X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fsifts%2FSiftsClient.java;h=0e9e88855704086a63f373c5c4fcd6c6dd78d0a9;hb=fa1b96bdca9954d44de8ed08e106ace44dcf66c3;hp=e85edd24d122f030f81c4a20f377af6b4054ce7f;hpb=290f1ace41a61281440573d87f8415e08978360a;p=jalview.git

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index e85edd2..0e9e888 100644
--- 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;
@@ -73,6 +76,12 @@ import MCview.PDBChain;
 
 public class SiftsClient implements SiftsClientI
 {
+  /*
+   * for use in mocking out file fetch for tests only
+   * - reset to null after testing!
+   */
+  private static File mockSiftsFile;
+
   private Entry siftsEntry;
 
   private StructureFile pdb;
@@ -186,6 +195,14 @@ public class SiftsClient implements SiftsClientI
    */
   public static File getSiftsFile(String pdbId) throws SiftsException
   {
+    /*
+     * return mocked file if it has been set
+     */
+    if (mockSiftsFile != null)
+    {
+      return mockSiftsFile;
+    }
+
     String siftsFileName = SiftsSettings.getSiftDownloadDirectory()
             + pdbId.toLowerCase() + ".xml.gz";
     File siftsFile = new File(siftsFileName);
@@ -211,6 +228,10 @@ public class SiftsClient implements SiftsClientI
           return new File(siftsFileName);
         }
       }
+      else
+      {
+        return siftsFile;
+      }
     }
     try
     {
@@ -276,6 +297,7 @@ 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 +311,8 @@ 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 +495,7 @@ 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 +533,13 @@ 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());
 
@@ -587,8 +609,12 @@ public class SiftsClient implements SiftsClientI
                     .getDbResNum());
           } catch (NumberFormatException nfe)
           {
-            resNum = (pdbRefDb == null) ? Integer.valueOf(residue
-                    .getDbResNum()) : Integer.valueOf(pdbRefDb
+            if (pdbRefDb == null || pdbRefDb.getDbResNum().equals("null"))
+            {
+              resNum = UNASSIGNED;
+              continue;
+            }
+            resNum = Integer.valueOf(pdbRefDb
                     .getDbResNum().split("[a-zA-Z]")[0]);
             continue;
           }
@@ -827,6 +853,10 @@ 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 +963,7 @@ public class SiftsClient implements SiftsClientI
   }
 
   @Override
-  public StringBuffer getMappingOutput(MappingOutputPojo mp)
+  public StringBuilder getMappingOutput(MappingOutputPojo mp)
           throws SiftsException
   {
     String seqRes = mp.getSeqResidue();
@@ -955,7 +985,7 @@ 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 +1006,7 @@ 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 +1025,29 @@ 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(".");
               }
@@ -1085,4 +1120,9 @@ public class SiftsClient implements SiftsClientI
     return siftsEntry.getDbVersion();
   }
 
+  public static void setMockSiftsFile(File file)
+  {
+    mockSiftsFile = file;
+  }
+
 }