X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=57a14a0cc38e01ca3047bb47bc318c475c981458;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=adbe90693129ce7349df2bdcdc04768dfef3bce2;hpb=6403e604c7be86f97af2f1900772f3fb31abfd58;p=jalview.git
diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
old mode 100755
new mode 100644
index adbe906..57a14a0
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -1,32 +1,52 @@
/*
- * 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 2.9)
+ * Copyright (C) 2015 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.print.*;
-import javax.swing.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.jbgui.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GPCAPanel;
+import jalview.schemes.ResidueProperties;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.PCAModel;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Graphics;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.print.PageFormat;
+import java.awt.print.Printable;
+import java.awt.print.PrinterException;
+import java.awt.print.PrinterJob;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JColorChooser;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JRadioButtonMenuItem;
/**
* DOCUMENT ME!
@@ -34,27 +54,21 @@ import jalview.jbgui.*;
* @author $author$
* @version $Revision$
*/
-public class PCAPanel extends GPCAPanel implements Runnable
+public class PCAPanel extends GPCAPanel implements Runnable,
+ IProgressIndicator
{
- PCA pca;
-
- int top;
+ private IProgressIndicator progressBar;
RotatableCanvas rc;
AlignmentPanel ap;
- AlignViewport av;
+ AlignmentViewport av;
- AlignmentView seqstrings;
+ PCAModel pcaModel;
- SequenceI[] seqs;
-
- /**
- * use the identity matrix for calculating similarity between sequences.
- */
- private boolean nucleotide=false;
+ int top = 0;
/**
* Creates a new PCAPanel object.
@@ -69,11 +83,15 @@ public class PCAPanel extends GPCAPanel implements Runnable
this.av = ap.av;
this.ap = ap;
- boolean sameLength = true;
+ progressBar = new ProgressBar(statusPanel, statusBar);
- seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
- nucleotide=av.getAlignment().isNucleotide();
- if (av.getSelectionGroup() == null)
+ boolean sameLength = true;
+ boolean selected = av.getSelectionGroup() != null
+ && av.getSelectionGroup().getSize() > 0;
+ AlignmentView seqstrings = av.getAlignmentView(selected);
+ boolean nucleotide = av.getAlignment().isNucleotide();
+ SequenceI[] seqs;
+ if (!selected)
{
seqs = av.getAlignment().getSequencesArray();
}
@@ -95,17 +113,14 @@ public class PCAPanel extends GPCAPanel implements Runnable
if (!sameLength)
{
- JOptionPane
- .showMessageDialog(
- Desktop.desktop,
- "The sequences must be aligned before calculating PCA.\n"
- + "Try using the Pad function in the edit menu,\n"
- + "or one of the multiple sequence alignment web services.",
- "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.pca_sequences_not_aligned"),
+ MessageManager.getString("label.sequences_not_aligned"),
+ JOptionPane.WARNING_MESSAGE);
return;
}
-
+ pcaModel = new PCAModel(seqstrings, seqs, nucleotide);
PaintRefresher.Register(this, av.getSequenceSetId());
rc = new RotatableCanvas(ap);
@@ -114,9 +129,48 @@ public class PCAPanel extends GPCAPanel implements Runnable
worker.start();
}
+ @Override
+ protected void scoreMatrix_menuSelected()
+ {
+ scoreMatrixMenu.removeAll();
+ for (final String sm : ResidueProperties.scoreMatrices.keySet())
+ {
+ if (ResidueProperties.getScoreMatrix(sm) != null)
+ {
+ // create an entry for this score matrix for use in PCA
+ JCheckBoxMenuItem jm = new JCheckBoxMenuItem();
+ jm.setText(MessageManager
+ .getStringOrReturn("label.score_model", sm));
+ jm.setSelected(pcaModel.getScore_matrix().equals(sm));
+ if ((ResidueProperties.scoreMatrices.get(sm).isDNA() && ResidueProperties.scoreMatrices
+ .get(sm).isProtein())
+ || pcaModel.isNucleotide() == ResidueProperties.scoreMatrices
+ .get(sm).isDNA())
+ {
+ final PCAPanel us = this;
+ jm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (!pcaModel.getScore_matrix().equals(sm))
+ {
+ pcaModel.setScore_matrix(sm);
+ Thread worker = new Thread(us);
+ worker.start();
+ }
+ }
+ });
+ scoreMatrixMenu.add(jm);
+ }
+ }
+ }
+ }
+
public void bgcolour_actionPerformed(ActionEvent e)
{
- Color col = JColorChooser.showDialog(this, "Select Background Colour",
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_backgroud_colour"),
rc.bgColour);
if (col != null)
@@ -131,78 +185,83 @@ public class PCAPanel extends GPCAPanel implements Runnable
*/
public void run()
{
+ long progId = System.currentTimeMillis();
+ IProgressIndicator progress = this;
+ String message = MessageManager.getString("label.pca_recalculating");
+ if (getParent() == null)
+ {
+ progress = ap.alignFrame;
+ message = MessageManager.getString("label.pca_calculating");
+ }
+ progress.setProgressBar(message, progId);
try
{
calcSettings.setEnabled(false);
- pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide);
- 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++)
- {
- if (pca.getEigenvalue(i) > 1e-4)
- {
- comps[i] = pca.component(i);
- }
- }
-
+ pcaModel.run();
// ////////////////
xCombobox.setSelectedIndex(0);
yCombobox.setSelectedIndex(1);
zCombobox.setSelectedIndex(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++)
- {
- SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
- points.addElement(sp);
- }
-
- rc.setPoints(points, pca.getM().rows);
+ pcaModel.updateRc(rc);
// rc.invalidate();
- nuclSetting.setSelected(nucleotide);
- protSetting.setSelected(!nucleotide);
+ nuclSetting.setSelected(pcaModel.isNucleotide());
+ protSetting.setSelected(!pcaModel.isNucleotide());
+ jvVersionSetting.setSelected(pcaModel.isJvCalcMode());
+ top = pcaModel.getTop();
} catch (OutOfMemoryError er)
{
new OOMWarning("calculating PCA", er);
return;
+ } finally
+ {
+ progress.setProgressBar("", progId);
}
calcSettings.setEnabled(true);
repaint();
- if (getParent()==null)
+ if (getParent() == null)
{
addKeyListener(rc);
- Desktop.addInternalFrame(this, "Principal component analysis", 475, 450);
+ Desktop.addInternalFrame(this, MessageManager
+ .getString("label.principal_component_analysis"), 475, 450);
}
}
+
@Override
protected void nuclSetting_actionPerfomed(ActionEvent arg0)
{
- nucleotide=true;
- Thread worker = new Thread(this);
- worker.start();
+ if (!pcaModel.isNucleotide())
+ {
+ pcaModel.setNucleotide(true);
+ pcaModel.setScore_matrix("DNA");
+ Thread worker = new Thread(this);
+ worker.start();
+ }
+
}
+
@Override
protected void protSetting_actionPerfomed(ActionEvent arg0)
{
- nucleotide=false;
+
+ if (pcaModel.isNucleotide())
+ {
+ pcaModel.setNucleotide(false);
+ pcaModel.setScore_matrix("BLOSUM62");
+ Thread worker = new Thread(this);
+ worker.start();
+ }
+ }
+
+ @Override
+ protected void jvVersionSetting_actionPerfomed(ActionEvent arg0)
+ {
+ pcaModel.setJvCalcMode(jvVersionSetting.isSelected());
Thread worker = new Thread(this);
worker.start();
}
+
/**
* DOCUMENT ME!
*/
@@ -216,14 +275,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
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];
- }
-
+ pcaModel.updateRcView(dim1, dim2, dim3);
rc.img = null;
rc.rotmat.setIdentity();
rc.initAxes();
@@ -268,8 +320,9 @@ public class PCAPanel extends GPCAPanel implements Runnable
CutAndPasteTransfer cap = new CutAndPasteTransfer();
try
{
- cap.setText(pca.getDetails());
- Desktop.addInternalFrame(cap, "PCA details", 500, 500);
+ cap.setText(pcaModel.getDetails());
+ Desktop.addInternalFrame(cap,
+ MessageManager.getString("label.pca_details"), 500, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("opening PCA details", oom);
@@ -292,7 +345,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
{
// this was cut'n'pasted from the equivalent TreePanel method - we should
// make this an abstract function of all jalview analysis windows
- if (seqstrings == null)
+ if (pcaModel.getSeqtrings() == null)
{
jalview.bin.Cache.log
.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
@@ -314,7 +367,8 @@ public class PCAPanel extends GPCAPanel implements Runnable
{
}
;
- Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(gc);
+ Object[] alAndColsel = pcaModel.getSeqtrings()
+ .getAlignmentAndColumnSelection(gc);
if (alAndColsel != null && alAndColsel[0] != null)
{
@@ -342,8 +396,10 @@ public class PCAPanel extends GPCAPanel implements Runnable
// af.addSortByOrderMenuItem(ServiceName + " Ordering",
// msaorder);
- Desktop.addInternalFrame(af, "Original Data for " + this.title,
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ Desktop.addInternalFrame(af, MessageManager.formatMessage(
+ "label.original_data_for_params",
+ new String[] { this.title }), AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
}
}
/*
@@ -408,7 +464,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
*/
public void eps_actionPerformed(ActionEvent e)
{
- makePCAImage(jalview.util.ImageMaker.EPS);
+ makePCAImage(jalview.util.ImageMaker.TYPE.EPS);
}
/**
@@ -419,26 +475,34 @@ public class PCAPanel extends GPCAPanel implements Runnable
*/
public void png_actionPerformed(ActionEvent e)
{
- makePCAImage(jalview.util.ImageMaker.PNG);
+ makePCAImage(jalview.util.ImageMaker.TYPE.PNG);
}
- void makePCAImage(int type)
+ void makePCAImage(jalview.util.ImageMaker.TYPE type)
{
int width = rc.getWidth();
int height = rc.getHeight();
jalview.util.ImageMaker im;
- if (type == jalview.util.ImageMaker.PNG)
+ if (type == jalview.util.ImageMaker.TYPE.PNG)
+ {
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from PCA",
+ width, height, null, null);
+ }
+ else if (type == jalview.util.ImageMaker.TYPE.EPS)
{
- im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
- "Make PNG image from PCA", width, height, null, null);
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from PCA",
+ width, height, null, this.getTitle());
}
else
{
- im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
- "Make EPS file from PCA", width, height, null,
- this.getTitle());
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
+ width, height, null, this.getTitle());
+
}
if (im.getGraphics() != null)
@@ -528,8 +592,12 @@ public class PCAPanel extends GPCAPanel implements Runnable
CutAndPasteTransfer cap = new CutAndPasteTransfer();
try
{
- cap.setText(getPointsasCsv(false));
- Desktop.addInternalFrame(cap, "Points for " + getTitle(), 500, 500);
+ cap.setText(pcaModel.getPointsasCsv(false,
+ xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
+ zCombobox.getSelectedIndex()));
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.points_for_params", new String[] { this.getTitle() }),
+ 500, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("exporting PCA points", oom);
@@ -537,56 +605,6 @@ public class PCAPanel extends GPCAPanel implements Runnable
}
}
- private String getPointsasCsv(boolean transformed)
- {
- StringBuffer csv = new StringBuffer();
- csv.append("\"Sequence\"");
- if (transformed)
- {
- csv.append(",");
- csv.append(xCombobox.getSelectedIndex());
- csv.append(",");
- csv.append(yCombobox.getSelectedIndex());
- csv.append(",");
- csv.append(zCombobox.getSelectedIndex());
- }
- else
- {
- for (int d = 1, dmax = pca.component(1).length; d <= dmax; d++)
- {
- csv.append("," + d);
- }
- }
- csv.append("\n");
- for (int s = 0; s < seqs.length; s++)
- {
- csv.append("\"" + seqs[s].getName() + "\"");
- double fl[];
- if (!transformed)
- {
- // output pca in correct order
- fl = pca.component(s);
- for (int d = fl.length - 1; d >= 0; d--)
- {
- csv.append(",");
- csv.append(fl[d]);
- }
- }
- else
- {
- // output current x,y,z coords for points
- fl = rc.getPointPosition(s);
- for (int d = 0; d < fl.length; d++)
- {
- csv.append(",");
- csv.append(fl[d]);
- }
- }
- csv.append("\n");
- }
- return csv.toString();
- }
-
/*
* (non-Javadoc)
*
@@ -599,9 +617,12 @@ public class PCAPanel extends GPCAPanel implements Runnable
CutAndPasteTransfer cap = new CutAndPasteTransfer();
try
{
- cap.setText(getPointsasCsv(true));
- Desktop.addInternalFrame(cap, "Transformed points for " + getTitle(),
- 500, 500);
+ cap.setText(pcaModel.getPointsasCsv(true,
+ xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
+ zCombobox.getSelectedIndex()));
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.transformed_points_for_params",
+ new String[] { this.getTitle() }), 500, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("exporting transformed PCA points", oom);
@@ -609,15 +630,110 @@ public class PCAPanel extends GPCAPanel implements Runnable
}
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
+ */
@Override
+ public void setProgressBar(String message, long id)
+ {
+ progressBar.setProgressBar(message, id);
+ // if (progressBars == null)
+ // {
+ // progressBars = new Hashtable();
+ // progressBarHandlers = new Hashtable();
+ // }
+ //
+ // JPanel progressPanel;
+ // Long lId = new Long(id);
+ // GridLayout layout = (GridLayout) statusPanel.getLayout();
+ // if (progressBars.get(lId) != null)
+ // {
+ // progressPanel = (JPanel) progressBars.get(new Long(id));
+ // statusPanel.remove(progressPanel);
+ // progressBars.remove(lId);
+ // progressPanel = null;
+ // if (message != null)
+ // {
+ // statusBar.setText(message);
+ // }
+ // if (progressBarHandlers.contains(lId))
+ // {
+ // progressBarHandlers.remove(lId);
+ // }
+ // layout.setRows(layout.getRows() - 1);
+ // }
+ // else
+ // {
+ // progressPanel = new JPanel(new BorderLayout(10, 5));
+ //
+ // JProgressBar progressBar = new JProgressBar();
+ // progressBar.setIndeterminate(true);
+ //
+ // progressPanel.add(new JLabel(message), BorderLayout.WEST);
+ // progressPanel.add(progressBar, BorderLayout.CENTER);
+ //
+ // layout.setRows(layout.getRows() + 1);
+ // statusPanel.add(progressPanel);
+ //
+ // progressBars.put(lId, progressPanel);
+ // }
+ // // update GUI
+ // // setMenusForViewport();
+ // validate();
+ }
+
+ @Override
+ public void registerHandler(final long id,
+ final IProgressIndicatorHandler handler)
+ {
+ progressBar.registerHandler(id, handler);
+ // if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
+ // {
+ // throw new
+ // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
+ // }
+ // progressBarHandlers.put(new Long(id), handler);
+ // final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
+ // if (handler.canCancel())
+ // {
+ // JButton cancel = new JButton(
+ // MessageManager.getString("action.cancel"));
+ // final IProgressIndicator us = this;
+ // cancel.addActionListener(new ActionListener()
+ // {
+ //
+ // @Override
+ // public void actionPerformed(ActionEvent e)
+ // {
+ // handler.cancelActivity(id);
+ // us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
+ // new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
+ // }
+ // });
+ // progressPanel.add(cancel, BorderLayout.EAST);
+ // }
+ }
+
+ /**
+ *
+ * @return true if any progress bars are still active
+ */
+ @Override
+ public boolean operationInProgress()
+ {
+ return progressBar.operationInProgress();
+ }
+
@Override
protected void resetButton_actionPerformed(ActionEvent e)
{
- int t=top;
- top=0; // ugly - prevents dimensionChanged events from being processed
+ int t = top;
+ top = 0; // ugly - prevents dimensionChanged events from being processed
xCombobox.setSelectedIndex(0);
yCombobox.setSelectedIndex(1);
- top=t;
+ top = t;
zCombobox.setSelectedIndex(2);
}
}