Merge pull request #89 from MesquiteProject/development

Development

Source/mesquite/Mesquite.java

@@ -37,24 +37,24 @@ public class Mesquite extends MesquiteTrunk
 {
 	/*.................................................................................................................*/
 	public String getCitation() {
-		return "Maddison, W.P. & D.R. Maddison. 2018. Mesquite: A modular system for evolutionary analysis.  Version 3.6.  http://www.mesquiteproject.org";
+		return "Maddison, W.P. & D.R. Maddison. 2019. Mesquite: A modular system for evolutionary analysis.  Version 3.61.  http://www.mesquiteproject.org";
 	}
 	/*.................................................................................................................*/
 	public String getVersion() {
-		return "3.6";
+		return "3.61";
 	}
 
 	/*.................................................................................................................*/
 	public int getVersionInt() {
-		return 360;
+		return 361;
 	}
 	/*.................................................................................................................*/
 	public double getMesquiteVersionNumber(){
-		return 3.6;
+		return 3.61;
 	}
 	/*.................................................................................................................*/
 	public String getDateReleased() {
-		return "December 2018"; //"April 2007";
+		return "December 2019"; //"April 2007";
 	}
 	/*.................................................................................................................*/
 	public boolean isPrerelease(){
@@ -380,7 +380,7 @@ else if (prefsFile.exists() || prefsFileXML.exists()) {
 		String logInitString = "Mesquite version " + getMesquiteVersion() + getBuildVersion() + "\n";
 		if (StringUtil.notEmpty(MesquiteModule.getSpecialVersion()))
 			logInitString  +="  " + MesquiteModule.getSpecialVersion()+ "\n";
-		logInitString  += ("Copyright (c) 1997-2018 W. Maddison and D. Maddison\n");
+		logInitString  += ("Copyright (c) 1997-2019 W. Maddison and D. Maddison\n");
 		logInitString  += "The basic Mesquite package (class library and basic modules) is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License. "
 				+ "  Mesquite is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.  For details on license and "
 				+ "lack of warranty see the GNU Lesser General Public License by selecting \"Display License\" from the Window menu or at www.gnu.org\n"

Source/mesquite/align/AlignDNAToProtein/AlignDNAToProtein.java

@@ -70,7 +70,7 @@ public boolean forceAlignment(DNAData dnaData, ProteinData proteinData, int it)
 		int numBases = dnaData.getNumberApplicableInTaxon(it, true);
 		int numAAs = proteinData.getNumberApplicableInTaxon(it, true);
 		if (numAAs*3!= numBases) {
-			logln("Number of nucleotides in sequence does not correspond to number of amino acids in protein sequence (taxon " + it+1 + ")");
+			logln("Number of nucleotides (\" + numBases + \") in sequence does not correspond to number of amino acids  (\" + numAAs + \") in protein sequence (taxon " + (it+1) + ")");
 			return false;
 		}
 

Source/mesquite/align/MuscleAlign/MuscleAlign.java

@@ -40,7 +40,7 @@ public boolean showCitation() {
 	}
 	/*.................................................................................................................*/
 	public String getCitation()  {
-		return "Please remember to cite the version of Muscle you used.";
+		return "Please remember to cite the version of MUSCLE you used.";
 	}
 	/*.................................................................................................................*/
 	public boolean isSubstantive(){
@@ -52,11 +52,11 @@ public boolean isPrerelease(){
 	}
 	/*.................................................................................................................*/
 	public String getName() {
-		return "Muscle Align";
+		return "MUSCLE Align";
 	}
 	/*.................................................................................................................*/
 	public String getNameForMenuItem() {
-		return "Muscle Align...";
+		return "MUSCLE Align...";
 	}
 	/*.................................................................................................................*/
 	/** returns an explanation of what the module does.*/
@@ -65,9 +65,13 @@ public String getExplanation() {
 	}
 
 	public String getProgramName(){
-		 return "Muscle";
+		 return "MUSCLE";
 	 }
-
+	/*.................................................................................................................*/
+	public String getHelpURL(){
+		return "http://www.drive5.com/muscle/manual/";
+	}
+
 	/*.................................................................................................................*/
 	public String getHelpString() {
 	  String s =  " In the Muscle Options field, place any Muscle options you wish to use.  For example, if you wished to change the"

Source/mesquite/align/lib/AlignUtil.java

@@ -590,7 +590,7 @@ public static boolean integrateAlignment(long[][] alignedMatrix, MolecularData d
 				data.setSelected(i, true);
 
 		}
-		MesquiteTrunk.mesquiteTrunk.logln("Alignment completed.");
+		MesquiteTrunk.mesquiteTrunk.logln("Alignment completed for " + data.getName());
 		data.removeCharactersThatAreEntirelyGaps(icStart, icEnd, true);  // added 1 June 2016
 
 		return true;

Source/mesquite/align/lib/ExternalSequenceAligner.java

@@ -450,15 +450,15 @@ else if (!(firstTaxon==0 && lastTaxon==matrix.getNumTaxa())) {  // we are doing
 				if (success) {
 					for (int i=1; i<alignedTaxa.getNumTaxa() ; i++) {
 						for (int j= i-1; j>=0 && j+1<keys.length && keys[j]>keys[j+1]; j--) {
-							alignedTaxa.swapParts(j, j+1);
+							alignedTaxa.swapParts(j, j+1, false);
 							int kj = keys[j];
 							keys[j] = keys[j+1];
 							keys[j+1] = kj;
 							//alignedData.swapTaxa(j, j+1);
 						}
 					}
+					alignedTaxa.notifyListeners(this, new Notification(MesquiteListener.PARTS_MOVED));
 					alignedData.changed(this, alignedTaxa, new Notification(MesquiteListener.PARTS_MOVED));
-
 					if (alignedData instanceof MolecularData){
 						aligned = new long[alignedData.getNumChars()][originalTaxa.getNumTaxa()];
 						for (int ic = 0; ic<alignedData.getNumChars(); ic++)

Source/mesquite/ancstates/TraceCharOverTrees/TraceCharOverTrees.java

@@ -921,7 +921,7 @@ else if (!tempCharStates.frequenciesExist() && mode == AVERAGE_FREQUENCIES) {
 				}
 				if (showNodeAbsent){
 					extraNames[NODE_ABSENT] = "Node Absent";
-					extraColors.setColor(NODE_ABSENT,Color.red);
+					extraColors.setColor(NODE_ABSENT,ColorDistribution.veryLightBlue);
 				}
 				charStates.setExtraFrequencyNames(extraNames);
 				charStates.setExtraFrequencyColors(extraColors);