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JAL-2674 Rewrote propagateInsertions
[jalview.git]
/
src
/
jalview
/
appletgui
/
PCAPanel.java
diff --git
a/src/jalview/appletgui/PCAPanel.java
b/src/jalview/appletgui/PCAPanel.java
index
2d77c59
..
fc1d359
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;
@@
-48,8
+48,8
@@
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
-public class PCAPanel extends EmbmenuFrame implements Runnable,
- ActionListener, ItemListener
+public class PCAPanel extends EmbmenuFrame
+ implements Runnable, ActionListener, ItemListener
{
RotatableCanvas rc;
{
RotatableCanvas rc;
@@
-88,7
+88,8
@@
public class PCAPanel extends EmbmenuFrame implements Runnable,
}
else
{
}
else
{
- seqs = viewport.getSelectionGroup().getSequencesInOrder(viewport.getAlignment());
+ seqs = viewport.getSelectionGroup()
+ .getSequencesInOrder(viewport.getAlignment());
}
SeqCigar sq[] = seqstrings.getSequences();
int length = sq[0].getWidth();
}
SeqCigar sq[] = seqstrings.getSequences();
int length = sq[0].getWidth();
@@
-103,8
+104,8
@@
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,
SimilarityParams.SeqSpace);
pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
SimilarityParams.SeqSpace);
@@
-216,8
+217,8
@@
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);
+ ScoreModelI scoreModel = ScoreModels.getInstance()
+ .getDefaultModel(false);
pcaModel.setScoreModel(scoreModel);
new Thread(this).start();
}
pcaModel.setScoreModel(scoreModel);
new Thread(this).start();
}
@@
-227,8
+228,8
@@
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);
+ ScoreModelI scoreModel = ScoreModels.getInstance()
+ .getDefaultModel(true);
pcaModel.setScoreModel(scoreModel);
new Thread(this).start();
}
pcaModel.setScoreModel(scoreModel);
new Thread(this).start();
}
@@
-281,15
+282,16
@@
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)
{
Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
if (alAndColsel != null && alAndColsel[0] != null)
{
Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
- 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]);
}
}
}
}
@@
-365,8
+367,8
@@
public class PCAPanel extends EmbmenuFrame implements Runnable,
values.setLabel(MessageManager.getString("label.output_values"));
values.addActionListener(this);
inputData.setLabel(MessageManager.getString("label.input_data"));
values.setLabel(MessageManager.getString("label.output_values"));
values.addActionListener(this);
inputData.setLabel(MessageManager.getString("label.input_data"));
- nuclSetting.setLabel(MessageManager
- .getString("label.nucleotide_matrix"));
+ nuclSetting
+ .setLabel(MessageManager.getString("label.nucleotide_matrix"));
nuclSetting.addItemListener(this);
protSetting.setLabel(MessageManager.getString("label.protein_matrix"));
protSetting.addItemListener(this);
nuclSetting.addItemListener(this);
protSetting.setLabel(MessageManager.getString("label.protein_matrix"));
protSetting.addItemListener(this);