X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSequenceFeatureFetcher.java;h=b3de0f3843346cd303d1cb4c7996881ecd021e1c;hb=32ce9ddb7ce1a68add53dd81785ae428ca136a83;hp=108fe08bb700ef980db56006230f09e80dbe5bc1;hpb=bc2ce1cf981d29d65f44cfcfa7bc4c8f00ee2354;p=jalview.git

diff --git a/src/jalview/io/SequenceFeatureFetcher.java b/src/jalview/io/SequenceFeatureFetcher.java
index 108fe08..b3de0f3 100755
--- a/src/jalview/io/SequenceFeatureFetcher.java
+++ b/src/jalview/io/SequenceFeatureFetcher.java
@@ -57,7 +57,7 @@ public class SequenceFeatureFetcher implements Runnable
     {
       // 1. Load the mapping information from the file
       Mapping map = new Mapping(uni.getClass().getClassLoader());
-      java.net.URL url = uni.getClass().getResource("/uniprot_mapping.xml");
+      java.net.URL url = getClass().getResource("/uniprot_mapping.xml");
       map.loadMapping(url);
 
       // 2. Unmarshal the data
@@ -112,7 +112,7 @@ public class SequenceFeatureFetcher implements Runnable
           if(!ids.contains(sequence.getName()))
           {
             ids.add(sequence.getName());
-            unknownSequences.add(sequence.getName());
+            unknownSequences.add(sequence);
           }
         }
 
@@ -156,19 +156,28 @@ public class SequenceFeatureFetcher implements Runnable
 
     }
 
-    if (unknownSequences.size() > 0)
-    {
-      int reply = javax.swing.JOptionPane.showInternalConfirmDialog(
-          Desktop.desktop, "Couldn't find a match for "+unknownSequences.size()+" sequences."
-              +"\nPerform blast for unknown sequences?",
-                  "Blast for Unidentified Sequences",
-                   javax.swing.JOptionPane.YES_NO_OPTION, javax.swing.JOptionPane.QUESTION_MESSAGE);
-
-      if(reply == javax.swing.JOptionPane.YES_OPTION)
-       new WSWUBlastClient(ap, align, unknownSequences);
-    }
-    else
-       ((Alignment)dataset).featuresAdded = true;
+    promptBeforeBlast();
+
+  }
+
+
+  void promptBeforeBlast()
+   {
+     // This must be outside the run() body as java 1.5
+     // will not return any value from the OptionPane to the expired thread.
+      if (unknownSequences.size() > 0)
+      {
+        int reply = javax.swing.JOptionPane.showConfirmDialog(
+            Desktop.desktop, "Couldn't find a match for "+unknownSequences.size()+" sequences."
+                +"\nPerform blast for unknown sequences?",
+                    "Blast for Unidentified Sequences",
+                     javax.swing.JOptionPane.YES_NO_OPTION, javax.swing.JOptionPane.QUESTION_MESSAGE);
+
+        if(reply == javax.swing.JOptionPane.YES_OPTION)
+         new WSWUBlastClient(ap, align, unknownSequences);
+      }
+      else
+         ((Alignment)dataset).featuresAdded = true;
 
 
     ap.repaint();
@@ -187,7 +196,6 @@ public class SequenceFeatureFetcher implements Runnable
       return;
 
     SequenceI sequence = null;
-    //       String pdb = null;
 
     Vector entries = getUniprotEntries(file);
 
@@ -202,25 +210,24 @@ public class SequenceFeatureFetcher implements Runnable
       if (sequence == null)
       {
         //Sequence maybe Name, not Accession
-        idmatch = entry.getName().elementAt(0).toString();;
+        idmatch = entry.getName().elementAt(0).toString();
         sequence = dataset.findName(idmatch);
       }
 
       if (sequence == null)
       {
-        System.out.println("not found");
+        System.out.println(idmatch+" not found");
         continue;
       }
 
       ids.remove(sequence.getName());
-      unknownSequences.remove(sequence.getName());
+      unknownSequences.remove(sequence);
 
       String nonGapped = AlignSeq.extractGaps("-. ", sequence.getSequence());
 
       int absStart = entry.getUniprotSequence().getContent().indexOf(
           nonGapped.toString());
 
-      int residueOffset = 0;
       if (absStart == -1)
       {
         // Is UniprotSequence contained in dataset sequence?
@@ -235,9 +242,9 @@ public class SequenceFeatureFetcher implements Runnable
         }
         else
         {
-          if(entry.getFeatures()!=null)
+          if(entry.getFeature()!=null)
           {
-            Enumeration e = entry.getFeatures().elements();
+            Enumeration e = entry.getFeature().elements();
             while (e.hasMoreElements())
             {
               SequenceFeature sf = (SequenceFeature) e.nextElement();
@@ -257,7 +264,19 @@ public class SequenceFeatureFetcher implements Runnable
       int absEnd = absStart + nonGapped.toString().length();
       absStart += 1;
 
-      sequence.setSequenceFeatures(entry.getFeatures());
+      Enumeration e = entry.getDbReference().elements();
+      Vector onlyPdbEntries = new Vector();
+      while(e.hasMoreElements())
+      {
+        PDBEntry pdb = (PDBEntry)e.nextElement();
+        if(!pdb.getType().equals("PDB"))
+          continue;
+
+        onlyPdbEntries.addElement(pdb);
+      }
+
+      sequence.setPDBId(onlyPdbEntries);
+      sequence.setSequenceFeatures(entry.getFeature());
       sequence.setStart(absStart);
       sequence.setEnd(absEnd);