X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FJPredThread.java;h=b4833b1b973e874b24341a1baf363aaa64f97d70;hb=bbc14e2d648fe667157c327043d9bbb238faf65e;hp=6aebfdce9c850887c6703157f93d6479b9c7b5ee;hpb=a5481d6e853a962af603f4a21b171ba6fc9c200d;p=jalview.git

diff --git a/src/jalview/ws/JPredThread.java b/src/jalview/ws/JPredThread.java
index 6aebfdc..b4833b1 100644
--- a/src/jalview/ws/JPredThread.java
+++ b/src/jalview/ws/JPredThread.java
@@ -6,14 +6,12 @@ import javax.swing.*;
 
 import vamsas.objects.simple.JpredResult;
 
-import ext.vamsas.*;
 import jalview.analysis.*;
 import jalview.bin.*;
 import jalview.datamodel.*;
 import jalview.gui.*;
 import jalview.io.*;
 import jalview.util.*;
-import jalview.ws.WSThread.*;
 
 class JPredThread
 extends WSThread
@@ -53,7 +51,7 @@ implements WSClientI
       return false;
     }
     /**
-     * 
+     *
      * @return null or Object[] { annotated alignment for this prediction, ColumnSelection for this prediction} or null if no results available.
      * @throws Exception
      */
@@ -95,14 +93,14 @@ implements WSClientI
             al = new Alignment(sqs);
             alcsel=(ColumnSelection) alandcolsel[1];
           } else {
-            al = new Alignment(new FormatAdapter().readFile(result.getAligfile(),
-                "Paste", format));
+            al = new FormatAdapter().readFile(result.getAligfile(),
+                "Paste", format);
             sqs = new SequenceI[al.getHeight()];
 
             for (int i = 0, j = al.getHeight(); i < j; i++)
             {
               sqs[i] = al.getSequenceAt(i);
-            } 
+            }
             if (!jalview.analysis.SeqsetUtils.deuniquify( (Hashtable)
                 SequenceInfo, sqs))
             {
@@ -133,9 +131,16 @@ implements WSClientI
           SequenceI[] sqs = (SequenceI[]) ((java.lang.Object[]) input.getAlignmentAndColumnSelection(gc))[0];
           if (this.msaIndex>=sqs.length)
             throw new Error("Implementation Error! Invalid msaIndex for JPredJob on parent MSA input object!");
-          sqs[msaIndex].removeGaps();
+
+          /////
+          //Uses RemoveGapsCommand
+          /////
+          new jalview.commands.RemoveGapsCommand("Remove Gaps",
+                                                 new SequenceI[] {sqs[msaIndex]},
+                                                 alignFrame.getCurrentView().getAlignment());
+
           SequenceI profileseq=al.getSequenceAt(FirstSeq);
-          profileseq.setSequence(sqs[msaIndex].getSequence());
+          profileseq.setSequence(sqs[msaIndex].getSequenceAsString());
         }
 
         if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
@@ -174,7 +179,7 @@ implements WSClientI
             sb.append(gc);
           }
           for (int s=1,ns=al.getHeight(); s<ns; s++) {
-            String sq = al.getSequenceAt(s).getSequence();
+            String sq = al.getSequenceAt(s).getSequenceAsString();
             int diff=gapMap[r]-sq.length();
             if (diff>0) {
               // pad gaps
@@ -218,7 +223,7 @@ implements WSClientI
           for (int s=0,ns=al.getHeight(); s<ns; s++) {
             SequenceI sqobj = al.getSequenceAt(s);
             if (sqobj!=profileseq) {
-              String sq = al.getSequenceAt(s).getSequence();
+              String sq = al.getSequenceAt(s).getSequenceAsString();
               if (sq.length()<=spos+offset) {
                 // pad sequence
                 int diff=spos+offset-sq.length()-1;
@@ -245,12 +250,12 @@ implements WSClientI
           sb.append(gc);
         }
         for (int s=1,ns=al.getHeight(); s<ns; s++) {
-          String sq = al.getSequenceAt(s).getSequence();
+          String sq = al.getSequenceAt(s).getSequenceAsString();
           // pad sequence
           int diff=origseq.getLength()-sq.length();
           while (diff>0) {
             sq=sq+((diff>=sb.length()) ? sb.toString() : sb.substring(0, diff));
-            diff=origseq.getLength()-sq.length();            
+            diff=origseq.getLength()-sq.length();
           }
         }
       }
@@ -261,7 +266,8 @@ implements WSClientI
     {
       super();
       this.predMap = delMap;
-      String sq = AlignSeq.extractGaps(Comparison.GapChars, seq.getSequence());
+      String sq = AlignSeq.extractGaps(Comparison.GapChars,
+                                       seq.getSequenceAsString());
       if (sq.length() >= 20)
       {
         this.SequenceInfo = SequenceInfo;
@@ -508,14 +514,14 @@ implements WSClientI
             if (((SequenceI[])alandcolsel[0])[0].getLength()!=res.getWidth()) {
               if (msa) {
                 throw new Error("Implementation Error! ColumnSelection from input alignment will not map to result alignment!");
-              } 
+              }
             }
             if (!msa) {
               // update hidden regions to account for loss of gaps in profile. - if any
               // gapMap returns insert list, interpreted as delete list by pruneDeletions
               //((ColumnSelection) alandcolsel[1]).pruneDeletions(ShiftList.parseMap(((SequenceI[]) alandcolsel[0])[0].gapMap()));
             }*/
-            
+
             af = new AlignFrame((Alignment) res[0], (ColumnSelection) res[1],AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
           }
           Desktop.addInternalFrame(af, altitle,