import jalview.analysis.*;
import jalview.datamodel.*;
import jalview.jbgui.*;
+import jalview.viewmodel.PCAModel;
/**
* DOCUMENT ME!
* @author $author$
* @version $Revision$
*/
-public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator
+public class PCAPanel extends GPCAPanel implements Runnable,
+ IProgressIndicator
{
- PCA pca;
-
- int top;
-
RotatableCanvas rc;
AlignmentPanel ap;
AlignViewport av;
- AlignmentView seqstrings;
-
- SequenceI[] seqs;
+ PCAModel pcaModel;
- /**
- * use the identity matrix for calculating similarity between sequences.
- */
- private boolean nucleotide=false;
+ int top = 0;
/**
* Creates a new PCAPanel object.
this.ap = ap;
boolean sameLength = true;
-
- seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
- nucleotide=av.getAlignment().isNucleotide();
- if (av.getSelectionGroup() == null)
+ 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();
}
return;
}
-
+ pcaModel = new PCAModel(seqstrings, seqs, nucleotide);
PaintRefresher.Register(this, av.getSequenceSetId());
rc = new RotatableCanvas(ap);
*/
public void run()
{
- long progId=System.currentTimeMillis();
- IProgressIndicator progress=this;
- String message="Recalculating PCA";
- if (getParent()==null) {
- progress=ap.alignFrame;
+ long progId = System.currentTimeMillis();
+ IProgressIndicator progress = this;
+ String message = "Recalculating PCA";
+ if (getParent() == null)
+ {
+ progress = ap.alignFrame;
message = "Calculating PCA";
}
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 {
+ } 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, "Principal component analysis", 475,
+ 450);
}
}
+
@Override
protected void nuclSetting_actionPerfomed(ActionEvent arg0)
{
- if (!nucleotide)
+ if (!pcaModel.isNucleotide())
{
- nucleotide=true;
- Thread worker = new Thread(this);
- worker.start();
+ pcaModel.setNucleotide(true);
+ Thread worker = new Thread(this);
+ worker.start();
}
-
+
}
+
@Override
protected void protSetting_actionPerfomed(ActionEvent arg0)
{
-
- if (nucleotide)
+
+ if (pcaModel.isNucleotide())
{
- nucleotide=false;
+ pcaModel.setNucleotide(false);
+ 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!
*/
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();
CutAndPasteTransfer cap = new CutAndPasteTransfer();
try
{
- cap.setText(pca.getDetails());
+ cap.setText(pcaModel.getDetails());
Desktop.addInternalFrame(cap, "PCA details", 500, 500);
} catch (OutOfMemoryError oom)
{
{
// 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.");
{
}
;
- Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(gc);
+ Object[] alAndColsel = pcaModel.getSeqtrings()
+ .getAlignmentAndColumnSelection(gc);
if (alAndColsel != null && alAndColsel[0] != null)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
try
{
- cap.setText(getPointsasCsv(false));
+ cap.setText(pcaModel.getPointsasCsv(false,
+ xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
+ zCombobox.getSelectedIndex()));
Desktop.addInternalFrame(cap, "Points for " + getTitle(), 500, 500);
} catch (OutOfMemoryError oom)
{
}
}
- 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)
*
CutAndPasteTransfer cap = new CutAndPasteTransfer();
try
{
- cap.setText(getPointsasCsv(true));
+ cap.setText(pcaModel.getPointsasCsv(true,
+ xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
+ zCombobox.getSelectedIndex()));
Desktop.addInternalFrame(cap, "Transformed points for " + getTitle(),
500, 500);
} catch (OutOfMemoryError oom)
/*
* (non-Javadoc)
- *
+ *
* @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
*/
@Override
}
/**
- *
+ *
* @return true if any progress bars are still active
*/
@Override
}
return false;
}
+
@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);
}
}
git://source.jalview.org / jalview.git / blobdiff