Sequence is char []

[jalview.git] / src / jalview / ws / JPredThread.java

diff --git a/src/jalview/ws/JPredThread.java b/src/jalview/ws/JPredThread.java
index 15b8bd8..f2592ff 100644 (file)
--- a/src/jalview/ws/JPredThread.java
+++ b/src/jalview/ws/JPredThread.java
@@ -142,7 +142,7 @@ implements WSClientI
                                                  gc);\r
 \r
           SequenceI profileseq=al.getSequenceAt(FirstSeq);\r
-          profileseq.setSequence(sqs[msaIndex].getSequence());\r
+          profileseq.setSequence(sqs[msaIndex].getSequenceAsString());\r
         }\r
 \r
         if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(\r
@@ -181,7 +181,7 @@ implements WSClientI
             sb.append(gc);\r
           }\r
           for (int s=1,ns=al.getHeight(); s<ns; s++) {\r
-            String sq = al.getSequenceAt(s).getSequence();\r
+            String sq = al.getSequenceAt(s).getSequenceAsString();\r
             int diff=gapMap[r]-sq.length();\r
             if (diff>0) {\r
               // pad gaps\r
@@ -225,7 +225,7 @@ implements WSClientI
           for (int s=0,ns=al.getHeight(); s<ns; s++) {\r
             SequenceI sqobj = al.getSequenceAt(s);\r
             if (sqobj!=profileseq) {\r
-              String sq = al.getSequenceAt(s).getSequence();\r
+              String sq = al.getSequenceAt(s).getSequenceAsString();\r
               if (sq.length()<=spos+offset) {\r
                 // pad sequence\r
                 int diff=spos+offset-sq.length()-1;\r
@@ -252,7 +252,7 @@ implements WSClientI
           sb.append(gc);\r
         }\r
         for (int s=1,ns=al.getHeight(); s<ns; s++) {\r
-          String sq = al.getSequenceAt(s).getSequence();\r
+          String sq = al.getSequenceAt(s).getSequenceAsString();\r
           // pad sequence\r
           int diff=origseq.getLength()-sq.length();\r
           while (diff>0) {\r
@@ -268,7 +268,8 @@ implements WSClientI
     {\r
       super();\r
       this.predMap = delMap;\r
-      String sq = AlignSeq.extractGaps(Comparison.GapChars, seq.getSequence());\r
+      String sq = AlignSeq.extractGaps(Comparison.GapChars,\r
+                                       seq.getSequenceAsString());\r
       if (sq.length() >= 20)\r
       {\r
         this.SequenceInfo = SequenceInfo;\r