Check for compatibility in AlterAllMatrices

Getting rid of green dot in NodeLocsCircular
MesquiteProject · Aug 23, 2014 · b0a7433 · b0a7433
1 parent 9b4ded3
commit b0a7433
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Showing 8 changed files with 13 additions and 14 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();

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/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/lib/MesquiteModule.java b/Source/mesquite/lib/MesquiteModule.java
@@ -68,7 +68,7 @@ public abstract class MesquiteModule extends EmployerEmployee implements Command
 	/*.................................................................................................................*/
 	/** returns build date of the Mesquite system (e.g., "22 September 2003") */
 	public final static String getBuildDate() {
-		return "22 August 2014";   
+		return "23 August 2014";   
 	}
 	/*.................................................................................................................*/
 	/** returns version of the Mesquite system */
@@ -89,7 +89,7 @@ public final static String getBuildLetter() {
 	public final static int getBuildNumber() {
 		//as of 26 Dec 08, build naming changed from letter + number to just number.  Accordingly j105 became 473, based on
 		// highest build numbers of d51+e81+g97+h66+i69+j105 + 3 for a, b, c
-		return 	629;  
+		return 	630;  
 	}
 	//0.95.80    14 Mar 01 - first beta release 
 	//0.96  2 April 01 beta  - second beta release

diff --git a/Source/mesquite/minimal/Installer/Installer.java b/Source/mesquite/minimal/Installer/Installer.java
@@ -209,7 +209,7 @@ void writeReceipts(){
 			buff.append("\t</installationReceipt>\n");
 		}
 		buff.append("\n</mesquite>");
-		MesquiteFile.createDirectory(getInstallationSettingsPath() );  //Debugg.println : this is a problem if user doesn't have write permission
+		MesquiteFile.createDirectory(getInstallationSettingsPath() );  
 		MesquiteFile.putFileContents(getInstallationSettingsPath() + "receipts.xml", buff.toString(), true, false);
 	}
 

diff --git a/Source/mesquite/minimal/Simplicity/SimplifyControlWindow.java b/Source/mesquite/minimal/Simplicity/SimplifyControlWindow.java
@@ -594,7 +594,7 @@ public SaveRenameDeleteButton(){
 		setForeground(ColorTheme.getExtInterfaceTextContrast());
 		//ColorTheme.getExtInterfaceElement());
 	}
-	void redoMenu() {//Debugg.println  don't use this if can't save because don't have permissions
+	void redoMenu() {// don't use this if can't save because don't have permissions
 		if (popup==null)
 			popup = new MesquitePopup(this);
 		popup.removeAll(); 

diff --git a/Source/mesquite/ornamental/NodeLocsCircular/NodeLocsCircular.java b/Source/mesquite/ornamental/NodeLocsCircular/NodeLocsCircular.java
@@ -441,8 +441,8 @@ public   String writeOnTree(Tree tree, int drawnRoot) {
 	public   void drawOnTree(Tree tree, int drawnRoot, Graphics g) {
 		if (locsModule.showScale.getValue() && locsModule.showBranchLengths.getValue())
 			locsModule.drawGrid(g, tree.tallestPathAboveNode(drawnRoot, 1.0), locsModule.scaling, locsModule.treeCenter);
-		g.setColor(Color.green);
-		g.fillOval(locsModule.centerx-8, locsModule.centery-8, 16, 16);
+		//g.setColor(Color.green);
+		//g.fillOval(locsModule.centerx-8, locsModule.centery-8, 16, 16);
 	}
 	/*.................................................................................................................*/
 	public   void printOnTree(Tree tree, int drawnRoot, Graphics g) {