From feb00a2deac901163f9d130b0ed0195b9ae73bfa Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 11 Feb 2005 10:39:20 +0000
Subject: [PATCH] bug fixed if featureEnd is beyond end of sequence

---
 src/jalview/analysis/SequenceFeatureFetcher.java |   25 ++++++++++++++++------
 src/jalview/gui/FeatureRenderer.java             |    3 +++
 2 files changed, 22 insertions(+), 6 deletions(-)

diff --git a/src/jalview/analysis/SequenceFeatureFetcher.java b/src/jalview/analysis/SequenceFeatureFetcher.java
index e034b3f..6560504 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)
@@ -98,6 +101,16 @@ public class SequenceFeatureFetcher implements Runnable
 
   ap.RefreshPanels();
   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)
   {
@@ -132,13 +145,13 @@ 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.
@@ -230,7 +243,7 @@ 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 +251,8 @@ 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);
diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 6a0daa8..59f446e 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -27,6 +27,9 @@ public class FeatureRenderer implements RendererI
     while( e.hasMoreElements() )
     {
       SequenceFeature sf = (SequenceFeature)e.nextElement();
+      if(sf.getStart()>seq.getEnd())
+        continue;
+
       int fstart = seq.findIndex(sf.getStart())-1;
       int fend = seq.findIndex(sf.getEnd())-1;
 
-- 
1.7.10.2