/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* 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.
*
* 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 .
*/
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.*;
/**
* DOCUMENT ME!
*
* @author $author$
* @version $Revision$
*/
public class PCAPanel extends GPCAPanel implements Runnable
{
PCA pca;
int top;
RotatableCanvas rc;
AlignmentPanel ap;
AlignViewport av;
AlignmentView seqstrings;
SequenceI[] seqs;
/**
* Creates a new PCAPanel object.
*
* @param av
* DOCUMENT ME!
* @param s
* DOCUMENT ME!
*/
public PCAPanel(AlignmentPanel ap)
{
this.av = ap.av;
this.ap = ap;
boolean sameLength = true;
seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
if (av.getSelectionGroup() == null)
{
seqs = av.alignment.getSequencesArray();
}
else
{
seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
}
SeqCigar sq[] = seqstrings.getSequences();
int length = sq[0].getWidth();
for (int i = 0; i < seqs.length; i++)
{
if (sq[i].getWidth() != length)
{
sameLength = false;
break;
}
}
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);
return;
}
Desktop
.addInternalFrame(this, "Principal component analysis", 400,
400);
PaintRefresher.Register(this, av.getSequenceSetId());
rc = new RotatableCanvas(ap);
this.getContentPane().add(rc, BorderLayout.CENTER);
Thread worker = new Thread(this);
worker.start();
}
public void bgcolour_actionPerformed(ActionEvent e)
{
Color col = JColorChooser.showDialog(this, "Select Background Colour",
rc.bgColour);
if (col != null)
{
rc.bgColour = col;
}
rc.repaint();
}
/**
* DOCUMENT ME!
*/
public void run()
{
try
{
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++)
{
if (pca.getEigenvalue(i) > 1e-4)
{
comps[i] = pca.component(i);
}
}
// ////////////////
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);
rc.repaint();
addKeyListener(rc);
} catch (OutOfMemoryError er)
{
new OOMWarning("calculating PCA", er);
}
}
/**
* DOCUMENT ME!
*/
void doDimensionChange()
{
if (top == 0)
{
return;
}
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();
rc.paint(rc.getGraphics());
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
protected void xCombobox_actionPerformed(ActionEvent e)
{
doDimensionChange();
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
protected void yCombobox_actionPerformed(ActionEvent e)
{
doDimensionChange();
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
protected void zCombobox_actionPerformed(ActionEvent e)
{
doDimensionChange();
}
public void outputValues_actionPerformed(ActionEvent e)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
try {
cap.setText(pca.getDetails());
Desktop.addInternalFrame(cap, "PCA details", 500, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("opening PCA details",oom);
cap.dispose();
}
}
public void showLabels_actionPerformed(ActionEvent e)
{
rc.showLabels(showLabels.getState());
}
public void print_actionPerformed(ActionEvent e)
{
PCAPrinter printer = new PCAPrinter();
printer.start();
}
public void originalSeqData_actionPerformed(ActionEvent e)
{
// 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)
{
jalview.bin.Cache.log
.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
return;
}
// decide if av alignment is sufficiently different to original data to
// warrant a new window to be created
// create new alignmnt window with hidden regions (unhiding hidden regions
// yields unaligned seqs)
// or create a selection box around columns in alignment view
// test Alignment(SeqCigar[])
char gc = '-';
try
{
// we try to get the associated view's gap character
// but this may fail if the view was closed...
gc = av.getGapCharacter();
} catch (Exception ex)
{
}
;
Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(gc);
if (alAndColsel != null && alAndColsel[0] != null)
{
// AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
Alignment dataset = (av != null && av.getAlignment() != null) ? av
.getAlignment().getDataset() : null;
if (dataset != null)
{
al.setDataset(dataset);
}
if (true)
{
// make a new frame!
AlignFrame af = new AlignFrame(al,
(ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
// >>>This is a fix for the moment, until a better solution is
// found!!<<<
// af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
// af.addSortByOrderMenuItem(ServiceName + " Ordering",
// msaorder);
Desktop.addInternalFrame(af, "Original Data for " + this.title,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
}
}
/*
* CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i <
* seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 +
* "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] +
* "\n"); }
*
* Desktop.addInternalFrame(cap, "Original Data", 400, 400);
*/
}
class PCAPrinter extends Thread implements Printable
{
public void run()
{
PrinterJob printJob = PrinterJob.getPrinterJob();
PageFormat pf = printJob.pageDialog(printJob.defaultPage());
printJob.setPrintable(this, pf);
if (printJob.printDialog())
{
try
{
printJob.print();
} catch (Exception PrintException)
{
PrintException.printStackTrace();
}
}
}
public int print(Graphics pg, PageFormat pf, int pi)
throws PrinterException
{
pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
rc.drawBackground(pg, rc.bgColour);
rc.drawScene(pg);
if (rc.drawAxes == true)
{
rc.drawAxes(pg);
}
if (pi == 0)
{
return Printable.PAGE_EXISTS;
}
else
{
return Printable.NO_SUCH_PAGE;
}
}
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
public void eps_actionPerformed(ActionEvent e)
{
makePCAImage(jalview.util.ImageMaker.EPS);
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
public void png_actionPerformed(ActionEvent e)
{
makePCAImage(jalview.util.ImageMaker.PNG);
}
void makePCAImage(int type)
{
int width = rc.getWidth();
int height = rc.getHeight();
jalview.util.ImageMaker im;
if (type == jalview.util.ImageMaker.PNG)
{
im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
"Make PNG image from PCA", width, height, null, null);
}
else
{
im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
"Make EPS file from PCA", width, height, null, this
.getTitle());
}
if (im.getGraphics() != null)
{
rc.drawBackground(im.getGraphics(), Color.black);
rc.drawScene(im.getGraphics());
if (rc.drawAxes == true)
{
rc.drawAxes(im.getGraphics());
}
im.writeImage();
}
}
public void viewMenu_menuSelected()
{
buildAssociatedViewMenu();
}
void buildAssociatedViewMenu()
{
AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
.getSequenceSetId());
if (aps.length == 1 && rc.av == aps[0].av)
{
associateViewsMenu.setVisible(false);
return;
}
associateViewsMenu.setVisible(true);
if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
{
viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
}
associateViewsMenu.removeAll();
JRadioButtonMenuItem item;
ButtonGroup buttonGroup = new ButtonGroup();
int i, iSize = aps.length;
final PCAPanel thisPCAPanel = this;
for (i = 0; i < iSize; i++)
{
final AlignmentPanel ap = aps[i];
item = new JRadioButtonMenuItem(ap.av.viewName, ap.av == rc.av);
buttonGroup.add(item);
item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent evt)
{
rc.applyToAllViews = false;
rc.av = ap.av;
rc.ap = ap;
PaintRefresher.Register(thisPCAPanel, ap.av.getSequenceSetId());
}
});
associateViewsMenu.add(item);
}
final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
buttonGroup.add(itemf);
itemf.setSelected(rc.applyToAllViews);
itemf.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent evt)
{
rc.applyToAllViews = itemf.isSelected();
}
});
associateViewsMenu.add(itemf);
}
/* (non-Javadoc)
* @see jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent)
*/
protected void outputPoints_actionPerformed(ActionEvent e)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
try {
cap.setText(getPointsasCsv(false));
Desktop.addInternalFrame(cap, "Points for "+getTitle(), 500, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("exporting PCA points",oom);
cap.dispose();
}
}
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=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