/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, 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 file is part of Jalview.
*
- * 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.
+ * 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.
*
- * 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 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;
*/
public class PCAPanel extends GPCAPanel implements Runnable
{
+
PCA pca;
int top;
* Creates a new PCAPanel object.
*
* @param av
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param s
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public PCAPanel(AlignmentPanel ap)
{
return;
}
- Desktop
- .addInternalFrame(this, "Principal component analysis", 400,
- 400);
+ Desktop.addInternalFrame(this, "Principal component analysis", 400, 400);
PaintRefresher.Register(this, av.getSequenceSetId());
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void xCombobox_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void yCombobox_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * 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)
* 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");
- * }
+ * "\n"); }
*
* Desktop.addInternalFrame(cap, "Original Data", 400, 400);
*/
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void eps_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void png_actionPerformed(ActionEvent e)
{
else
{
im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
- "Make EPS file from PCA", width, height, null, this
- .getTitle());
+ "Make EPS file from PCA", width, height, null,
+ this.getTitle());
}
if (im.getGraphics() != null)
}
+ /*
+ * (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