git://source.jalview.org
/
jalview.git
/ commitdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
| commitdiff |
tree
raw
|
patch
|
inline
| side by side (parent:
9a419b6
)
Fix PaSiMap on selected sequences
author
MorellThomas
<morellth@yahoo.co.jp>
Wed, 6 Mar 2024 14:29:15 +0000
(15:29 +0100)
committer
MorellThomas
<morellth@yahoo.co.jp>
Wed, 6 Mar 2024 14:29:15 +0000
(15:29 +0100)
src/jalview/analysis/Connectivity.java
patch
|
blob
|
history
diff --git
a/src/jalview/analysis/Connectivity.java
b/src/jalview/analysis/Connectivity.java
index
0f849e3
..
a9cd46c
100644
(file)
--- a/
src/jalview/analysis/Connectivity.java
+++ b/
src/jalview/analysis/Connectivity.java
@@
-45,7
+45,14
@@
public class Connectivity
*/
public static Hashtable<SequenceI, Integer> getConnectivity(AlignmentViewport av, float[][] scores, byte dim) throws RuntimeException
{
*/
public static Hashtable<SequenceI, Integer> getConnectivity(AlignmentViewport av, float[][] scores, byte dim) throws RuntimeException
{
- SequenceI[] sequences = av.getAlignment().getSequencesArray();
+ boolean isSelection = av.getSelectionGroup() != null && av.getSelectionGroup().getSize() > 0;
+ SequenceI[] sequences;
+ if (isSelection)
+ {
+ sequences = (SequenceI[]) av.getAlignmentView(isSelection).getAlignmentAndHiddenColumns(av.getGapCharacter())[0];
+ } else {
+ sequences = av.getAlignment().getSequencesArray();
+ }
Hashtable<SequenceI, Integer> connectivity = new Hashtable<SequenceI, Integer>();
// for each unique connection
Hashtable<SequenceI, Integer> connectivity = new Hashtable<SequenceI, Integer>();
// for each unique connection