JAL-2446 merged to spike branch

[jalview.git] / src / jalview / ws / sifts / SiftsClient.java

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index ea65125..2ff4a8b 100644 (file)
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -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;
@@ -575,18 +577,8 @@ public class SiftsClient implements SiftsClientI
                   .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
@@ -599,19 +591,11 @@ public class SiftsClient implements SiftsClientI
         }
         if (currSeqIndex >= seq.getStart() && currSeqIndex <= seq.getEnd())
         {
-          int resNum;
-          try
-          {
-            resNum = (pdbRefDb == null) ? Integer.valueOf(residue
-                    .getDbResNum()) : Integer.valueOf(pdbRefDb
-                    .getDbResNum());
-          } catch (NumberFormatException nfe)
-          {
-            resNum = (pdbRefDb == null) ? Integer.valueOf(residue
-                    .getDbResNum()) : 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)
@@ -634,6 +618,30 @@ public class SiftsClient implements SiftsClientI
   }
 
   /**
+   * 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.
@@ -957,7 +965,7 @@ public class SiftsClient implements SiftsClientI
   }
 
   @Override
-  public StringBuffer getMappingOutput(MappingOutputPojo mp)
+  public StringBuilder getMappingOutput(MappingOutputPojo mp)
           throws SiftsException
   {
     String seqRes = mp.getSeqResidue();
@@ -979,7 +987,7 @@ public class SiftsClient implements SiftsClientI
     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);
@@ -1000,6 +1008,7 @@ public class SiftsClient implements SiftsClientI
     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++)
     {
@@ -1018,27 +1027,29 @@ public class SiftsClient implements SiftsClientI
       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(".");
               }