/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * 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 <http://www.gnu.org/licenses/>.
*/
package jalview.gui;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class PCAPanel
- extends GPCAPanel implements Runnable
+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!
+ *
+ * @param av
+ * DOCUMENT ME!
+ * @param s
+ * DOCUMENT ME!
*/
public PCAPanel(AlignmentPanel ap)
{
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,
+ "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);
+ Desktop
+ .addInternalFrame(this, "Principal component analysis", 400,
+ 400);
PaintRefresher.Register(this, av.getSequenceSetId());
public void bgcolour_actionPerformed(ActionEvent e)
{
Color col = JColorChooser.showDialog(this, "Select Background Colour",
- rc.bgColour);
+ rc.bgColour);
if (col != null)
{
// Now find the component coordinates
int ii = 0;
- while ( (ii < seqs.length) && (seqs[ii] != null))
+ while ((ii < seqs.length) && (seqs[ii] != null))
{
ii++;
}
}
}
- //////////////////
+ // ////////////////
xCombobox.setSelectedIndex(0);
yCombobox.setSelectedIndex(1);
zCombobox.setSelectedIndex(2);
addKeyListener(rc);
- }
- catch (OutOfMemoryError er)
+ } catch (OutOfMemoryError er)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Out of memory calculating PCA!!"
- +
- "\nSee help files for increasing Java Virtual Machine memory."
- , "Out of memory",
- JOptionPane.WARNING_MESSAGE);
- System.out.println("PCAPanel: " + er);
- System.gc();
+ new OOMWarning("calculating PCA", er);
}
for (int i = 0; i < pca.getM().rows; i++)
{
- ( (SequencePoint) rc.points.elementAt(i)).coord = scores[i];
+ ((SequencePoint) rc.points.elementAt(i)).coord = scores[i];
}
rc.img = null;
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void xCombobox_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void yCombobox_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void zCombobox_actionPerformed(ActionEvent e)
{
public void outputValues_actionPerformed(ActionEvent e)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
- Desktop.addInternalFrame(cap, "PCA details", 500,
- 500);
-
- cap.setText(pca.getDetails());
+ 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)
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
+ // 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.");
+ 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)
+ // 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 {
+ 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) {};
+ 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.getAlignment().getDataset();
+ 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
- );
+ 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!!<<<
+ // >>>This is a fix for the moment, until a better solution is
+ // found!!<<<
// af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
- // af.addSortByOrderMenuItem(ServiceName + " Ordering",
- // msaorder);
+ // af.addSortByOrderMenuItem(ServiceName + " Ordering",
+ // msaorder);
Desktop.addInternalFrame(af, "Original Data for " + this.title,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ 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);
+ /*
+ * 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
+ class PCAPrinter extends Thread implements Printable
{
public void run()
{
try
{
printJob.print();
- }
- catch (Exception PrintException)
+ } catch (Exception PrintException)
{
PrintException.printStackTrace();
}
}
public int print(Graphics pg, PageFormat pf, int pi)
- throws PrinterException
+ throws PrinterException
{
- pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
+ pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
rc.drawBackground(pg, rc.bgColour);
rc.drawScene(pg);
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void eps_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void png_actionPerformed(ActionEvent e)
{
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);
+ 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());
+ im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
+ "Make EPS file from PCA", width, height, null, this
+ .getTitle());
}
if (im.getGraphics() != null)
void buildAssociatedViewMenu()
{
- AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av.
- getSequenceSetId());
+ AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
+ .getSequenceSetId());
if (aps.length == 1 && rc.av == aps[0].av)
{
associateViewsMenu.setVisible(false);
associateViewsMenu.setVisible(true);
- if ( (viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
+ if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
{
viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
}
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<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)
+ * @see jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event.ActionEvent)
+ */
+ protected void outputProjPoints_actionPerformed(ActionEvent e)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ try {
+ cap.setText(getPointsasCsv(true));
+ Desktop.addInternalFrame(cap, "Transformed points for "+getTitle(), 500, 500);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("exporting transformed PCA points",oom);
+ cap.dispose();
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff