Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

[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..ea65125 100644 (file)
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -29,6 +29,7 @@ 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 +74,12 @@ 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 +193,14 @@ 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 +226,10 @@ public class SiftsClient implements SiftsClientI
           return new File(siftsFileName);
         }
       }
+      else
+      {
+        return siftsFile;
+      }
     }
     try
     {
@@ -276,6 +295,7 @@ 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 +309,8 @@ 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 +493,7 @@ 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 +531,13 @@ 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 +847,10 @@ 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))
@@ -1001,8 +1025,10 @@ public class SiftsClient implements SiftsClientI
         {
           if ((i + (j * len)) < seqRes.length())
           {
-            if (seqRes.charAt(i + (j * len)) == strRes
-                    .charAt(i + (j * len))
+            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))))
             {
@@ -1085,4 +1111,9 @@ public class SiftsClient implements SiftsClientI
     return siftsEntry.getDbVersion();
   }
 
+  public static void setMockSiftsFile(File file)
+  {
+    mockSiftsFile = file;
+  }
+
 }