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JAL-3633 Help documentation updated
[jalview.git]
/
src
/
jalview
/
appletgui
/
PCAPanel.java
diff --git
a/src/jalview/appletgui/PCAPanel.java
b/src/jalview/appletgui/PCAPanel.java
index
0d607c0
..
7c0dfa9
100644
(file)
--- a/
src/jalview/appletgui/PCAPanel.java
+++ b/
src/jalview/appletgui/PCAPanel.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-20,9
+20,12
@@
*/
package jalview.appletgui;
*/
package jalview.appletgui;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.analysis.scoremodels.SimilarityParams;
+import jalview.api.analysis.ScoreModelI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentView;
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;
@@
-45,8
+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;
@@
-56,7
+59,7
@@
public class PCAPanel extends EmbmenuFrame implements Runnable,
int top = 0;
int top = 0;
- public PCAPanel(AlignViewport av)
+ public PCAPanel(AlignViewport viewport)
{
try
{
{
try
{
@@
-73,19
+76,20
@@
public class PCAPanel extends EmbmenuFrame implements Runnable,
zCombobox.addItem("dim " + i);
}
zCombobox.addItem("dim " + i);
}
- this.av = av;
- boolean selected = av.getSelectionGroup() != null
- && av.getSelectionGroup().getSize() > 0;
- AlignmentView seqstrings = av.getAlignmentView(selected);
- boolean nucleotide = av.getAlignment().isNucleotide();
+ this.av = viewport;
+ boolean selected = viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() > 0;
+ AlignmentView seqstrings = viewport.getAlignmentView(selected);
+ boolean nucleotide = viewport.getAlignment().isNucleotide();
SequenceI[] seqs;
if (!selected)
{
SequenceI[] seqs;
if (!selected)
{
- seqs = av.getAlignment().getSequencesArray();
+ seqs = viewport.getAlignment().getSequencesArray();
}
else
{
}
else
{
- seqs = av.getSelectionGroup().getSequencesInOrder(av.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();
@@
-99,9
+103,13
@@
public class PCAPanel extends EmbmenuFrame implements Runnable,
return;
}
}
return;
}
}
- pcaModel = new PCAModel(seqstrings, seqs, nucleotide);
- rc = new RotatableCanvas(av);
+ ScoreModelI scoreModel = ScoreModels.getInstance()
+ .getDefaultModel(!nucleotide);
+ pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
+ SimilarityParams.SeqSpace);
+
+ rc = new RotatableCanvas(viewport);
embedMenuIfNeeded(rc);
add(rc, BorderLayout.CENTER);
embedMenuIfNeeded(rc);
add(rc, BorderLayout.CENTER);
@@
-116,6
+124,7
@@
public class PCAPanel extends EmbmenuFrame implements Runnable,
/**
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
*/
+ @Override
public void run()
{
// TODO progress indicator
public void run()
{
// TODO progress indicator
@@
-125,7
+134,7
@@
public class PCAPanel extends EmbmenuFrame implements Runnable,
{
nuclSetting.setState(pcaModel.isNucleotide());
protSetting.setState(!pcaModel.isNucleotide());
{
nuclSetting.setState(pcaModel.isNucleotide());
protSetting.setState(!pcaModel.isNucleotide());
- pcaModel.run();
+ pcaModel.calculate();
// ////////////////
xCombobox.select(0);
yCombobox.select(1);
// ////////////////
xCombobox.select(0);
yCombobox.select(1);
@@
-158,12
+167,11
@@
public class PCAPanel extends EmbmenuFrame implements Runnable,
int dim2 = top - yCombobox.getSelectedIndex();
int dim3 = top - zCombobox.getSelectedIndex();
pcaModel.updateRcView(dim1, dim2, dim3);
int dim2 = top - yCombobox.getSelectedIndex();
int dim3 = top - zCombobox.getSelectedIndex();
pcaModel.updateRcView(dim1, dim2, dim3);
- rc.img = null;
- rc.rotmat.setIdentity();
- rc.initAxes();
+ rc.resetView();
rc.paint(rc.getGraphics());
}
rc.paint(rc.getGraphics());
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == inputData)
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == inputData)
@@
-183,6
+191,7
@@
public class PCAPanel extends EmbmenuFrame implements Runnable,
}
}
}
}
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (evt.getSource() == xCombobox)
public void itemStateChanged(ItemEvent evt)
{
if (evt.getSource() == xCombobox)
@@
-206,6
+215,9
@@
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();
}
}
@@
-214,6
+226,9
@@
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();
}
}
@@
-264,16
+279,17
@@
public class PCAPanel extends EmbmenuFrame implements Runnable,
{
}
;
{
}
;
- Object[] alAndColsel = pcaModel.getSeqtrings()
- .getAlignmentAndColumnSelection(gc);
+ Object[] alAndColsel = pcaModel.getInputData()
+ .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]);
}
}
}
}
@@
-349,8
+365,8
@@
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);