git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
(JAL-969) refactored alignmentViewport base class to own package and pulled up most...
[jalview.git]
/
src
/
jalview
/
appletgui
/
TreePanel.java
diff --git
a/src/jalview/appletgui/TreePanel.java
b/src/jalview/appletgui/TreePanel.java
index
29e5654
..
aa57908
100644
(file)
--- a/
src/jalview/appletgui/TreePanel.java
+++ b/
src/jalview/appletgui/TreePanel.java
@@
-186,11
+186,11
@@
public class TreePanel extends EmbmenuFrame implements ActionListener,
{
if (odata == null)
{
{
if (odata == null)
{
- tree = new NJTree(av.alignment.getSequencesArray(), newtree);
+ tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
}
else
{
}
else
{
- tree = new NJTree(av.alignment.getSequencesArray(), odata,
+ tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
newtree);
}
newtree);
}
@@
-204,14
+204,14
@@
public class TreePanel extends EmbmenuFrame implements ActionListener,
if (av.getSelectionGroup() == null)
{
start = 0;
if (av.getSelectionGroup() == null)
{
start = 0;
- end = av.alignment.getWidth();
- seqs = av.alignment.getSequencesArray();
+ end = av.getAlignment().getWidth();
+ seqs = av.getAlignment().getSequencesArray();
}
else
{
start = av.getSelectionGroup().getStartRes();
end = av.getSelectionGroup().getEndRes() + 1;
}
else
{
start = av.getSelectionGroup().getStartRes();
end = av.getSelectionGroup().getEndRes() + 1;
- seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+ seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
}
tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
}
tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);