X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSequenceFeatureFetcher.java;h=2c0aaac9d15fbcd82f26c2987105286679a1c486;hb=ebb52a433edbbdbd31ab82cbb1c59fc116a72b1d;hp=dc8a3cdb460e61629cdcdab846f9f32a9f8b82f3;hpb=44b659b39011c69e40b43610c4a9b94501fd1bd5;p=jalview.git

diff --git a/src/jalview/analysis/SequenceFeatureFetcher.java b/src/jalview/analysis/SequenceFeatureFetcher.java
index dc8a3cd..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.*;
@@ -10,9 +11,14 @@ 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)
   {
+    unknownSequences = new ArrayList();
     this.align = align;
     this.ap = ap;
     Thread thread = new Thread(this);
@@ -29,7 +35,8 @@ public class SequenceFeatureFetcher implements Runnable
   try{
     if (cache == null)
     {
-      jalview.bin.Cache.setProperty("UNIPROT_CACHE", System.getProperty("user.home/uniprot.xml"));
+      jalview.bin.Cache.setProperty("UNIPROT_CACHE", System.getProperty("user.home")+"/uniprot.xml");
+      cache = jalview.bin.Cache.getProperty("UNIPROT_CACHE");
     }
 
 
@@ -77,7 +84,7 @@ public class SequenceFeatureFetcher implements Runnable
           remainingIds.append(ids.get(i) + ";");
 
          EBIFetchClient ebi = new EBIFetchClient();
-        String[] result = ebi.fetchData(remainingIds.toString(), "xml", null);
+         String[] result = ebi.fetchData(remainingIds.toString(), "xml", null);
 
         if(result!=null)
           ReadUniprotFile(result, out, align);
@@ -92,6 +99,24 @@ public class SequenceFeatureFetcher implements Runnable
     }
   }catch(Exception ex){ex.printStackTrace();}
 
+  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)
+  {
+    //ignore for now!!!!!!!!!!
+  //  WSWUBlastClient blastClient = new WSWUBlastClient(align, unknownSequences);
+  }
 
 }
 
@@ -114,10 +139,21 @@ void ReadUniprotFile(String [] result, RandomAccessFile out, AlignmentI align)
         out.writeBytes("<entry>\n");
       }catch(Exception ex){}
 
-      sequence = align.findName( parseElement( result[r], "<name>" , out)) ;
+      String seqName = parseElement( result[r], "<name>" , out);
+      sequence = align.findName( seqName ) ;
       if(sequence==null)
       {
-        System.out.println("Couldnt find sequence id. Suggestion is "+result[r]);
+        sequence = align.findName( seqName.substring(0, seqName.indexOf('_')));
+        if(sequence!=null)
+        {
+          sbuffer.append("changing "+sequence.getName()+" to "+seqName+"\n");
+          sequence.setName(seqName);
+        }
+      }
+      if(sequence==null)
+      {
+        sbuffer.append("UNIPROT updated suggestion is "+result[r]+"\n");
+        sequence = align.findName( result[r] ) ;
 
         // this entry has been suggested by ebi.
         // doesn't match id in alignment file
@@ -167,16 +203,58 @@ 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)
+     {
+       StringBuffer seqString = new StringBuffer();
+
+       if(out!=null)
+         try  {  out.writeBytes(result[r]+"\n"); }   catch (Exception ex){}
+
+       while(result[++r].indexOf("</sequence>")==-1)
+       {
+         seqString.append(result[r]);
+         if(out!=null)
+         try  {  out.writeBytes(result[r]+"\n"); }   catch (Exception ex){}
+       }
+
+       if(out!=null)
+         try  {  out.writeBytes(result[r]+"\n"); }   catch (Exception ex){}
+
+       StringBuffer nonGapped = new StringBuffer();
+       for (int i = 0; i < sequence.getSequence().length(); i++)
+       {
+         if (!jalview.util.Comparison.isGap(sequence.getCharAt(i)))
+           nonGapped.append(sequence.getCharAt(i));
+       }
+
+       int absStart = seqString.toString().indexOf(nonGapped.toString());
+       if(absStart==-1)
+       {
+         unknownSequences.add(sequence.getName());
+         features = null;
+         sbuffer.append(sequence.getName()+ " SEQUENCE NOT %100 MATCH \n");
+         continue;
        }
+
+       int absEnd =   absStart + nonGapped.toString().length();
+       absStart+=1;
+
+       if(absStart!=sequence.getStart() || absEnd!=sequence.getEnd())
+         sbuffer.append("Updated: "+sequence.getName()+" "+
+                           sequence.getStart()+"/"+sequence.getEnd()+"  to  "+ absStart+"/"+absEnd+"\n");
+
+
+       sequence.setStart(absStart);
+       sequence.setEnd(absEnd);
+
      }
 
      if(result[r].indexOf("</entry>")>-1)
@@ -190,8 +268,34 @@ void ReadUniprotFile(String [] result, RandomAccessFile out, AlignmentI align)
 
      }
   }
+}
+
+void findMissingIds(AlignmentI align)
+{
+  String data;
+  ArrayList cachedIds = new ArrayList();
+
+  try
+  {
+    BufferedReader in = new BufferedReader(
+        new FileReader(jalview.bin.Cache.getProperty("UNIPROT_CACHE")));
+
+    while ( (data = in.readLine()) != null)
+    {
+      if (data.indexOf("name") > -1)
+      {
+        String name = parseElement(data, "<name>", null);
+        cachedIds.add(name);
+      }
+    }
+  }
+  catch (Exception ex)
+  {   ex.printStackTrace();  }
+
+  for(int i=0; i<align.getHeight(); i++)
+    if( !cachedIds.contains( align.getSequenceAt(i).getName() ) )
+      unknownSequences.add( align.getSequenceAt(i).getName() );
 
-  ap.RefreshPanels();
 
 }