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

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