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JAL-1031 JAL-1032 if selection is non-null but empty, then calculate PCA or tree...
author
jprocter
<jprocter@compbio.dundee.ac.uk>
Tue, 25 Sep 2012 14:21:04 +0000
(15:21 +0100)
committer
jprocter
<jprocter@compbio.dundee.ac.uk>
Tue, 25 Sep 2012 14:21:04 +0000
(15:21 +0100)
src/jalview/appletgui/PCAPanel.java
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src/jalview/appletgui/TreePanel.java
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src/jalview/gui/AlignFrame.java
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src/jalview/gui/PCAPanel.java
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src/jalview/gui/TreePanel.java
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diff --git
a/src/jalview/appletgui/PCAPanel.java
b/src/jalview/appletgui/PCAPanel.java
index
44711d7
..
ff8b506
100755
(executable)
--- a/
src/jalview/appletgui/PCAPanel.java
+++ b/
src/jalview/appletgui/PCAPanel.java
@@
-55,11
+55,12
@@
public class PCAPanel extends EmbmenuFrame implements Runnable,
}
this.av = av;
}
this.av = av;
+ boolean selected=av.getSelectionGroup()!=null && av.getSelectionGroup().getSize()>0;
AlignmentView seqstrings = av
AlignmentView seqstrings = av
- .getAlignmentView(av.getSelectionGroup() != null);
+ .getAlignmentView(selected);
boolean nucleotide = av.getAlignment().isNucleotide();
SequenceI[] seqs;
boolean nucleotide = av.getAlignment().isNucleotide();
SequenceI[] seqs;
- if (av.getSelectionGroup() == null)
+ if (!selected)
{
seqs = av.getAlignment().getSequencesArray();
}
{
seqs = av.getAlignment().getSequencesArray();
}
diff --git
a/src/jalview/appletgui/TreePanel.java
b/src/jalview/appletgui/TreePanel.java
index
aa57908
..
ec2512f
100644
(file)
--- a/
src/jalview/appletgui/TreePanel.java
+++ b/
src/jalview/appletgui/TreePanel.java
@@
-199,9
+199,11
@@
public class TreePanel extends EmbmenuFrame implements ActionListener,
{
int start, end;
SequenceI[] seqs;
{
int start, end;
SequenceI[] seqs;
- AlignmentView seqStrings = av.getAlignmentView(av
- .getSelectionGroup() != null);
- if (av.getSelectionGroup() == null)
+ boolean selview=(av
+ .getSelectionGroup() != null) && (av
+ .getSelectionGroup().getSize()>1);
+ AlignmentView seqStrings = av.getAlignmentView(selview);
+ if (!selview)
{
start = 0;
end = av.getAlignment().getWidth();
{
start = 0;
end = av.getAlignment().getWidth();
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
8396e6a
..
39884ce
100755
(executable)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-3668,7
+3668,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
TreePanel tp;
{
TreePanel tp;
- if (viewport.getSelectionGroup() != null)
+ if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)
{
if (viewport.getSelectionGroup().getSize() < 3)
{
{
if (viewport.getSelectionGroup().getSize() < 3)
{
diff --git
a/src/jalview/gui/PCAPanel.java
b/src/jalview/gui/PCAPanel.java
index
ad7d1fd
..
bafacc5
100755
(executable)
--- a/
src/jalview/gui/PCAPanel.java
+++ b/
src/jalview/gui/PCAPanel.java
@@
-63,12
+63,12
@@
public class PCAPanel extends GPCAPanel implements Runnable,
this.ap = ap;
boolean sameLength = true;
this.ap = ap;
boolean sameLength = true;
-
+ boolean selected=av.getSelectionGroup()!=null && av.getSelectionGroup().getSize()>0;
AlignmentView seqstrings = av
AlignmentView seqstrings = av
- .getAlignmentView(av.getSelectionGroup() != null);
+ .getAlignmentView(selected);
boolean nucleotide = av.getAlignment().isNucleotide();
SequenceI[] seqs;
boolean nucleotide = av.getAlignment().isNucleotide();
SequenceI[] seqs;
- if (av.getSelectionGroup() == null)
+ if (!selected)
{
seqs = av.getAlignment().getSequencesArray();
}
{
seqs = av.getAlignment().getSequencesArray();
}
diff --git
a/src/jalview/gui/TreePanel.java
b/src/jalview/gui/TreePanel.java
index
14802e7
..
60557ca
100755
(executable)
--- a/
src/jalview/gui/TreePanel.java
+++ b/
src/jalview/gui/TreePanel.java
@@
-273,9
+273,11
@@
public class TreePanel extends GTreePanel
{
int start, end;
SequenceI[] seqs;
{
int start, end;
SequenceI[] seqs;
- AlignmentView seqStrings = av.getAlignmentView(av
- .getSelectionGroup() != null);
- if (av.getSelectionGroup() == null)
+ boolean selview=av
+ .getSelectionGroup() != null & av
+ .getSelectionGroup().getSize()>1;
+ AlignmentView seqStrings = av.getAlignmentView(selview);
+ if (!selview)
{
start = 0;
end = av.getAlignment().getWidth();
{
start = 0;
end = av.getAlignment().getWidth();