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 6aebfdc..f2592ff 100644 (file)
--- a/src/jalview/ws/JPredThread.java
+++ b/src/jalview/ws/JPredThread.java
@@ -53,7 +53,7 @@ implements WSClientI
       return false;\r
     }\r
     /**\r
-     * \r
+     *\r
      * @return null or Object[] { annotated alignment for this prediction, ColumnSelection for this prediction} or null if no results available.\r
      * @throws Exception\r
      */\r
@@ -102,7 +102,7 @@ implements WSClientI
             for (int i = 0, j = al.getHeight(); i < j; i++)\r
             {\r
               sqs[i] = al.getSequenceAt(i);\r
-            } \r
+            }\r
             if (!jalview.analysis.SeqsetUtils.deuniquify( (Hashtable)\r
                 SequenceInfo, sqs))\r
             {\r
@@ -133,9 +133,16 @@ implements WSClientI
           SequenceI[] sqs = (SequenceI[]) ((java.lang.Object[]) input.getAlignmentAndColumnSelection(gc))[0];\r
           if (this.msaIndex>=sqs.length)\r
             throw new Error("Implementation Error! Invalid msaIndex for JPredJob on parent MSA input object!");\r
-          sqs[msaIndex].removeGaps();\r
+\r
+          /////\r
+          //Uses RemoveGapsCommand\r
+          /////\r
+          new jalview.commands.RemoveGapsCommand("Remove Gaps",\r
+                                                 new SequenceI[] {sqs[msaIndex]},\r
+                                                 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
@@ -174,7 +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
@@ -218,7 +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
@@ -245,12 +252,12 @@ 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
             sq=sq+((diff>=sb.length()) ? sb.toString() : sb.substring(0, diff));\r
-            diff=origseq.getLength()-sq.length();            \r
+            diff=origseq.getLength()-sq.length();\r
           }\r
         }\r
       }\r
@@ -261,7 +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
@@ -508,14 +516,14 @@ implements WSClientI
             if (((SequenceI[])alandcolsel[0])[0].getLength()!=res.getWidth()) {\r
               if (msa) {\r
                 throw new Error("Implementation Error! ColumnSelection from input alignment will not map to result alignment!");\r
-              } \r
+              }\r
             }\r
             if (!msa) {\r
               // update hidden regions to account for loss of gaps in profile. - if any\r
               // gapMap returns insert list, interpreted as delete list by pruneDeletions\r
               //((ColumnSelection) alandcolsel[1]).pruneDeletions(ShiftList.parseMap(((SequenceI[]) alandcolsel[0])[0].gapMap()));\r
             }*/\r
-            \r
+\r
             af = new AlignFrame((Alignment) res[0], (ColumnSelection) res[1],AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);\r
           }\r
           Desktop.addInternalFrame(af, altitle,\r