X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FPCAPanel.java;h=44711d77c42d5ee2d9019c1f1999d8acc974258e;hb=0899f9541714086b75987a4ba3d35037a6d6224b;hp=3e87f17a07073741689c867da1ec503e30b2a93c;hpb=6dd0025ba30d818f7112e2edd4a6c0becdee4910;p=jalview.git diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java index 3e87f17..44711d7 100755 --- a/src/jalview/appletgui/PCAPanel.java +++ b/src/jalview/appletgui/PCAPanel.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -24,28 +24,18 @@ import java.awt.event.*; import jalview.analysis.*; import jalview.datamodel.*; +import jalview.viewmodel.PCAModel; public class PCAPanel extends EmbmenuFrame implements Runnable, ActionListener, ItemListener { - PCA pca; - - int top; - RotatableCanvas rc; AlignViewport av; - AlignmentView seqstrings; - - SequenceI[] seqs; - - - /** - * use the identity matrix for calculating similarity between sequences. - */ - private boolean useidentity=false; + PCAModel pcaModel; + int top = 0; public PCAPanel(AlignViewport av) { @@ -65,15 +55,17 @@ public class PCAPanel extends EmbmenuFrame implements Runnable, } this.av = av; - seqstrings = av.getAlignmentView(av.getSelectionGroup() != null); - useidentity=av.getAlignment().isNucleotide(); + AlignmentView seqstrings = av + .getAlignmentView(av.getSelectionGroup() != null); + boolean nucleotide = av.getAlignment().isNucleotide(); + SequenceI[] seqs; if (av.getSelectionGroup() == null) { - seqs = av.alignment.getSequencesArray(); + seqs = av.getAlignment().getSequencesArray(); } else { - seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment); + seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment()); } SeqCigar sq[] = seqstrings.getSequences(); int length = sq[0].getWidth(); @@ -87,13 +79,14 @@ public class PCAPanel extends EmbmenuFrame implements Runnable, return; } } + pcaModel = new PCAModel(seqstrings, seqs, nucleotide); rc = new RotatableCanvas(av); embedMenuIfNeeded(rc); add(rc, BorderLayout.CENTER); jalview.bin.JalviewLite.addFrame(this, "Principal component analysis", - 400, 400); + 475, 400); Thread worker = new Thread(this); worker.start(); @@ -104,46 +97,32 @@ public class PCAPanel extends EmbmenuFrame implements Runnable, */ public void run() { - pca = new PCA(seqstrings.getSequenceStrings(' '), useidentity); - 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++) + // TODO progress indicator + calcSettings.setEnabled(false); + rc.setEnabled(false); + try { - if (pca.getEigenvalue(i) > 1e-4) - { - comps[i] = pca.component(i); - } - } - - // //////////////// - xCombobox.select(0); - yCombobox.select(1); - zCombobox.select(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++) + nuclSetting.setState(pcaModel.isNucleotide()); + protSetting.setState(!pcaModel.isNucleotide()); + pcaModel.run(); + // //////////////// + xCombobox.select(0); + yCombobox.select(1); + zCombobox.select(2); + + pcaModel.updateRc(rc); + // rc.invalidate(); + top = pcaModel.getTop(); + } catch (OutOfMemoryError x) { - SequencePoint sp = new SequencePoint(seqs[i], scores[i]); - points.addElement(sp); + System.err.println("Out of memory when calculating PCA."); + return; } + calcSettings.setEnabled(true); - rc.setPoints(points, pca.getM().rows); + // TODO revert progress indicator + rc.setEnabled(true); rc.repaint(); - seqs = null; this.repaint(); } @@ -153,17 +132,11 @@ public class PCAPanel extends EmbmenuFrame implements Runnable, { return; } - + 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(); @@ -176,7 +149,14 @@ public class PCAPanel extends EmbmenuFrame implements Runnable, { showOriginalData(); } - else + if (evt.getSource() == resetButton) + { + xCombobox.select(0); + yCombobox.select(1); + zCombobox.select(2); + doDimensionChange(); + } + if (evt.getSource() == values) { values_actionPerformed(); } @@ -196,6 +176,26 @@ public class PCAPanel extends EmbmenuFrame implements Runnable, { zCombobox_actionPerformed(); } + else if (evt.getSource() == labels) + { + labels_itemStateChanged(evt); + } + else if (evt.getSource() == nuclSetting) + { + if (!pcaModel.isNucleotide()) + { + pcaModel.setNucleotide(true); + new Thread(this).start(); + } + } + else if (evt.getSource() == protSetting) + { + if (pcaModel.isNucleotide()) + { + pcaModel.setNucleotide(false); + new Thread(this).start(); + } + } } protected void xCombobox_actionPerformed() @@ -221,7 +221,7 @@ public class PCAPanel extends EmbmenuFrame implements Runnable, frame.add(cap); jalview.bin.JalviewLite.addFrame(frame, "PCA details", 500, 500); - cap.setText(pca.getDetails()); + cap.setText(pcaModel.getDetails()); } void showOriginalData() @@ -242,7 +242,8 @@ public class PCAPanel extends EmbmenuFrame implements Runnable, { } ; - Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(gc); + Object[] alAndColsel = pcaModel.getSeqtrings() + .getAlignmentAndColumnSelection(gc); if (alAndColsel != null && alAndColsel[0] != null) { @@ -273,6 +274,8 @@ public class PCAPanel extends EmbmenuFrame implements Runnable, protected Choice zCombobox = new Choice(); + protected Button resetButton = new Button(); + FlowLayout flowLayout1 = new FlowLayout(); BorderLayout borderLayout1 = new BorderLayout(); @@ -283,8 +286,14 @@ public class PCAPanel extends EmbmenuFrame implements Runnable, Menu menu2 = new Menu(); + Menu calcSettings = new Menu(); + protected CheckboxMenuItem labels = new CheckboxMenuItem(); + protected CheckboxMenuItem protSetting = new CheckboxMenuItem(); + + protected CheckboxMenuItem nuclSetting = new CheckboxMenuItem(); + MenuItem values = new MenuItem(); MenuItem inputData = new MenuItem(); @@ -306,14 +315,22 @@ public class PCAPanel extends EmbmenuFrame implements Runnable, yCombobox.addItemListener(this); xCombobox.setFont(new java.awt.Font("Verdana", 0, 12)); xCombobox.addItemListener(this); + resetButton.setFont(new java.awt.Font("Verdana", 0, 12)); + resetButton.setLabel("Reset"); + resetButton.addActionListener(this); this.setMenuBar(menuBar1); menu1.setLabel("File"); menu2.setLabel("View"); + calcSettings.setLabel("Change Parameters"); labels.setLabel("Labels"); labels.addItemListener(this); values.setLabel("Output Values..."); values.addActionListener(this); inputData.setLabel("Input Data..."); + nuclSetting.setLabel("Nucleotide matrix"); + nuclSetting.addItemListener(this); + protSetting.setLabel("Protein matrix"); + protSetting.addItemListener(this); this.add(jPanel2, BorderLayout.SOUTH); jPanel2.add(jLabel1, null); jPanel2.add(xCombobox, null); @@ -321,11 +338,15 @@ public class PCAPanel extends EmbmenuFrame implements Runnable, jPanel2.add(yCombobox, null); jPanel2.add(jLabel3, null); jPanel2.add(zCombobox, null); + jPanel2.add(resetButton, null); menuBar1.add(menu1); menuBar1.add(menu2); + menuBar1.add(calcSettings); menu2.add(labels); menu1.add(values); menu1.add(inputData); + calcSettings.add(nuclSetting); + calcSettings.add(protSetting); inputData.addActionListener(this); }