From d86deeaf2bf1128ff2d4e610c9a715c9970fb3ad Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 24 Oct 2006 11:19:30 +0000
Subject: [PATCH] Uses RemoveGapsCommand

---
 src/jalview/ws/JPredThread.java |   19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

diff --git a/src/jalview/ws/JPredThread.java b/src/jalview/ws/JPredThread.java
index 6aebfdc..15b8bd8 100644
--- a/src/jalview/ws/JPredThread.java
+++ b/src/jalview/ws/JPredThread.java
@@ -53,7 +53,7 @@ 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
      */
@@ -102,7 +102,7 @@ implements WSClientI
             for (int i = 0, j = al.getHeight(); i < j; i++)
             {
               sqs[i] = al.getSequenceAt(i);
-            } 
+            }
             if (!jalview.analysis.SeqsetUtils.deuniquify( (Hashtable)
                 SequenceInfo, sqs))
             {
@@ -133,7 +133,14 @@ 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]},
+                                                 gc);
+
           SequenceI profileseq=al.getSequenceAt(FirstSeq);
           profileseq.setSequence(sqs[msaIndex].getSequence());
         }
@@ -250,7 +257,7 @@ implements WSClientI
           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();
           }
         }
       }
@@ -508,14 +515,14 @@ 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,
-- 
1.7.10.2