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JAL-2526 correct boundary conditions for sequence left/right of cursor
[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
078f189
..
b0210d8
100644
(file)
--- a/
src/jalview/ws/jws1/JPredThread.java
+++ b/
src/jalview/ws/jws1/JPredThread.java
@@
-27,7
+27,6
@@
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.datamodel.HiddenColumns;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
@@
-115,7
+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;
@@
-145,7
+144,7
@@
class JPredThread extends JWS1Thread implements WSClientI
.getAlignmentAndHiddenColumns(getGapChar());
sqs = (SequenceI[]) alandcolsel[0];
al = new Alignment(sqs);
.getAlignmentAndHiddenColumns(getGapChar());
sqs = (SequenceI[]) alandcolsel[0];
al = new Alignment(sqs);
- alcsel = (ColumnSelection) alandcolsel[1];
+ alhidden = (HiddenColumns) alandcolsel[1];
}
else
{
}
else
{
@@
-238,7
+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);
}
}
@@
-253,7
+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};
}
/**
}
/**