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
Merge branch 'develop' into features/JAL-2446NCList
[jalview.git]
/
src
/
jalview
/
appletgui
/
PCAPanel.java
diff --git
a/src/jalview/appletgui/PCAPanel.java
b/src/jalview/appletgui/PCAPanel.java
index
efb204e
..
5dc57f9
100644
(file)
--- a/
src/jalview/appletgui/PCAPanel.java
+++ b/
src/jalview/appletgui/PCAPanel.java
@@
-25,7
+25,7
@@
import jalview.analysis.scoremodels.SimilarityParams;
import jalview.api.analysis.ScoreModelI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentView;
import jalview.api.analysis.ScoreModelI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentView;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SeqCigar;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
import jalview.datamodel.SeqCigar;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
@@
-105,8
+105,7
@@
public class PCAPanel extends EmbmenuFrame implements Runnable,
ScoreModelI scoreModel = ScoreModels.getInstance().getDefaultModel(
!nucleotide);
ScoreModelI scoreModel = ScoreModels.getInstance().getDefaultModel(
!nucleotide);
- pcaModel = new PCAModel(seqstrings, seqs, nucleotide,
- scoreModel,
+ pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
SimilarityParams.SeqSpace);
rc = new RotatableCanvas(viewport);
SimilarityParams.SeqSpace);
rc = new RotatableCanvas(viewport);
@@
-217,6
+216,9
@@
public class PCAPanel extends EmbmenuFrame implements Runnable,
if (!pcaModel.isNucleotide())
{
pcaModel.setNucleotide(true);
if (!pcaModel.isNucleotide())
{
pcaModel.setNucleotide(true);
+ ScoreModelI scoreModel = ScoreModels.getInstance().getDefaultModel(
+ false);
+ pcaModel.setScoreModel(scoreModel);
new Thread(this).start();
}
}
new Thread(this).start();
}
}
@@
-225,6
+227,9
@@
public class PCAPanel extends EmbmenuFrame implements Runnable,
if (pcaModel.isNucleotide())
{
pcaModel.setNucleotide(false);
if (pcaModel.isNucleotide())
{
pcaModel.setNucleotide(false);
+ ScoreModelI scoreModel = ScoreModels.getInstance().getDefaultModel(
+ true);
+ pcaModel.setScoreModel(scoreModel);
new Thread(this).start();
}
}
new Thread(this).start();
}
}
@@
-276,7
+281,7
@@
public class PCAPanel extends EmbmenuFrame implements Runnable,
}
;
Object[] alAndColsel = pcaModel.getSeqtrings()
}
;
Object[] alAndColsel = pcaModel.getSeqtrings()
- .getAlignmentAndColumnSelection(gc);
+ .getAlignmentAndHiddenColumns(gc);
if (alAndColsel != null && alAndColsel[0] != null)
{
if (alAndColsel != null && alAndColsel[0] != null)
{
@@
-284,7
+289,8
@@
public class PCAPanel extends EmbmenuFrame implements Runnable,
AlignFrame af = new AlignFrame(al, av.applet,
"Original Data for PCA", false);
AlignFrame af = new AlignFrame(al, av.applet,
"Original Data for PCA", false);
- af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]);
+ af.viewport.getAlignment().setHiddenColumns(
+ (HiddenColumns) alAndColsel[1]);
}
}
}
}