\r
import vamsas.objects.simple.JpredResult;\r
\r
-import ext.vamsas.*;\r
import jalview.analysis.*;\r
import jalview.bin.*;\r
import jalview.datamodel.*;\r
import jalview.gui.*;\r
import jalview.io.*;\r
import jalview.util.*;\r
-import jalview.ws.WSThread.*;\r
\r
class JPredThread\r
extends WSThread\r
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
al = new Alignment(sqs);\r
alcsel=(ColumnSelection) alandcolsel[1];\r
} else {\r
- al = new Alignment(new FormatAdapter().readFile(result.getAligfile(),\r
- "Paste", format));\r
+ al = new FormatAdapter().readFile(result.getAligfile(),\r
+ "Paste", format);\r
sqs = new SequenceI[al.getHeight()];\r
\r
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
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
+ alignFrame.getCurrentView().getAlignment());\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
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
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
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
{\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
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