X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FJPredThread.java;h=f2592ff715f64e4a4fbe2205eb37d40c56571be4;hb=4d2e0d36506302cc00677527725bcccbdf27d766;hp=15b8bd894342cc8f5337fa6c85c3a698b399645a;hpb=dc5507ccf4bf0c8b20f86aee7175c16b68ef52ea;p=jalview.git

diff --git a/src/jalview/ws/JPredThread.java b/src/jalview/ws/JPredThread.java
index 15b8bd8..f2592ff 100644
--- a/src/jalview/ws/JPredThread.java
+++ b/src/jalview/ws/JPredThread.java
@@ -142,7 +142,7 @@ implements WSClientI
                                                  gc);
 
           SequenceI profileseq=al.getSequenceAt(FirstSeq);
-          profileseq.setSequence(sqs[msaIndex].getSequence());
+          profileseq.setSequence(sqs[msaIndex].getSequenceAsString());
         }
 
         if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
@@ -181,7 +181,7 @@ 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 +225,7 @@ 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 +252,7 @@ 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 +268,8 @@ 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;