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fix for JAL-1398 - original colourscheme is enabled if colourscheme has a BaseColour...
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceGroup.java
diff --git
a/src/jalview/datamodel/SequenceGroup.java
b/src/jalview/datamodel/SequenceGroup.java
index
c42a955
..
9ed3a53
100755
(executable)
--- a/
src/jalview/datamodel/SequenceGroup.java
+++ b/
src/jalview/datamodel/SequenceGroup.java
@@
-493,7
+493,7
@@
public class SequenceGroup implements AnnotatedCollectionI
endRes + 1, showSequenceLogo);
if (consensus != null)
{
endRes + 1, showSequenceLogo);
if (consensus != null)
{
- _updateConsensusRow(cnsns);
+ _updateConsensusRow(cnsns, sequences.size());
}
if (cs != null)
{
}
if (cs != null)
{
@@
-552,7
+552,7
@@
public class SequenceGroup implements AnnotatedCollectionI
public Hashtable[] consensusData = null;
public Hashtable[] consensusData = null;
- private void _updateConsensusRow(Hashtable[] cnsns)
+ private void _updateConsensusRow(Hashtable[] cnsns, long nseq)
{
if (consensus == null)
{
{
if (consensus == null)
{
@@
-569,7
+569,7
@@
public class SequenceGroup implements AnnotatedCollectionI
consensus.annotations = new Annotation[aWidth]; // should be alignment width
AAFrequency.completeConsensus(consensus, cnsns, startRes, endRes + 1,
consensus.annotations = new Annotation[aWidth]; // should be alignment width
AAFrequency.completeConsensus(consensus, cnsns, startRes, endRes + 1,
- ignoreGapsInConsensus, showSequenceLogo); // TODO: setting container
+ ignoreGapsInConsensus, showSequenceLogo, nseq); // TODO: setting container
// for
// ignoreGapsInConsensusCalculation);
}
// for
// ignoreGapsInConsensusCalculation);
}
@@
-612,9
+612,9
@@
public class SequenceGroup implements AnnotatedCollectionI
}
/**
}
/**
- * DOCUMENT ME!
*
*
- * @return DOCUMENT ME!
+ *
+ * @return the first column selected by this group. Runs from 0<=i<N_cols
*/
public int getStartRes()
{
*/
public int getStartRes()
{
@@
-622,9
+622,8
@@
public class SequenceGroup implements AnnotatedCollectionI
}
/**
}
/**
- * DOCUMENT ME!
*
*
- * @return DOCUMENT ME!
+ * @return the groups last selected column. Runs from 0<=i<N_cols
*/
public int getEndRes()
{
*/
public int getEndRes()
{
@@
-1034,12
+1033,12
@@
public class SequenceGroup implements AnnotatedCollectionI
{
consensus = new AlignmentAnnotation("", "", new Annotation[1], 0f,
100f, AlignmentAnnotation.BAR_GRAPH);
{
consensus = new AlignmentAnnotation("", "", new Annotation[1], 0f,
100f, AlignmentAnnotation.BAR_GRAPH);
+ consensus.hasText = true;
+ consensus.autoCalculated = true;
+ consensus.groupRef = this;
+ consensus.label = "Consensus for " + getName();
+ consensus.description = "Percent Identity";
}
}
- consensus.hasText = true;
- consensus.autoCalculated = true;
- consensus.groupRef = this;
- consensus.label = "Consensus for " + getName();
- consensus.description = "Percent Identity";
return consensus;
}
return consensus;
}