X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FJPredThread.java;h=b4833b1b973e874b24341a1baf363aaa64f97d70;hb=c858b2b71816055429bd496a7158973ad8acec57;hp=15b8bd894342cc8f5337fa6c85c3a698b399645a;hpb=d86deeaf2bf1128ff2d4e610c9a715c9970fb3ad;p=jalview.git

diff --git a/src/jalview/ws/JPredThread.java b/src/jalview/ws/JPredThread.java
index 15b8bd8..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
@@ -95,8 +93,8 @@ 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++)
@@ -139,10 +137,10 @@ implements WSClientI
           /////
           new jalview.commands.RemoveGapsCommand("Remove Gaps",
                                                  new SequenceI[] {sqs[msaIndex]},
-                                                 gc);
+                                                 alignFrame.getCurrentView().getAlignment());
 
           SequenceI profileseq=al.getSequenceAt(FirstSeq);
-          profileseq.setSequence(sqs[msaIndex].getSequence());
+          profileseq.setSequence(sqs[msaIndex].getSequenceAsString());
         }
 
         if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
@@ -181,7 +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
@@ -225,7 +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;
@@ -252,7 +250,7 @@ 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();
           // pad sequence
           int diff=origseq.getLength()-sq.length();
           while (diff>0) {
@@ -268,7 +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;