X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSequenceFeatureFetcher.java;h=2c0aaac9d15fbcd82f26c2987105286679a1c486;hb=ebb52a433edbbdbd31ab82cbb1c59fc116a72b1d;hp=e034b3fb49f0f179421ed716ce75d15672886db5;hpb=b100e1ff9a2e736a5535dda3abded2bf59144af4;p=jalview.git

diff --git a/src/jalview/analysis/SequenceFeatureFetcher.java b/src/jalview/analysis/SequenceFeatureFetcher.java
index e034b3f..2c0aaac 100755
--- a/src/jalview/analysis/SequenceFeatureFetcher.java
+++ b/src/jalview/analysis/SequenceFeatureFetcher.java
@@ -2,6 +2,7 @@ package jalview.analysis;
 
 import java.io.*;
 import java.util.*;
+import javax.swing.*;
 import jalview.io.*;
 import jalview.gui.*;
 import jalview.datamodel.*;
@@ -11,6 +12,9 @@ public class SequenceFeatureFetcher implements Runnable
   AlignmentI align;
   AlignmentPanel ap;
   ArrayList unknownSequences;
+  JInternalFrame outputFrame = new JInternalFrame();
+  CutAndPasteTransfer output = new CutAndPasteTransfer(false);
+  StringBuffer sbuffer = new StringBuffer();
 
   public SequenceFeatureFetcher(AlignmentI align, AlignmentPanel ap)
   {
@@ -80,7 +84,6 @@ public class SequenceFeatureFetcher implements Runnable
           remainingIds.append(ids.get(i) + ";");
 
          EBIFetchClient ebi = new EBIFetchClient();
-         System.out.println(remainingIds.toString());
          String[] result = ebi.fetchData(remainingIds.toString(), "xml", null);
 
         if(result!=null)
@@ -96,12 +99,23 @@ public class SequenceFeatureFetcher implements Runnable
     }
   }catch(Exception ex){ex.printStackTrace();}
 
-  ap.RefreshPanels();
+  ap.repaint();
   findMissingIds(align);
+  if(sbuffer.length()>0)
+  {
+    output.formatForOutput();
+    outputFrame.setContentPane(output);
+    output.setText("Your sequences have been matched to Uniprot. Some of the ids have been\n"
+                   +"altered, most likely the start/end residue will have been updated.\n"
+                   +"Save your alignment to maintain the updated id.\n\n"+sbuffer.toString());
+  Desktop.addInternalFrame(outputFrame, "Sequence names updated ", 600,300);
+
+  }
 
   if(unknownSequences.size()>0)
   {
-    WSWUBlastClient blastClient = new WSWUBlastClient(align, unknownSequences);
+    //ignore for now!!!!!!!!!!
+  //  WSWUBlastClient blastClient = new WSWUBlastClient(align, unknownSequences);
   }
 
 }
@@ -132,13 +146,13 @@ void ReadUniprotFile(String [] result, RandomAccessFile out, AlignmentI align)
         sequence = align.findName( seqName.substring(0, seqName.indexOf('_')));
         if(sequence!=null)
         {
-          System.out.println("changing "+sequence.getName()+" to "+seqName);
+          sbuffer.append("changing "+sequence.getName()+" to "+seqName+"\n");
           sequence.setName(seqName);
         }
       }
       if(sequence==null)
       {
-        System.out.println("UNIPROT updated suggestion is "+result[r]);
+        sbuffer.append("UNIPROT updated suggestion is "+result[r]+"\n");
         sequence = align.findName( result[r] ) ;
 
         // this entry has been suggested by ebi.
@@ -189,16 +203,12 @@ void ReadUniprotFile(String [] result, RandomAccessFile out, AlignmentI align)
        if(out!=null)
          try{ out.writeBytes("</feature>\n"); }catch(Exception ex){}
 
-
-       if(sstart>=sequence.getStart() && eend<=sequence.getEnd())
-       {
          SequenceFeature sf = new SequenceFeature(type,
              sstart,
              eend,
              description,
              status);
          features.add(sf);
-       }
      }
 
      if(result[r].indexOf("<sequence")>-1)
@@ -230,7 +240,7 @@ void ReadUniprotFile(String [] result, RandomAccessFile out, AlignmentI align)
        {
          unknownSequences.add(sequence.getName());
          features = null;
-         System.out.println(sequence.getName()+ "does not match ");
+         sbuffer.append(sequence.getName()+ " SEQUENCE NOT %100 MATCH \n");
          continue;
        }
 
@@ -238,8 +248,8 @@ void ReadUniprotFile(String [] result, RandomAccessFile out, AlignmentI align)
        absStart+=1;
 
        if(absStart!=sequence.getStart() || absEnd!=sequence.getEnd())
-         System.out.println("Updated: "+sequence.getName()+" "+
-                           sequence.getStart()+"/"+sequence.getEnd()+"  to  "+ absStart+"/"+absEnd);
+         sbuffer.append("Updated: "+sequence.getName()+" "+
+                           sequence.getStart()+"/"+sequence.getEnd()+"  to  "+ absStart+"/"+absEnd+"\n");
 
 
        sequence.setStart(absStart);