Move start and end before parsing name

[jalview.git] / src / jalview / io / SequenceFeatureFetcher.java

diff --git a/src/jalview/io/SequenceFeatureFetcher.java b/src/jalview/io/SequenceFeatureFetcher.java
index 8bd9bab..a70aaef 100755 (executable)
--- a/src/jalview/io/SequenceFeatureFetcher.java
+++ b/src/jalview/io/SequenceFeatureFetcher.java
@@ -109,10 +109,10 @@ public class SequenceFeatureFetcher implements Runnable
              seqIndex++, i++)\r
         {\r
           SequenceI sequence = (SequenceI) sequences.get(seqIndex);\r
-          if(!ids.contains(sequence.getName()))\r
+          if(!ids.contains(sequence.getShortName()))\r
           {\r
-            ids.add(sequence.getName());\r
-            unknownSequences.add(sequence.getName());\r
+            ids.add(sequence.getShortName());\r
+            unknownSequences.add(sequence);\r
           }\r
         }\r
 \r
@@ -196,7 +196,6 @@ public class SequenceFeatureFetcher implements Runnable
       return;\r
 \r
     SequenceI sequence = null;\r
-    //       String pdb = null;\r
 \r
     Vector entries = getUniprotEntries(file);\r
 \r
@@ -206,30 +205,29 @@ public class SequenceFeatureFetcher implements Runnable
     {\r
       entry = (UniprotEntry) entries.elementAt(i);\r
       String idmatch = entry.getAccession().elementAt(0).toString();\r
-      sequence = dataset.findName(idmatch);\r
+      sequence = dataset.findShortName(idmatch);\r
 \r
       if (sequence == null)\r
       {\r
         //Sequence maybe Name, not Accession\r
         idmatch = entry.getName().elementAt(0).toString();;\r
-        sequence = dataset.findName(idmatch);\r
+        sequence = dataset.findShortName(idmatch);\r
       }\r
 \r
       if (sequence == null)\r
       {\r
-        System.out.println("not found");\r
+        System.out.println(idmatch+" not found");\r
         continue;\r
       }\r
 \r
       ids.remove(sequence.getName());\r
-      unknownSequences.remove(sequence.getName());\r
+      unknownSequences.remove(sequence);\r
 \r
       String nonGapped = AlignSeq.extractGaps("-. ", sequence.getSequence());\r
 \r
       int absStart = entry.getUniprotSequence().getContent().indexOf(\r
           nonGapped.toString());\r
 \r
-      int residueOffset = 0;\r
       if (absStart == -1)\r
       {\r
         // Is UniprotSequence contained in dataset sequence?\r
@@ -244,9 +242,9 @@ public class SequenceFeatureFetcher implements Runnable
         }\r
         else\r
         {\r
-          if(entry.getFeatures()!=null)\r
+          if(entry.getFeature()!=null)\r
           {\r
-            Enumeration e = entry.getFeatures().elements();\r
+            Enumeration e = entry.getFeature().elements();\r
             while (e.hasMoreElements())\r
             {\r
               SequenceFeature sf = (SequenceFeature) e.nextElement();\r
@@ -266,7 +264,19 @@ public class SequenceFeatureFetcher implements Runnable
       int absEnd = absStart + nonGapped.toString().length();\r
       absStart += 1;\r
 \r
-      sequence.setSequenceFeatures(entry.getFeatures());\r
+      Enumeration e = entry.getDbReference().elements();\r
+      Vector onlyPdbEntries = new Vector();\r
+      while(e.hasMoreElements())\r
+      {\r
+        PDBEntry pdb = (PDBEntry)e.nextElement();\r
+        if(!pdb.getType().equals("PDB"))\r
+          continue;\r
+\r
+        onlyPdbEntries.addElement(pdb);\r
+      }\r
+\r
+      sequence.setPDBId(onlyPdbEntries);\r
+      sequence.setSequenceFeatures(entry.getFeature());\r
       sequence.setStart(absStart);\r
       sequence.setEnd(absEnd);\r
 \r