git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-2446 merged to spike branch
[jalview.git]
/
src
/
jalview
/
ws
/
jws1
/
JPredThread.java
diff --git
a/src/jalview/ws/jws1/JPredThread.java
b/src/jalview/ws/jws1/JPredThread.java
index
e685d00
..
b0210d8
100644
(file)
--- a/
src/jalview/ws/jws1/JPredThread.java
+++ b/
src/jalview/ws/jws1/JPredThread.java
@@
-27,7
+27,7
@@
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
@@
-114,7
+114,7
@@
class JPredThread extends JWS1Thread implements WSClientI
return null;
}
AlignmentI al = null;
return null;
}
AlignmentI al = null;
- ColumnSelection alcsel = null;
+ HiddenColumns alhidden = null;
int FirstSeq = -1; // the position of the query sequence in Alignment al
JpredResult result = (JpredResult) this.result;
int FirstSeq = -1; // the position of the query sequence in Alignment al
JpredResult result = (JpredResult) this.result;
@@
-141,10
+141,10
@@
class JPredThread extends JWS1Thread implements WSClientI
if (predMap != null)
{
Object[] alandcolsel = input
if (predMap != null)
{
Object[] alandcolsel = input
- .getAlignmentAndColumnSelection(getGapChar());
+ .getAlignmentAndHiddenColumns(getGapChar());
sqs = (SequenceI[]) alandcolsel[0];
al = new Alignment(sqs);
sqs = (SequenceI[]) alandcolsel[0];
al = new Alignment(sqs);
- alcsel = (ColumnSelection) alandcolsel[1];
+ alhidden = (HiddenColumns) alandcolsel[1];
}
else
{
}
else
{
@@
-192,7
+192,7
@@
class JPredThread extends JWS1Thread implements WSClientI
{
char gc = getGapChar();
SequenceI[] sqs = (SequenceI[]) input
{
char gc = getGapChar();
SequenceI[] sqs = (SequenceI[]) input
- .getAlignmentAndColumnSelection(gc)[0];
+ .getAlignmentAndHiddenColumns(gc)[0];
if (this.msaIndex >= sqs.length)
{
throw new Error(
if (this.msaIndex >= sqs.length)
{
throw new Error(
@@
-237,7
+237,7
@@
class JPredThread extends JWS1Thread implements WSClientI
{
// Adjust input view for gaps
// propagate insertions into profile
{
// Adjust input view for gaps
// propagate insertions into profile
- alcsel = ColumnSelection.propagateInsertions(profileseq, al,
+ alhidden = HiddenColumns.propagateInsertions(profileseq, al,
input);
}
}
input);
}
}
@@
-252,7
+252,7
@@
class JPredThread extends JWS1Thread implements WSClientI
alant.sequenceRef);
}
}
alant.sequenceRef);
}
}
- return new Object[] { al, alcsel }; // , FirstSeq, noMsa};
+ return new Object[] { al, alhidden }; // , FirstSeq, noMsa};
}
/**
}
/**
@@
-625,7
+625,7
@@
class JPredThread extends JWS1Thread implements WSClientI
if (res[1] != null)
{
af = new AlignFrame((Alignment) res[0],
if (res[1] != null)
{
af = new AlignFrame((Alignment) res[0],
- (ColumnSelection) res[1], AlignFrame.DEFAULT_WIDTH,
+ (HiddenColumns) res[1], AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
}
else
AlignFrame.DEFAULT_HEIGHT);
}
else
@@
-651,7
+651,8
@@
class JPredThread extends JWS1Thread implements WSClientI
*/
af = new AlignFrame((Alignment) res[0],
*/
af = new AlignFrame((Alignment) res[0],
- (ColumnSelection) res[1], AlignFrame.DEFAULT_WIDTH,
+ (HiddenColumns) res[1],
+ AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
}
Desktop.addInternalFrame(af, altitle, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
}
Desktop.addInternalFrame(af, altitle, AlignFrame.DEFAULT_WIDTH,