/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-
-public class PCAPanel extends EmbmenuFrame implements Runnable,
- ActionListener, ItemListener
+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.HiddenColumns;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+import jalview.viewmodel.PCAModel;
+
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.CheckboxMenuItem;
+import java.awt.Choice;
+import java.awt.Color;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.Label;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+
+public class PCAPanel extends EmbmenuFrame
+ implements Runnable, ActionListener, ItemListener
{
- PCA pca;
-
- int top;
-
RotatableCanvas rc;
AlignViewport av;
- SequenceI[] seqs;
+ PCAModel pcaModel;
- AlignmentView seqstrings;
+ int top = 0;
- public PCAPanel(AlignViewport av)
+ public PCAPanel(AlignViewport viewport)
{
try
{
zCombobox.addItem("dim " + i);
}
- this.av = av;
- seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
- if (av.getSelectionGroup() == null)
+ 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)
{
- seqs = av.getAlignment().getSequencesArray();
+ seqs = viewport.getAlignment().getSequencesArray();
}
else
{
- seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
+ seqs = viewport.getSelectionGroup()
+ .getSequencesInOrder(viewport.getAlignment());
}
SeqCigar sq[] = seqstrings.getSequences();
int length = sq[0].getWidth();
}
}
- 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);
- jalview.bin.JalviewLite.addFrame(this, "Principal component analysis",
- 400, 400);
+ jalview.bin.JalviewLite.addFrame(this,
+ MessageManager.getString("label.principal_component_analysis"),
+ 475, 400);
- Thread worker = new Thread(this);
+ Thread worker = new Thread(this, "PCACalcThread");
worker.start();
}
/**
* DOCUMENT ME!
*/
+ @Override
public void run()
{
- pca = new PCA(seqstrings.getSequenceStrings(' '));
- pca.run();
-
- // Now find the component coordinates
- int ii = 0;
-
- while ((ii < seqs.length) && (seqs[ii] != null))
- {
- ii++;
- }
-
- double[][] comps = new double[ii][ii];
-
- for (int i = 0; i < ii; i++)
+ // TODO progress indicator
+ calcSettings.setEnabled(false);
+ rc.setEnabled(false);
+ try
{
- if (pca.getEigenvalue(i) > 1e-4)
- {
- comps[i] = pca.component(i);
- }
- }
-
- // ////////////////
- xCombobox.select(0);
- yCombobox.select(1);
- zCombobox.select(2);
-
- top = pca.getM().rows - 1;
-
- Vector points = new Vector();
- float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
-
- for (int i = 0; i < pca.getM().rows; i++)
+ nuclSetting.setState(pcaModel.isNucleotide());
+ protSetting.setState(!pcaModel.isNucleotide());
+ pcaModel.calculate();
+ // ////////////////
+ xCombobox.select(0);
+ yCombobox.select(1);
+ zCombobox.select(2);
+
+ pcaModel.updateRc(rc);
+ // rc.invalidate();
+ top = pcaModel.getTop();
+ } catch (OutOfMemoryError x)
{
- SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
- points.addElement(sp);
+ System.err.println("Out of memory when calculating PCA.");
+ return;
}
+ calcSettings.setEnabled(true);
- rc.setPoints(points, pca.getM().rows);
+ // TODO revert progress indicator
+ rc.setEnabled(true);
rc.repaint();
- seqs = null;
this.repaint();
}
int dim1 = top - xCombobox.getSelectedIndex();
int dim2 = top - yCombobox.getSelectedIndex();
int dim3 = top - zCombobox.getSelectedIndex();
-
- float[][] scores = pca.getComponents(dim1, dim2, dim3, 100);
- for (int i = 0; i < pca.getM().rows; i++)
- {
- ((SequencePoint) rc.points.elementAt(i)).coord = scores[i];
- }
-
- rc.img = null;
- rc.rotmat.setIdentity();
- rc.initAxes();
+ pcaModel.updateRcView(dim1, dim2, dim3);
+ rc.resetView();
rc.paint(rc.getGraphics());
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == inputData)
{
showOriginalData();
}
- else
+ if (evt.getSource() == resetButton)
+ {
+ xCombobox.select(0);
+ yCombobox.select(1);
+ zCombobox.select(2);
+ doDimensionChange();
+ }
+ if (evt.getSource() == values)
{
values_actionPerformed();
}
}
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (evt.getSource() == xCombobox)
{
zCombobox_actionPerformed();
}
+ else if (evt.getSource() == labels)
+ {
+ labels_itemStateChanged(evt);
+ }
+ else if (evt.getSource() == nuclSetting)
+ {
+ if (!pcaModel.isNucleotide())
+ {
+ pcaModel.setNucleotide(true);
+ ScoreModelI scoreModel = ScoreModels.getInstance()
+ .getDefaultModel(false);
+ pcaModel.setScoreModel(scoreModel);
+ new Thread(this, "PCARecalcThread").start();
+ }
+ }
+ else if (evt.getSource() == protSetting)
+ {
+ if (pcaModel.isNucleotide())
+ {
+ pcaModel.setNucleotide(false);
+ ScoreModelI scoreModel = ScoreModels.getInstance()
+ .getDefaultModel(true);
+ pcaModel.setScoreModel(scoreModel);
+ new Thread(this, "PCARecalcThread").start();
+ }
+ }
}
protected void xCombobox_actionPerformed()
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "PCA details", 500, 500);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.pca_details"), 500, 500);
- cap.setText(pca.getDetails());
+ cap.setText(pcaModel.getDetails());
}
void showOriginalData()
{
}
;
- Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(gc);
+ Object[] alAndColsel = pcaModel.getInputData()
+ .getAlignmentAndHiddenColumns(gc);
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]);
}
}
protected Choice zCombobox = new Choice();
+ protected Button resetButton = new Button();
+
FlowLayout flowLayout1 = new FlowLayout();
BorderLayout borderLayout1 = new BorderLayout();
Menu menu2 = new Menu();
+ Menu calcSettings = new Menu();
+
protected CheckboxMenuItem labels = new CheckboxMenuItem();
+ protected CheckboxMenuItem protSetting = new CheckboxMenuItem();
+
+ protected CheckboxMenuItem nuclSetting = new CheckboxMenuItem();
+
MenuItem values = new MenuItem();
MenuItem inputData = new MenuItem();
yCombobox.addItemListener(this);
xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
xCombobox.addItemListener(this);
+ resetButton.setFont(new java.awt.Font("Verdana", 0, 12));
+ resetButton.setLabel(MessageManager.getString("action.reset"));
+ resetButton.addActionListener(this);
this.setMenuBar(menuBar1);
- menu1.setLabel("File");
- menu2.setLabel("View");
- labels.setLabel("Labels");
+ menu1.setLabel(MessageManager.getString("action.file"));
+ menu2.setLabel(MessageManager.getString("action.view"));
+ calcSettings.setLabel(MessageManager.getString("action.change_params"));
+ labels.setLabel(MessageManager.getString("label.labels"));
labels.addItemListener(this);
- values.setLabel("Output Values...");
+ values.setLabel(MessageManager.getString("label.output_values"));
values.addActionListener(this);
- inputData.setLabel("Input Data...");
+ inputData.setLabel(MessageManager.getString("label.input_data"));
+ nuclSetting
+ .setLabel(MessageManager.getString("label.nucleotide_matrix"));
+ nuclSetting.addItemListener(this);
+ protSetting.setLabel(MessageManager.getString("label.protein_matrix"));
+ protSetting.addItemListener(this);
this.add(jPanel2, BorderLayout.SOUTH);
jPanel2.add(jLabel1, null);
jPanel2.add(xCombobox, null);
jPanel2.add(yCombobox, null);
jPanel2.add(jLabel3, null);
jPanel2.add(zCombobox, null);
+ jPanel2.add(resetButton, null);
menuBar1.add(menu1);
menuBar1.add(menu2);
+ menuBar1.add(calcSettings);
menu2.add(labels);
menu1.add(values);
menu1.add(inputData);
+ calcSettings.add(nuclSetting);
+ calcSettings.add(protSetting);
inputData.addActionListener(this);
}
git://source.jalview.org / jalview.git / blobdiff