JAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix delegate of

[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 e85edd2..df5aee9 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;
@@ -29,6 +31,7 @@ import jalview.datamodel.SequenceI;
 import jalview.io.StructureFile;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureMapping;
+import jalview.util.Comparison;
 import jalview.util.DBRefUtils;
 import jalview.util.Format;
 import jalview.xml.binding.sifts.Entry;
@@ -211,6 +214,10 @@ public class SiftsClient implements SiftsClientI
           return new File(siftsFileName);
         }
       }
+      else
+      {
+        return siftsFile;
+      }
     }
     try
     {
@@ -276,6 +283,7 @@ public class SiftsClient implements SiftsClientI
       siftsDownloadDir.mkdirs();
     }
     // System.out.println(">> Download ftp url : " + siftsFileFTPURL);
+    // long now = System.currentTimeMillis();
     URL url = new URL(siftsFileFTPURL);
     URLConnection conn = url.openConnection();
     InputStream inputStream = conn.getInputStream();
@@ -289,7 +297,8 @@ public class SiftsClient implements SiftsClientI
     }
     outputStream.close();
     inputStream.close();
-    // System.out.println(">>> File downloaded : " + downloadedSiftsFile);
+//    System.out.println(">>> File downloaded : " + downloadedSiftsFile
+//            + " took " + (System.currentTimeMillis() - now) + "ms");
     return new File(downloadedSiftsFile);
   }
 
@@ -472,8 +481,7 @@ public class SiftsClient implements SiftsClientI
 
     if (mapping.isEmpty())
     {
-      throw new SiftsException(
-              "SIFTS mapping failed - falling back on Needleman-Wunsch");
+      throw new SiftsException("SIFTS mapping failed");
     }
 
     Integer[] keys = mapping.keySet().toArray(new Integer[0]);
@@ -511,13 +519,13 @@ public class SiftsClient implements SiftsClientI
     if (os != null)
     {
       MappingOutputPojo mop = new MappingOutputPojo();
-      mop.setSeqStart(pdbStart);
-      mop.setSeqEnd(pdbEnd);
+      mop.setSeqStart(seqStart);
+      mop.setSeqEnd(seqEnd);
       mop.setSeqName(seq.getName());
       mop.setSeqResidue(matchedSeq);
 
-      mop.setStrStart(seqStart);
-      mop.setStrEnd(seqEnd);
+      mop.setStrStart(pdbStart);
+      mop.setStrEnd(pdbEnd);
       mop.setStrName(structId);
       mop.setStrResidue(targetStrucSeqs.toString());
 
@@ -827,6 +835,10 @@ public class SiftsClient implements SiftsClientI
 
     if (sPojo[0].entityId != null)
     {
+      if (sPojo[0].pid < 1)
+      {
+        return null;
+      }
       for (Entity entity : entities)
       {
         if (!entity.getEntityId().equalsIgnoreCase(sPojo[0].entityId))
@@ -933,7 +945,7 @@ public class SiftsClient implements SiftsClientI
   }
 
   @Override
-  public StringBuffer getMappingOutput(MappingOutputPojo mp)
+  public StringBuilder getMappingOutput(MappingOutputPojo mp)
           throws SiftsException
   {
     String seqRes = mp.getSeqResidue();
@@ -955,7 +967,7 @@ 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);
@@ -976,6 +988,7 @@ 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++)
     {
@@ -994,25 +1007,29 @@ 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())
           {
-            if (seqRes.charAt(i + (j * len)) == strRes
-                    .charAt(i + (j * len))
-                    && !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(".");
               }