X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=ad7d1fda22de641062de622c77c8b5be35c0ee74;hb=b9fbdac95abae11673f09be76494032ec0bbca74;hp=4c8a2516f65949b7f97354b20d71ac8d681ede51;hpb=4e06055734abdda4bc0dbbe9a1b88dcb806cdd2b;p=jalview.git diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index 4c8a251..ad7d1fd 100755 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -27,6 +27,7 @@ import javax.swing.*; import jalview.analysis.*; import jalview.datamodel.*; import jalview.jbgui.*; +import jalview.viewmodel.PCAModel; /** * DOCUMENT ME! @@ -34,27 +35,19 @@ import jalview.jbgui.*; * @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. @@ -71,8 +64,10 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator boolean sameLength = true; - seqstrings = av.getAlignmentView(av.getSelectionGroup() != null); - nucleotide=av.getAlignment().isNucleotide(); + AlignmentView seqstrings = av + .getAlignmentView(av.getSelectionGroup() != null); + boolean nucleotide = av.getAlignment().isNucleotide(); + SequenceI[] seqs; if (av.getSelectionGroup() == null) { seqs = av.getAlignment().getSequencesArray(); @@ -105,7 +100,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator return; } - + pcaModel = new PCAModel(seqstrings, seqs, nucleotide); PaintRefresher.Register(this, av.getSequenceSetId()); rc = new RotatableCanvas(ap); @@ -131,98 +126,81 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator */ 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! */ @@ -236,14 +214,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator 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(); @@ -288,7 +259,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator CutAndPasteTransfer cap = new CutAndPasteTransfer(); try { - cap.setText(pca.getDetails()); + cap.setText(pcaModel.getDetails()); Desktop.addInternalFrame(cap, "PCA details", 500, 500); } catch (OutOfMemoryError oom) { @@ -312,7 +283,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator { // 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."); @@ -334,7 +305,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator { } ; - Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(gc); + Object[] alAndColsel = pcaModel.getSeqtrings() + .getAlignmentAndColumnSelection(gc); if (alAndColsel != null && alAndColsel[0] != null) { @@ -548,7 +520,9 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator 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) { @@ -557,56 +531,6 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator } } - 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) * @@ -619,7 +543,9 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator 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) @@ -635,7 +561,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator /* * (non-Javadoc) - * + * * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long) */ @Override @@ -719,7 +645,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator } /** - * + * * @return true if any progress bars are still active */ @Override @@ -731,14 +657,15 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator } 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); } }