/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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
*
* This file is part of Jalview.
*
return;
}
- Desktop
- .addInternalFrame(this, "Principal component analysis", 400,
- 400);
+ Desktop.addInternalFrame(this, "Principal component analysis", 400, 400);
PaintRefresher.Register(this, av.getSequenceSetId());
public void outputValues_actionPerformed(ActionEvent e)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
- try {
+ try
+ {
cap.setText(pca.getDetails());
Desktop.addInternalFrame(cap, "PCA details", 500, 500);
} catch (OutOfMemoryError oom)
{
- new OOMWarning("opening PCA details",oom);
+ new OOMWarning("opening PCA details", oom);
cap.dispose();
}
}
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)
associateViewsMenu.add(itemf);
}
- /* (non-Javadoc)
- * @see jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent)
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
+ * )
*/
protected void outputPoints_actionPerformed(ActionEvent e)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
- try {
+ try
+ {
cap.setText(getPointsasCsv(false));
- Desktop.addInternalFrame(cap, "Points for "+getTitle(), 500, 500);
+ Desktop.addInternalFrame(cap, "Points for " + getTitle(), 500, 500);
} catch (OutOfMemoryError oom)
{
- new OOMWarning("exporting PCA points",oom);
+ new OOMWarning("exporting PCA points", oom);
cap.dispose();
}
}
{
StringBuffer csv = new StringBuffer();
csv.append("\"Sequence\"");
- if (transformed) {
+ 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++)
+ }
+ else
+ {
+ for (int d = 1, dmax = pca.component(1).length; d <= dmax; d++)
{
- csv.append(","+d);
+ csv.append("," + d);
}
}
csv.append("\n");
- for (int s=0;s<seqs.length;s++)
+ for (int s = 0; s < seqs.length; s++)
{
- csv.append("\""+seqs[s].getName()+"\"");
+ csv.append("\"" + seqs[s].getName() + "\"");
double fl[];
- if (!transformed) {
+ if (!transformed)
+ {
// output pca in correct order
fl = pca.component(s);
- for (int d=fl.length-1; d>=0;d--)
+ for (int d = fl.length - 1; d >= 0; d--)
{
csv.append(",");
csv.append(fl[d]);
}
- } else {
- // output current x,y,z coords for points
+ }
+ else
+ {
+ // output current x,y,z coords for points
fl = rc.getPointPosition(s);
- for (int d=0; d<fl.length;d++)
+ for (int d = 0; d < fl.length; d++)
{
csv.append(",");
csv.append(fl[d]);
return csv.toString();
}
- /* (non-Javadoc)
- * @see jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event.ActionEvent)
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event
+ * .ActionEvent)
*/
protected void outputProjPoints_actionPerformed(ActionEvent e)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
- try {
+ try
+ {
cap.setText(getPointsasCsv(true));
- Desktop.addInternalFrame(cap, "Transformed points for "+getTitle(), 500, 500);
+ Desktop.addInternalFrame(cap, "Transformed points for " + getTitle(),
+ 500, 500);
} catch (OutOfMemoryError oom)
{
- new OOMWarning("exporting transformed PCA points",oom);
+ new OOMWarning("exporting transformed PCA points", oom);
cap.dispose();
}
}