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total annotation score is a double for maximum precision.
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceGroup.java
diff --git
a/src/jalview/datamodel/SequenceGroup.java
b/src/jalview/datamodel/SequenceGroup.java
index
bae5863
..
47d56b7
100755
(executable)
--- a/
src/jalview/datamodel/SequenceGroup.java
+++ b/
src/jalview/datamodel/SequenceGroup.java
@@
-39,7
+39,7
@@
public class SequenceGroup
Vector aaFrequency;
boolean displayBoxes = true;
boolean displayText = true;
Vector aaFrequency;
boolean displayBoxes = true;
boolean displayText = true;
- boolean colourText = true;
+ boolean colourText = false;
private Vector sequences = new Vector();
int width = -1;
private Vector sequences = new Vector();
int width = -1;
@@
-98,10
+98,7
@@
public class SequenceGroup
{
SequenceI seq = inorder[i];
{
SequenceI seq = inorder[i];
- seqs[i] = new Sequence(seq.getName(),
- seq.getSequence(startRes, endRes + 1),
- seq.findPosition(startRes),
- findEndRes(seq));
+ seqs[i] = seq.getSubSequence(startRes, endRes+1);
seqs[i].setDescription(seq.getDescription());
seqs[i].setDBRef(seq.getDBRef());
seqs[i].setDescription(seq.getDescription());
seqs[i].setDBRef(seq.getDBRef());
@@
-115,7
+112,11
@@
public class SequenceGroup
{
for (int a = 0; a < seq.getAnnotation().length; a++)
{
{
for (int a = 0; a < seq.getAnnotation().length; a++)
{
- seqs[i].addAlignmentAnnotation(new AlignmentAnnotation(seq.getAnnotation()[a]));
+ AlignmentAnnotation newannot = new AlignmentAnnotation(seq.getAnnotation()[a]);
+ newannot.restrict(startRes, endRes);
+ newannot.setSequenceRef(seqs[i]);
+ newannot.adjustForAlignment();
+ seqs[i].addAlignmentAnnotation(newannot);
}
}
}
}
}
}