Allow for uniprot in name

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

diff --git a/src/jalview/io/SequenceFeatureFetcher.java b/src/jalview/io/SequenceFeatureFetcher.java
index 2bfbfd9..d980b0a 100755 (executable)
--- a/src/jalview/io/SequenceFeatureFetcher.java
+++ b/src/jalview/io/SequenceFeatureFetcher.java
@@ -48,8 +48,12 @@ public class SequenceFeatureFetcher implements Runnable
   ArrayList unknownSequences;\r
   CutAndPasteTransfer output = new CutAndPasteTransfer();\r
   StringBuffer sbuffer = new StringBuffer();\r
+  boolean uniprotFlag = false;\r
 \r
-  Vector getUniprotEntries(File file)\r
+  public SequenceFeatureFetcher()\r
+  {}\r
+\r
+  public Vector getUniprotEntries(File file)\r
   {\r
 \r
     UniprotFile uni = new UniprotFile();\r
@@ -108,11 +112,14 @@ public class SequenceFeatureFetcher implements Runnable
         for (int i = 0; (seqIndex < sequences.size()) && (i < 50);\r
              seqIndex++, i++)\r
         {\r
-          SequenceI sequence = (SequenceI) sequences.get(seqIndex);\r
-          if(!ids.contains(sequence.getName()))\r
+          Sequence sequence = (Sequence) sequences.get(seqIndex);\r
+          if(sequence.getSequenceFeatures()==null)\r
           {\r
-            ids.add(sequence.getName());\r
-            unknownSequences.add(sequence.getName());\r
+            if (!ids.contains(sequence.getName()))\r
+            {\r
+              ids.add(sequence.getName());\r
+              unknownSequences.add(sequence);\r
+            }\r
           }\r
         }\r
 \r
@@ -123,11 +130,17 @@ public class SequenceFeatureFetcher implements Runnable
           StringBuffer remainingIds = new StringBuffer("uniprot:");\r
           for (int i = 0; i < ids.size(); i++)\r
            {\r
+             if(ids.get(i).toString().indexOf("|")>-1)\r
+             {\r
+               remainingIds.append(ids.get(i).toString().substring(\r
+                   ids.get(i).toString().lastIndexOf("|") + 1));\r
+               uniprotFlag = true;\r
+             }\r
              remainingIds.append(ids.get(i) + ";");\r
            }\r
           EBIFetchClient ebi = new EBIFetchClient();\r
           File file = ebi.fetchDataAsFile(remainingIds.toString(),\r
-                                          "xml", null);\r
+                                          "xml", "raw");\r
 \r
 \r
 \r
@@ -173,12 +186,9 @@ public class SequenceFeatureFetcher implements Runnable
                     "Blast for Unidentified Sequences",\r
                      javax.swing.JOptionPane.YES_NO_OPTION, javax.swing.JOptionPane.QUESTION_MESSAGE);\r
 \r
-        System.out.println("response ?? "+reply);\r
         if(reply == javax.swing.JOptionPane.YES_OPTION)\r
          new WSWUBlastClient(ap, align, unknownSequences);\r
       }\r
-      else\r
-         ((Alignment)dataset).featuresAdded = true;\r
 \r
 \r
     ap.repaint();\r
@@ -197,7 +207,6 @@ public class SequenceFeatureFetcher implements Runnable
       return;\r
 \r
     SequenceI sequence = null;\r
-    //       String pdb = null;\r
 \r
     Vector entries = getUniprotEntries(file);\r
 \r
@@ -212,25 +221,32 @@ public class SequenceFeatureFetcher implements Runnable
       if (sequence == null)\r
       {\r
         //Sequence maybe Name, not Accession\r
-        idmatch = entry.getName().elementAt(0).toString();;\r
+        idmatch = entry.getName().elementAt(0).toString();\r
         sequence = dataset.findName(idmatch);\r
       }\r
 \r
-      if (sequence == null)\r
+      if(sequence!=null)\r
+        ids.remove(sequence.getName());\r
+\r
+      else  if (sequence == null && uniprotFlag)\r
       {\r
-        System.out.println("not found");\r
+          sequence = dataset.findName("UniProt/Swiss-Prot|"+entry.getAccession().elementAt(0)+"|"+idmatch);\r
+          ids.remove(idmatch);\r
+      }\r
+\r
+      if(sequence ==null)\r
+      {\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
@@ -245,9 +261,9 @@ 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
@@ -267,7 +283,19 @@ 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