From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 14 Nov 2005 12:00:03 +0000 (+0000)
Subject: Use shortname
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5aeb9ce3b99be8cbe7ca47c04a31dca3e3bbc282;p=jalview.git

Use shortname
---

diff --git a/src/jalview/io/SequenceFeatureFetcher.java b/src/jalview/io/SequenceFeatureFetcher.java
index 5ecb417..a70aaef 100755
--- a/src/jalview/io/SequenceFeatureFetcher.java
+++ b/src/jalview/io/SequenceFeatureFetcher.java
@@ -109,10 +109,10 @@ public class SequenceFeatureFetcher implements Runnable
              seqIndex++, i++)
         {
           SequenceI sequence = (SequenceI) sequences.get(seqIndex);
-          if(!ids.contains(sequence.getName()))
+          if(!ids.contains(sequence.getShortName()))
           {
-            ids.add(sequence.getName());
-            unknownSequences.add(sequence.getName());
+            ids.add(sequence.getShortName());
+            unknownSequences.add(sequence);
           }
         }
 
@@ -205,13 +205,13 @@ public class SequenceFeatureFetcher implements Runnable
     {
       entry = (UniprotEntry) entries.elementAt(i);
       String idmatch = entry.getAccession().elementAt(0).toString();
-      sequence = dataset.findName(idmatch);
+      sequence = dataset.findShortName(idmatch);
 
       if (sequence == null)
       {
         //Sequence maybe Name, not Accession
         idmatch = entry.getName().elementAt(0).toString();;
-        sequence = dataset.findName(idmatch);
+        sequence = dataset.findShortName(idmatch);
       }
 
       if (sequence == null)
@@ -221,7 +221,7 @@ public class SequenceFeatureFetcher implements Runnable
       }
 
       ids.remove(sequence.getName());
-      unknownSequences.remove(sequence.getName());
+      unknownSequences.remove(sequence);
 
       String nonGapped = AlignSeq.extractGaps("-. ", sequence.getSequence());
 
diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
index 99beb5f..e6800bc 100755
--- a/src/jalview/io/WSWUBlastClient.java
+++ b/src/jalview/io/WSWUBlastClient.java
@@ -29,6 +29,7 @@ import java.util.*;
 import javax.swing.*;
 
 import javax.xml.namespace.QName;
+import jalview.analysis.AlignSeq;
 
 
 /**
@@ -44,7 +45,7 @@ public class WSWUBlastClient
     CutAndPasteTransfer output = new CutAndPasteTransfer();
     int jobsRunning = 0;
 
-    Hashtable suggestedIds = new Hashtable();
+    Vector suggestedIds = new Vector();
     /**
      * Creates a new WSWUBlastClient object.
      *
@@ -63,21 +64,10 @@ public class WSWUBlastClient
 
         for (int i = 0; i < ids.size(); i++)
         {
-            SequenceI sequence = al.findName(ids.get(i).toString());
-            System.out.println(ids.get(i).toString());
-            StringBuffer nonGapped = new StringBuffer();
+            Sequence sequence = (Sequence)ids.get(i);
+            System.out.println(sequence.getName());
 
-
-            for (int n = 0; n < sequence.getSequence().length(); n++)
-            {
-                if (!jalview.util.Comparison.isGap(sequence.getCharAt(n)))
-                {
-                    nonGapped.append(sequence.getCharAt(n));
-                }
-            }
-
-            BlastThread thread = new BlastThread(ids.get(i).toString(),
-                    nonGapped.toString());
+            BlastThread thread = new BlastThread(sequence);
             thread.start();
             jobsRunning++;
         }
@@ -93,13 +83,13 @@ public class WSWUBlastClient
      * @param id1 DOCUMENT ME!
      * @param res DOCUMENT ME!
      */
-    void parseResult(String id1, String res)
+    void parseResult(Sequence seq, String res)
     {
         StringTokenizer st = new StringTokenizer(res, "\n");
         String data;
         String id2;
         int maxFound = 90;
-        StringBuffer buffer = new StringBuffer("\n\n" + id1 + " :");
+        StringBuffer buffer = new StringBuffer("\n\n" + seq.getShortName() + " :");
 
         while (st.hasMoreTokens())
         {
@@ -127,10 +117,7 @@ public class WSWUBlastClient
                         {
                             maxFound = value;
                             buffer.append(" " + id2 + " " + value + "%; ");
-                            if(!suggestedIds.containsKey(id1))
-                             {
-                               suggestedIds.put(id1, id2);
-                             }
+                            suggestedIds.addElement( new Object[]{seq, id2});
                         }
                     }
                 }
@@ -150,29 +137,35 @@ public class WSWUBlastClient
 
       if (reply == JOptionPane.YES_OPTION)
       {
-        Enumeration keys = suggestedIds.keys();
+        Enumeration keys = suggestedIds.elements();
         while(keys.hasMoreElements())
         {
-          String oldid = keys.nextElement().toString();
-          SequenceI sequence = al.findName(oldid);
-          sequence.setName( suggestedIds.get(oldid).toString() );
+          Object [] object = (Object[])keys.nextElement();
 
-          sequence = sequence.getDatasetSequence();
-          if(sequence!=null)
-          {
+          Sequence oldseq = (Sequence)object[0];
 
-            sequence.setName(suggestedIds.get(oldid).toString());
+          oldseq.setName( object[1].toString() );
 
-            Vector entries = sequence.getDBRef();
-            if(entries!=null)
+          // Oldseq is actually in the dataset, we must find the
+          // Visible seq and change its name also.
+          for (int i = 0; i < al.getHeight(); i++)
+          {
+            if (al.getSequenceAt(i).getDatasetSequence() == oldseq)
             {
-              DBRefEntry entry = (DBRefEntry) entries.elementAt(0);
-              sequence.addDBRef(new jalview.datamodel.DBRefEntry("UNIPROT",
-                  "0",
-                  entry.getAccessionId()));
+              al.getSequenceAt(i).setName(oldseq.getName());
+              break;
             }
           }
-          System.out.println("replace "+oldid+" with "+suggestedIds.get(oldid));
+
+          Vector entries = oldseq.getDBRef();
+          if (entries != null)
+          {
+            DBRefEntry entry = (DBRefEntry) entries.elementAt(0);
+            oldseq.addDBRef(new jalview.datamodel.
+                                                 DBRefEntry("UNIPROT",
+                "0",
+                entry.getAccessionId()));
+          }
         }
       }
       ap.repaint();
@@ -227,16 +220,14 @@ public class WSWUBlastClient
 
     class BlastThread extends Thread
     {
-        String sequence;
-        String seqid;
+        Sequence sequence;
         String jobid;
         boolean jobComplete = false;
 
-        BlastThread(String id, String sequence)
+        BlastThread(Sequence sequence)
         {
-          System.out.println("blasting for: "+id);
-            this.sequence = sequence;
-            seqid = id;
+          System.out.println("blasting for: "+sequence.getName());
+          this.sequence = sequence;
         }
 
         public void run()
@@ -259,14 +250,14 @@ public class WSWUBlastClient
 
                     if(object instanceof String)
                     {
-                      parseResult(seqid, (String)object);
+                      parseResult(sequence, (String)object);
                       jobComplete = true;
                       jobsRunning--;
                     }
 
                     Thread.sleep(5000);
 
-                    System.out.println("WSWuBlastClient: I'm alive "+seqid+" "+jobid); // log.debug
+                    System.out.println("WSWuBlastClient: I'm alive "+sequence.getShortName()+" "+jobid); // log.debug
                 }
                 catch (Exception ex)
                 {
@@ -286,7 +277,8 @@ public class WSWUBlastClient
             params.put("type", "xml");
             params.put("async", "true");
 
-            byte[] seqbytes = sequence.getBytes();
+            byte[] seqbytes = AlignSeq.extractGaps("-. ",
+                                                  sequence.getSequence()).getBytes();
 
             try
             {
@@ -307,7 +299,7 @@ public class WSWUBlastClient
                 {
                   jobComplete = true;
                   jobsRunning--;
-                  parseResult(seqid, (String)object);
+                  parseResult(sequence, (String)object);
                 }
 
             }