootPath() + "images/equivocal.gif"));
 		} catch (IOException e) {
-			Debugg.println(" IOException trying to read equivocal texture ");
+			MesquiteMessage.println(" IOException trying to read equivocal texture ");
 		}
 		GraphicsUtil.missingDataTexture = new TexturePaint(equiv, new Rectangle(0, 0, 16, 16));
 
@@ -748,7 +748,7 @@ private void findMesquiteDirectory(){
 			String manualString = mesquiteDirectory  + sep + "docs/mesquite" + sep + "manual.html";
 			File manual = new File(manualString);
 
-			storedManualString = manualString;  //Debugg.println get rid of this stuff!
+			storedManualString = manualString; 
 		}
 
 		setMesquiteDirectoryPath();
@@ -1479,6 +1479,18 @@ public void searchData(String s, MesquiteWindow window){
 		if (helpSearchManager != null)
 			helpSearchManager.searchData(s, window);
 	}
+
+	public String getNumModuleStarts() {
+		StringBuffer sb=new StringBuffer();
+		for (int i= 0; i<mesquiteModulesInfoVector.size(); i++){
+			MesquiteModuleInfo mmi = (MesquiteModuleInfo)mesquiteModulesInfoVector.elementAt(i);
+			int starts = mmi.getNumStarts();
+			if (starts>0)
+				sb.append(mmi.getClassName() + "\t" + starts+StringUtil.lineEnding());
+		}
+		return sb.toString();
+	}
+
 	/*.................................................................................................................*/
 	MesquiteInteger pos = new MesquiteInteger();
 	String noticeLocation = "http://"; //before release, change URL to "http://"
@@ -1820,7 +1832,11 @@ else if (checker.compare(this.getClass(), "Quits Mesquite", null, commandName, "
 					reportMemory();
 					logln("==^^^^^^^^^^^^^^^^^^^^==");
 				}
+
 			}
+			logln("\n");
+			logln("All modules that have been started at least once, and the number of times they have been started:");
+			logln(getNumModuleStarts());
 			/*
 				if (Listened.listenersRemaining>0) {
 					for (int i = 0; i<Listened.allListeners.size(); i++){

diff --git a/Source/mesquite/align/MAFFTAlign/MAFFTAlign.java b/Source/mesquite/align/MAFFTAlign/MAFFTAlign.java
@@ -233,7 +233,7 @@ public void appendDefaultOptions(StringBuffer shellScript, String inFilePath, St
 		if (!MesquiteTrunk.isWindows())
 			shellScript.append("  " + StringUtil.protectForUnix(inFilePath) + " > " + StringUtil.protectForUnix(outFilePath));
 		else
-			shellScript.append(" --out " + StringUtil.protectForUnix(outFilePath) + " " + StringUtil.protectForUnix(inFilePath));  //Debugg.println need to check MAFFT windows format
+			shellScript.append(" --out " + StringUtil.protectForUnix(outFilePath) + " " + StringUtil.protectForUnix(inFilePath));  
 	}
 
 

diff --git a/Source/mesquite/align/lib/ExternalSequenceAligner.java b/Source/mesquite/align/lib/ExternalSequenceAligner.java
@@ -111,7 +111,7 @@ public String getQueryProgramOptions() {
 	}
 	/*.................................................................................................................*/
 	public boolean queryOptions() {
-		if (!okToInteractWithUser(CAN_PROCEED_ANYWAY, "Querying Options"))  //Debugg.println needs to check that options set well enough to proceed anyway
+		if (!okToInteractWithUser(CAN_PROCEED_ANYWAY, "Querying Options"))  
 			return true;
 		MesquiteInteger buttonPressed = new MesquiteInteger(1);
 		ExtensibleDialog dialog = new ExtensibleDialog(containerOfModule(), getProgramName() + " Locations & Options",buttonPressed);  //MesquiteTrunk.mesquiteTrunk.containerOfModule()

diff --git a/Source/mesquite/basic/PrefixedStringMatcher/PrefixedStringMatcher.java b/Source/mesquite/basic/PrefixedStringMatcher/PrefixedStringMatcher.java
@@ -29,7 +29,7 @@ public boolean startJob(String arguments, Object condition, boolean hiredByName)
 	}
 	/** returns true if the options are set and accepted.*/
 	public  boolean queryOptions(){
-			if (!okToInteractWithUser(CAN_PROCEED_ANYWAY, "Querying Options"))  //Debugg.println needs to check that options set well enough to proceed anyway
+			if (!okToInteractWithUser(CAN_PROCEED_ANYWAY, "Querying Options")) 
 				return true;
 
 			MesquiteInteger buttonPressed = new MesquiteInteger(1);
@@ -64,7 +64,6 @@ public boolean stringsMatch(String s1, String s2) {
 		catch (Exception e) {
 			return false;
 		}
-		//Debugg.println("nextChars1: " + nextChars1 + ",   nextChars2: " + nextChars2 + "     " + nextChars1.equalsIgnoreCase(nextChars2));
 		if (StringUtil.blank(nextChars1) || StringUtil.blank(nextChars2))
 			return false;
 		return nextChars1.equalsIgnoreCase(nextChars2);

diff --git a/Source/mesquite/categ/ManageCategoricalChars/ManageCategoricalChars.java b/Source/mesquite/categ/ManageCategoricalChars/ManageCategoricalChars.java
@@ -84,6 +84,8 @@ public CharacterData processFormat(MesquiteFile file, Taxa taxa, String dataType
 				data.setName(title);  //because otherwise titles are not set for fused matrices within ManageCharacters, since on the outside they don't know if it's new
 		}
 		else {
+			if (fuse)
+				data.setSuppressSpecssetReading(true);
 			if (taxa == null)
 				taxa = data.getTaxa();
 			data.suppressChecksum = true;

diff --git a/Source/mesquite/categ/ManageDNARNAChars/ManageDNARNAChars.java b/Source/mesquite/categ/ManageDNARNAChars/ManageDNARNAChars.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.categ.ManageDNARNAChars;
 
 import java.util.*;
@@ -24,11 +24,11 @@
 /* ======================================================================== 
 Manages DNA and RNA data matrices */
 public class ManageDNARNAChars extends CategMatrixManager {
-	
+
 	/*.................................................................................................................*/
 	public boolean startJob(String arguments, Object condition, boolean hiredByName) {
 		return true;
-  	 }
+	}
 	public Class getDataClass(){
 		return DNAData.class;
 	}
@@ -64,7 +64,7 @@ public CharacterData processFormat(MesquiteFile file, Taxa taxa, String dataType
 		else
 			proj = getProject();
 		CategoricalData data= null;
-		
+
 		//@@@@@@@@@@@@@@@@@@@@
 		boolean fuse = parser.hasFileReadingArgument(fileReadingArguments, "fuseTaxaCharBlocks");
 
@@ -82,8 +82,11 @@ public CharacterData processFormat(MesquiteFile file, Taxa taxa, String dataType
 				if (fuse)
 					data.setName(title);  //because otherwise titles are not set for fused matrices within ManageCharacters, since on the outside they don't know if it's new
 			}
-			else
+			else {
+				if (fuse)
+					data.setSuppressSpecssetReading(true);
 				data.suppressChecksum = true;
+			}
 			((DNAData)data).setDisplayAsRNA(true);
 		}
 		else {
@@ -100,8 +103,11 @@ public CharacterData processFormat(MesquiteFile file, Taxa taxa, String dataType
 				if (fuse)
 					data.setName(title);  //because otherwise titles are not set for fused matrices within ManageCharacters, since on the outside they don't know if it's new
 			}
-		else
-			data.suppressChecksum = true;
+			else{
+				if (fuse)
+					data.setSuppressSpecssetReading(true);
+				data.suppressChecksum = true;
+			}
 		}
 		data.interleaved = false;   //reset default in case this is fused
 		//@@@@@@@@@@@@@@@@@@@@
@@ -117,7 +123,7 @@ else if (tok.equalsIgnoreCase("interleave")) {
 				if ("=".equals(e)){
 					String y = ParseUtil.getToken(formatCommand, stringPos); //yes or no ?
 					data.interleaved = ("yes".equalsIgnoreCase(y));
-						
+
 				}
 				else {
 					stringPos.setValue(sp);
@@ -301,7 +307,7 @@ else if (file.writeOnlySelectedTaxa)
 			blocks.append(getCharStateLabels(data));
 
 		writeNexusMatrix(data, cB, blocks, file, progIndicator);
-		
+
 		blocks.append( StringUtil.lineEnding());
 		if (!file.useSimplifiedNexus){
 			String idsCommand = null;
@@ -313,23 +319,23 @@ else if (file.writeOnlySelectedTaxa)
 		if (cB !=null)
 			blocks.append(cB.getUnrecognizedCommands() + StringUtil.lineEnding());
 		blocks.append("END;" + StringUtil.lineEnding());
-	//	MesquiteModule.mesquiteTrunk.mesquiteMessage("DNA matrix composed", 1, 0);
+		//	MesquiteModule.mesquiteTrunk.mesquiteMessage("DNA matrix composed", 1, 0);
 
 		file.writeLine( blocks.toString());
 	}
 
 
 	/*.................................................................................................................*/
-    	 public String getName() {
+	public String getName() {
 		return "Manage DNA/RNA matrices";
-   	 }
-   	 
+	}
+
 	/*.................................................................................................................*/
- 	/** returns an explanation of what the module does.*/
- 	public String getExplanation() {
- 		return "Manages DNA/RNA data matrices (including read/write in NEXUS file)." ;
-   	 }
+	/** returns an explanation of what the module does.*/
+	public String getExplanation() {
+		return "Manages DNA/RNA data matrices (including read/write in NEXUS file)." ;
+	}
 }
-	
-	
+
+
 
diff --git a/Source/mesquite/categ/ManageProteinChars/ManageProteinChars.java b/Source/mesquite/categ/ManageProteinChars/ManageProteinChars.java
@@ -76,8 +76,11 @@ public CharacterData processFormat(MesquiteFile file, Taxa taxa, String dataType
 			if (fuse)
 				data.setName(title);  //because otherwise titles are not set for fused matrices within ManageCharacters, since on the outside they don't know if it's new
 		}
-		else
+		else {
+			if (fuse)
+				data.setSuppressSpecssetReading(true);
 			data.suppressChecksum = true;
+		}
 		//@@@@@@@@@@@@@@@@@@@@
 		String tok = ParseUtil.getToken(formatCommand, stringPos);
 		while (!tok.equals(";")) {

diff --git a/Source/mesquite/charMatrices/AlterAllMatrices/AlterAllMatrices.java b/Source/mesquite/charMatrices/AlterAllMatrices/AlterAllMatrices.java
@@ -93,12 +93,11 @@ public boolean processFile(MesquiteFile file){
    		if (proj == null)
    			return false;
    		boolean success = true;
+   		CompatibilityTest test = alterTask.getCompatibilityTest();
    		for (int im = 0; im < proj.getNumberCharMatrices(file); im++){
    			CharacterData data = proj.getCharacterMatrix(file, im);
-   			//Debugg.println checkCompatibility
-
-   			Debugg.println("Altering matrix " + im + " (" + data.getName() + ", id = " + data.getID() + ")");
-   			success = success && alterTask.alterData(data, null, null);
+   			if (test.isCompatible(data.getStateClass(), getProject(), this))
+   				success = success && alterTask.alterData(data, null, null);
    		}
 
    		return success;

diff --git a/Source/mesquite/charMatrices/BasicDataWindowMaker/BasicDataWindowMaker.java b/Source/mesquite/charMatrices/BasicDataWindowMaker/BasicDataWindowMaker.java
@@ -2246,7 +2246,7 @@ public boolean requestCellColorer(MesquiteModule mb, int ic, int it, String mess
 		if (ic >= 0 && it >= 0) { // matrix cells
 			if (table.cellColorer == mb)
 				return true;
-			if ((table.cellColorer == null || table.cellColorer instanceof mesquite.charMatrices.NoColor.NoColor) || (message != null && AlertDialog.query(this, "Cell colors", message, "Yes", "No"))) {
+			if ((table.cellColorer == null || table.cellColorer instanceof mesquite.charMatrices.NoColor.NoColor) && (message != null && AlertDialog.query(this, "Cell colors", message, "Yes", "No"))) {
 				setCellColorer(mb);
 				table.repaintAll();
 				return true;
@@ -2255,7 +2255,7 @@ public boolean requestCellColorer(MesquiteModule mb, int ic, int it, String mess
 		else if (ic < 0 && it >= 0) { // row names
 			if (table.rowNamesColorer == mb)
 				return true;
-			if ((table.rowNamesColorer == null || table.rowNamesColorer instanceof mesquite.charMatrices.NoColor.NoColor) || (message != null && AlertDialog.query(this, "Row name colors", message, "Yes", "No"))) {
+			if ((table.rowNamesColorer == null || table.rowNamesColorer instanceof mesquite.charMatrices.NoColor.NoColor) && (message != null && AlertDialog.query(this, "Row name colors", message, "Yes", "No"))) {
 				setRowNamesColorer(mb);
 				table.repaintAll();
 				return true;
@@ -2264,7 +2264,7 @@ else if (ic < 0 && it >= 0) { // row names
 		else if (ic >= 0 && it < 0) { // column names
 			if (table.columnNamesColorer == mb)
 				return true;
-			if ((table.columnNamesColorer == null || table.columnNamesColorer instanceof mesquite.charMatrices.NoColor.NoColor) || (message != null && AlertDialog.query(this, "Column name colors", message, "Yes", "No"))) {
+			if ((table.columnNamesColorer == null || table.columnNamesColorer instanceof mesquite.charMatrices.NoColor.NoColor) && (message != null && AlertDialog.query(this, "Column name colors", message, "Yes", "No"))) {
 				setColumnNamesColorer(mb);
 				table.repaintAll();
 				return true;

diff --git a/Source/mesquite/charMatrices/StoredMatrices/StoredMatrices.java b/Source/mesquite/charMatrices/StoredMatrices/StoredMatrices.java
@@ -157,20 +157,20 @@ public void disposing(Object obj){
 
 			if (taxa !=null && taxa.isDoomed()) {
 				taxa = null;
-				if (!okToInteractWithUser(CAN_PROCEED_ANYWAY, "Taxa block that is in use has been deleted"))  //Debugg.println needs to check that options set well enough to proceed anyway
+				if (!okToInteractWithUser(CAN_PROCEED_ANYWAY, "Taxa block that is in use has been deleted"))  
 					return;
 
-				logln("Taxa null or being disposed; StoredMatrices will quit.");//Debugg.println
+				logln("Taxa null or being disposed; StoredMatrices will quit.");
 				iQuit();
 				return;
 
 			}
 			data = null;
 			dataName.setValue("No matrix is currently in use");
-			if (!okToInteractWithUser(CAN_PROCEED_ANYWAY, "Character matrix that is in use has been deleted"))  //Debugg.println needs to check that options set well enough to proceed anyway
+			if (!okToInteractWithUser(CAN_PROCEED_ANYWAY, "Character matrix that is in use has been deleted"))  
 				return;
 
-			discreetAlert("A character data matrix in use (for " + getEmployer().getName() + ") has been deleted.  Another matrix will be sought.");  //Debugg.println
+			discreetAlert("A character data matrix in use (for " + getEmployer().getName() + ") has been deleted.  Another matrix will be sought.");  
 			if (dataClass!=null) {
 				if (getProject().getNumberCharMatricesVisible(taxa, dataClass)<=0) {
 					alert("No compatible character matrices were found, and so Stored Matrices cannot be used.");

diff --git a/Source/mesquite/cont/lib/ManageContCharsA.java b/Source/mesquite/cont/lib/ManageContCharsA.java
@@ -84,8 +84,11 @@ public CharacterData processFormat(MesquiteFile file, Taxa taxa, String dataType
 			if (fuse)
 				data.setName(title);  //because otherwise titles are not set for fused matrices within ManageCharacters, since on the outside they don't know if it's new
 		}
-		else
+		else {
+			if (fuse)
+				data.setSuppressSpecssetReading(true);
 			data.suppressChecksum = true;
+		}
 		data.interleaved = false;   //reset default in case this is fused
 
 		//@@@@@@@@@@@@@@@@@@@@

diff --git a/Source/mesquite/correl/lib/PagelMatrixModel.java b/Source/mesquite/correl/lib/PagelMatrixModel.java
@@ -385,7 +385,7 @@ private double[] prepareQList(double[] values){
 
 		for (int i=0;i<qMapping.length;i++) {
 			if (qMapping[i]>= values.length)
-				Debugg.println("values length " + values.length + " [qMapping[i] " + qMapping[i]);
+				MesquiteMessage.println("values length " + values.length + " [qMapping[i] " + qMapping[i]);
 			qList[i] = values[qMapping[i]];
 		}
 		return qList;

diff --git a/Source/mesquite/lib/EmployerEmployee.java b/Source/mesquite/lib/EmployerEmployee.java
@@ -1040,11 +1040,15 @@ private boolean startupEmployee(MesquiteModule mb, Class dutyClass, Object condi
 				started = mb.superStartJob(null, null, false);
 				if (started)
 					started = mb.startJob(null, null, false);
+				if (started)
+					mb.incrementNumStarts();
 			}
 			else {
 				started = mb.superStartJob(arguments, condition, false);
 				if (started)
 					started = mb.startJob(arguments, condition, false);
+				if (started)
+					mb.incrementNumStarts();
 			}
 		} 
 		catch (Exception e) {