Merge branch 'develop' into features/JAL-2393customMatrices

diff --combined src/jalview/ws/sifts/SiftsClient.java
index 0e9e888,fe3a25b..2ff4a8b
--- 1/src/jalview/ws/sifts/SiftsClient.java
--- 2/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@@ -21,8 -21,6 +21,8 @@@
  package jalview.ws.sifts;
  
  import jalview.analysis.AlignSeq;
 +import jalview.analysis.scoremodels.ScoreMatrix;
 +import jalview.analysis.scoremodels.ScoreModels;
  import jalview.api.DBRefEntryI;
  import jalview.api.SiftsClientI;
  import jalview.datamodel.DBRefEntry;
@@@ -577,18 -575,8 +577,8 @@@ public class SiftsClient implements Sif
                    .equalsIgnoreCase(seqCoordSys.getName())
                    && isAccessionMatched(cRefDb.getDbAccessionId()))
            {
-             String resNumIndexString = cRefDb.getDbResNum()
-                     .equalsIgnoreCase("None") ? String.valueOf(UNASSIGNED)
-                     : cRefDb.getDbResNum();
-             try
-             {
-               currSeqIndex = Integer.valueOf(resNumIndexString);
-             } catch (NumberFormatException nfe)
-             {
-               currSeqIndex = Integer.valueOf(resNumIndexString
-                       .split("[a-zA-Z]")[0]);
-               continue;
-             }
+             currSeqIndex = getLeadingIntegerValue(
+                     cRefDb.getDbResNum(), UNASSIGNED);
              if (pdbRefDb != null)
              {
                break;// exit loop if pdb and uniprot are already found
@@@ -601,23 -589,11 +591,11 @@@
          }
          if (currSeqIndex >= seq.getStart() && currSeqIndex <= seq.getEnd())
          {
-           int resNum;
-           try
-           {
-             resNum = (pdbRefDb == null) ? Integer.valueOf(residue
-                     .getDbResNum()) : Integer.valueOf(pdbRefDb
-                     .getDbResNum());
-           } catch (NumberFormatException nfe)
-           {
-             if (pdbRefDb == null || pdbRefDb.getDbResNum().equals("null"))
-             {
-               resNum = UNASSIGNED;
-               continue;
-             }
-             resNum = Integer.valueOf(pdbRefDb
-                     .getDbResNum().split("[a-zA-Z]")[0]);
-             continue;
-           }
+ 
+           int resNum = (pdbRefDb == null) ? getLeadingIntegerValue(
+                   residue.getDbResNum(), UNASSIGNED)
+                   : getLeadingIntegerValue(pdbRefDb.getDbResNum(),
+                           UNASSIGNED);
  
            if (isResidueObserved(residue)
                    || seqCoordSys == CoordinateSys.UNIPROT)
@@@ -640,6 -616,30 +618,30 @@@
    }
  
    /**
+    * Get the leading integer part of a string that begins with an integer.
+    * 
+    * @param input
+    *          - the string input to process
+    * @param failValue
+    *          - value returned if unsuccessful
+    * @return
+    */
+   static int getLeadingIntegerValue(String input, int failValue)
+   {
+     if (input == null)
+     {
+       return failValue;
+     }
+     String[] parts = input.split("(?=\\D)(?<=\\d)");
+     if (parts != null && parts.length > 0 && parts[0].matches("[0-9]+"))
+     {
+       return Integer.valueOf(parts[0]);
+     }
+     return failValue;
+   }
+ 
+ 
+   /**
     * 
     * @param chainId
     *          Target chain to populate mapping of its atom positions.
@@@ -963,7 -963,7 +965,7 @@@
    }
  
    @Override
 -  public StringBuffer getMappingOutput(MappingOutputPojo mp)
 +  public StringBuilder getMappingOutput(MappingOutputPojo mp)
            throws SiftsException
    {
      String seqRes = mp.getSeqResidue();
@@@ -985,7 -985,7 +987,7 @@@
      int nochunks = ((seqRes.length()) / len)
              + ((seqRes.length()) % len > 0 ? 1 : 0);
      // output mappings
 -    StringBuffer output = new StringBuffer();
 +    StringBuilder output = new StringBuilder(512);
      output.append(NEWLINE);
      output.append("Sequence \u27f7 Structure mapping details").append(
              NEWLINE);
@@@ -1006,7 -1006,6 +1008,7 @@@
      output.append(String.valueOf(pdbEnd));
      output.append(NEWLINE).append(NEWLINE);
  
 +    ScoreMatrix pam250 = ScoreModels.getInstance().getPam250();
      int matchedSeqCount = 0;
      for (int j = 0; j < nochunks; j++)
      {
@@@ -1025,29 -1024,27 +1027,29 @@@
        output.append(NEWLINE);
        output.append(new Format("%" + (maxid) + "s").form(" ")).append(" ");
  
 -      // Print out the matching chars
 +      /*
 +       * Print out the match symbols:
 +       * | for exact match (ignoring case)
 +       * . if PAM250 score is positive
 +       * else a space
 +       */
        for (int i = 0; i < len; i++)
        {
          try
          {
            if ((i + (j * len)) < seqRes.length())
            {
 -            boolean sameChar = Comparison.isSameResidue(
 -                    seqRes.charAt(i + (j * len)),
 -                    strRes.charAt(i + (j * len)), false);
 -            if (sameChar
 -                    && !jalview.util.Comparison.isGap(seqRes.charAt(i
 -                            + (j * len))))
 +            char c1 = seqRes.charAt(i + (j * len));
 +            char c2 = strRes.charAt(i + (j * len));
 +            boolean sameChar = Comparison.isSameResidue(c1, c2, false);
 +            if (sameChar && !Comparison.isGap(c1))
              {
                matchedSeqCount++;
                output.append("|");
              }
              else if (type.equals("pep"))
              {
 -              if (ResidueProperties.getPAM250(seqRes.charAt(i + (j * len)),
 -                      strRes.charAt(i + (j * len))) > 0)
 +              if (pam250.getPairwiseScore(c1, c2) > 0)
                {
                  output.append(".");
                }