Merge pull request #60 from MesquiteProject/fixingCodonPositionsWriti…

…ng20161202 3.11 fix of bug writing codon positions
MesquiteProject · Dec 3, 2016 · bbb7e30 · bbb7e30
2 parents cc1efa2 + e8b8c53
commit bbb7e30
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Showing 3 changed files with 24 additions and 16 deletions.
diff --git a/Source/mesquite/Mesquite.java b/Source/mesquite/Mesquite.java
@@ -38,24 +38,24 @@ public class Mesquite extends MesquiteTrunk
 {
 	/*.................................................................................................................*/
 	public String getCitation() {
-		return "Maddison, W.P. & D.R. Maddison. 2016. Mesquite: A modular system for evolutionary analysis.  Version 3.1.  http://mesquiteproject.org";
+		return "Maddison, W.P. & D.R. Maddison. 2016. Mesquite: A modular system for evolutionary analysis.  Version 3.11.  http://mesquiteproject.org";
 	}
 	/*.................................................................................................................*/
 	public String getVersion() {
-		return "3.1";
+		return "3.11";
 	}
 
 	/*.................................................................................................................*/
 	public int getVersionInt() {
-		return 310;
+		return 311;
 	}
 	/*.................................................................................................................*/
 	public double getMesquiteVersionNumber(){
-		return 3.10;
+		return 3.11;
 	}
 	/*.................................................................................................................*/
 	public String getDateReleased() {
-		return "June 2016"; //"April 2007";
+		return "December 2016"; //"April 2007";
 	}
 	/*.................................................................................................................*/
 	/** returns the URL of the notices file for this module so that it can phone home and check for messages */

diff --git a/Source/mesquite/lib/MesquiteModule.java b/Source/mesquite/lib/MesquiteModule.java
@@ -68,12 +68,12 @@ 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 "27 June 2016";
+		return "3 Dec 2016";
 	}
 	/*.................................................................................................................*/
 	/** returns version of the Mesquite system */
 	public final static String getMesquiteVersion() {
-		return "3.10";
+		return "3.11";
 	}
 	/*.................................................................................................................*/
 	/*.................................................................................................................*/
@@ -90,7 +90,7 @@ 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 	765;  
+		return 	766;  
 	}
 	//0.95.80    14 Mar 01 - first beta release 
 	//0.96  2 April 01 beta  - second beta release
@@ -134,6 +134,7 @@ public final static int getBuildNumber() {
 	//3.03  = 702 released 31 March 2015
 	//3.04  = 725 released 16 August 2015
 	//3.10  = 765 released 27 June 2016
+	//3.11  = 766 released 3 December 2016,  fix of miswriting of codon positions
 	/*.................................................................................................................*/
 	/** returns a string if this is a special version of Mesquite */
 	public final static String getSpecialVersion() {

diff --git a/Source/mesquite/lib/characters/CodonPositionsSet.java b/Source/mesquite/lib/characters/CodonPositionsSet.java
@@ -91,7 +91,7 @@ public String getListOfMatches(int targetPos, int offset, boolean[] include){
  		return getListOfMatches(targetPos, offset, include, false);
  	}
  	public String getListOfMatches(int targetPos, int offset, boolean[] include, boolean writeCommas){  //offset is number to add to character numbers
-
+ 		//this had been badly broken in 310 (commas written everywhere...
  		int lastWritten = -1;
 		int unassignedPosition=4;
 		String list = "";
@@ -109,17 +109,21 @@ public String getListOfMatches(int targetPos, int offset, boolean[] include, boo
 						int lastThird = endSequenceByThree(targetPos, getNumberOfParts(), ic, count, include, charNumberOfLastThird);
 						//if so, then go the series of thirds 
 						if (lastThird != count){
-							if (writeSeparator)
-								list += ",";
+							if (writeSeparator) {
+								list += ", ";
+								writeSeparator=false;
+							}
 
 							list += " " + CharacterStates.toExternal(count+offset) + " - " +  CharacterStates.toExternal(lastThird+offset) + "\\3";
 							ic = charNumberOfLastThird.getValue();
 							count = lastThird;
 
 						}
 						else { //otherwise write as normal*/
-							if (writeSeparator)
-								list += ",";
+							if (writeSeparator) {
+								list += ", ";
+								writeSeparator=false;
+							}
 							lastWritten = count;
 							list += " " + CharacterStates.toExternal(count+offset);
 							continuing = 1;
@@ -132,13 +136,16 @@ else if (continuing == 1) {  // we know there are at least two in a row of the s
 				}
 				else if (continuing>0) {   // we are in a contiguous stretch of the same thing
 					if (lastWritten != count-1){  // last one we wrote wasn't the one just before
-						if (writeSeparator)
-							list += ",";
+						if (writeSeparator) {
+							list += ", ";
+							writeSeparator=false;
+						}
 						list += " " + CharacterStates.toExternal(count-1+offset);
 						lastWritten = count-1;
 					}
 					else {
-						writeSeparator=true;
+						if (writeCommas)
+							writeSeparator=true;
 						lastWritten = -1;
 					}
 					continuing = 0;