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New view copies annotations across
[jalview.git]
/
src
/
jalview
/
ws
/
JPredThread.java
diff --git
a/src/jalview/ws/JPredThread.java
b/src/jalview/ws/JPredThread.java
index
6aebfdc
..
b4833b1
100644
(file)
--- a/
src/jalview/ws/JPredThread.java
+++ b/
src/jalview/ws/JPredThread.java
@@
-6,14
+6,12
@@
import javax.swing.*;
\r
import vamsas.objects.simple.JpredResult;
\r
\r
\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.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
\r
class JPredThread
\r
extends WSThread
\r
@@
-53,7
+51,7
@@
implements WSClientI
return false;
\r
}
\r
/**
\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
* @return null or Object[] { annotated alignment for this prediction, ColumnSelection for this prediction} or null if no results available.
\r
* @throws Exception
\r
*/
\r
@@
-95,14
+93,14
@@
implements WSClientI
al = new Alignment(sqs);
\r
alcsel=(ColumnSelection) alandcolsel[1];
\r
} else {
\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
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
if (!jalview.analysis.SeqsetUtils.deuniquify( (Hashtable)
\r
SequenceInfo, sqs))
\r
{
\r
@@
-133,9
+131,16
@@
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
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
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
}
\r
\r
if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
\r
@@
-174,7
+179,7
@@
implements WSClientI
sb.append(gc);
\r
}
\r
for (int s=1,ns=al.getHeight(); s<ns; s++) {
\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
int diff=gapMap[r]-sq.length();
\r
if (diff>0) {
\r
// pad gaps
\r
@@
-218,7
+223,7
@@
implements WSClientI
for (int s=0,ns=al.getHeight(); s<ns; s++) {
\r
SequenceI sqobj = al.getSequenceAt(s);
\r
if (sqobj!=profileseq) {
\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
if (sq.length()<=spos+offset) {
\r
// pad sequence
\r
int diff=spos+offset-sq.length()-1;
\r
@@
-245,12
+250,12
@@
implements WSClientI
sb.append(gc);
\r
}
\r
for (int s=1,ns=al.getHeight(); s<ns; s++) {
\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
// 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
}
\r
}
\r
@@
-261,7
+266,8
@@
implements WSClientI
{
\r
super();
\r
this.predMap = delMap;
\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 (sq.length() >= 20)
\r
{
\r
this.SequenceInfo = SequenceInfo;
\r
@@
-508,14
+514,14
@@
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
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
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
af = new AlignFrame((Alignment) res[0], (ColumnSelection) res[1],AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
\r
}
\r
Desktop.addInternalFrame(af, altitle,
\r