\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
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
new jalview.commands.RemoveGapsCommand("Remove Gaps",\r
new SequenceI[] {sqs[msaIndex]},\r
- gc);\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
{\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