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[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceGroup.java
diff --git
a/src/jalview/datamodel/SequenceGroup.java
b/src/jalview/datamodel/SequenceGroup.java
index
2bdd5f8
..
df8c6ea
100755
(executable)
--- a/
src/jalview/datamodel/SequenceGroup.java
+++ b/
src/jalview/datamodel/SequenceGroup.java
@@
-119,6
+119,7
@@
public class SequenceGroup
SequenceI [] seqs = new SequenceI[iSize];
\r
SequenceI [] inorder = getSequencesInOrder(align);
\r
\r
SequenceI [] seqs = new SequenceI[iSize];
\r
SequenceI [] inorder = getSequencesInOrder(align);
\r
\r
+
\r
for (int i = 0; i < iSize; i++)
\r
{
\r
SequenceI seq = inorder[i];
\r
for (int i = 0; i < iSize; i++)
\r
{
\r
SequenceI seq = inorder[i];
\r
@@
-316,7
+317,7
@@
public class SequenceGroup
*/
\r
public void addSequence(SequenceI s, boolean recalc)
\r
{
\r
*/
\r
public void addSequence(SequenceI s, boolean recalc)
\r
{
\r
- if (!sequences.contains(s))
\r
+ if (s!=null && !sequences.contains(s))
\r
{
\r
sequences.addElement(s);
\r
}
\r
{
\r
sequences.addElement(s);
\r
}
\r
@@
-337,7
+338,7
@@
public class SequenceGroup
\r
try
\r
{
\r
\r
try
\r
{
\r
- cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));
\r
+ cs.setConsensus(AAFrequency.calculate(sequences, startRes, endRes+1));
\r
\r
if (cs instanceof ClustalxColourScheme)
\r
{
\r
\r
if (cs instanceof ClustalxColourScheme)
\r
{
\r
@@
-348,7
+349,7
@@
public class SequenceGroup
{
\r
Conservation c = new Conservation(groupName,
\r
ResidueProperties.propHash, 3, sequences,
\r
{
\r
Conservation c = new Conservation(groupName,
\r
ResidueProperties.propHash, 3, sequences,
\r
- 0, getWidth());
\r
+ startRes, endRes+1);
\r
c.calculate();
\r
c.verdict(false, 25);
\r
\r
c.calculate();
\r
c.verdict(false, 25);
\r
\r