X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPCAPanel.java;h=0a4e1c55f2143b7b669ee45f81a6428f617c585b;hb=4a3def9f59cefe629c9a33d87483283aee085928;hp=a5268bff97b2cd22c9424d5464aab1840d9a3556;hpb=3d136290d42e4f4ae2deeed8ce3b9dae7c6e2eec;p=jalview.git diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java old mode 100755 new mode 100644 index a5268bf..0a4e1c5 --- a/src/jalview/appletgui/PCAPanel.java +++ b/src/jalview/appletgui/PCAPanel.java @@ -1,49 +1,70 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, 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 + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * 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. - * - * 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 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ - package jalview.appletgui; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import jalview.analysis.*; -import jalview.datamodel.*; - -public class PCAPanel - extends EmbmenuFrame implements Runnable, ActionListener, ItemListener +import jalview.analysis.scoremodels.ScoreModels; +import jalview.analysis.scoremodels.SimilarityParams; +import jalview.api.analysis.ScoreModelI; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentView; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.SeqCigar; +import jalview.datamodel.SequenceI; +import jalview.util.MessageManager; +import jalview.viewmodel.PCAModel; + +import java.awt.BorderLayout; +import java.awt.Button; +import java.awt.CheckboxMenuItem; +import java.awt.Choice; +import java.awt.Color; +import java.awt.FlowLayout; +import java.awt.Frame; +import java.awt.Label; +import java.awt.Menu; +import java.awt.MenuBar; +import java.awt.MenuItem; +import java.awt.Panel; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; + +public class PCAPanel extends EmbmenuFrame + implements Runnable, ActionListener, ItemListener { - PCA pca; - int top; RotatableCanvas rc; + AlignViewport av; - SequenceI[] seqs; - AlignmentView seqstrings; - public PCAPanel(AlignViewport av) + PCAModel pcaModel; + + int top = 0; + + public PCAPanel(AlignViewport viewport) { try { jbInit(); - } - catch (Exception e) + } catch (Exception e) { e.printStackTrace(); } @@ -55,15 +76,20 @@ public class PCAPanel zCombobox.addItem("dim " + i); } - this.av = av; - seqstrings = av.getAlignmentView(av.getSelectionGroup() != null); - if (av.getSelectionGroup() == null) + this.av = viewport; + boolean selected = viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().getSize() > 0; + AlignmentView seqstrings = viewport.getAlignmentView(selected); + boolean nucleotide = viewport.getAlignment().isNucleotide(); + SequenceI[] seqs; + if (!selected) { - seqs = av.alignment.getSequencesArray(); + seqs = viewport.getAlignment().getSequencesArray(); } else { - seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment); + seqs = viewport.getSelectionGroup() + .getSequencesInOrder(viewport.getAlignment()); } SeqCigar sq[] = seqstrings.getSequences(); int length = sq[0].getWidth(); @@ -72,67 +98,61 @@ public class PCAPanel { if (sq[i].getWidth() != length) { - System.out.println("Sequences must be equal length for PCA analysis"); + System.out + .println("Sequences must be equal length for PCA analysis"); return; } } - rc = new RotatableCanvas(av); + ScoreModelI scoreModel = ScoreModels.getInstance() + .getDefaultModel(!nucleotide); + pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel, + SimilarityParams.SeqSpace); + + rc = new RotatableCanvas(viewport); embedMenuIfNeeded(rc); add(rc, BorderLayout.CENTER); - jalview.bin.JalviewLite.addFrame(this, "Principal component analysis", - 400, 400); + jalview.bin.JalviewLite.addFrame(this, + MessageManager.getString("label.principal_component_analysis"), + 475, 400); - Thread worker = new Thread(this); + Thread worker = new Thread(this, "PCACalc"); worker.start(); } /** * DOCUMENT ME! */ + @Override public void run() { - pca = new PCA(seqstrings.getSequenceStrings(' ')); - 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.calculate(); + // //////////////// + 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(); } @@ -146,31 +166,32 @@ public class PCAPanel 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]; - } - - rc.img = null; - rc.rotmat.setIdentity(); - rc.initAxes(); + pcaModel.updateRcView(dim1, dim2, dim3); + rc.resetView(); rc.paint(rc.getGraphics()); } + @Override public void actionPerformed(ActionEvent evt) { if (evt.getSource() == inputData) { showOriginalData(); } - else + if (evt.getSource() == resetButton) + { + xCombobox.select(0); + yCombobox.select(1); + zCombobox.select(2); + doDimensionChange(); + } + if (evt.getSource() == values) { values_actionPerformed(); } } + @Override public void itemStateChanged(ItemEvent evt) { if (evt.getSource() == xCombobox) @@ -185,6 +206,32 @@ public class PCAPanel { zCombobox_actionPerformed(); } + else if (evt.getSource() == labels) + { + labels_itemStateChanged(evt); + } + else if (evt.getSource() == nuclSetting) + { + if (!pcaModel.isNucleotide()) + { + pcaModel.setNucleotide(true); + ScoreModelI scoreModel = ScoreModels.getInstance() + .getDefaultModel(false); + pcaModel.setScoreModel(scoreModel); + new Thread(this, "PCARecalc").start(); + } + } + else if (evt.getSource() == protSetting) + { + if (pcaModel.isNucleotide()) + { + pcaModel.setNucleotide(false); + ScoreModelI scoreModel = ScoreModels.getInstance() + .getDefaultModel(true); + pcaModel.setScoreModel(scoreModel); + new Thread(this, "PCARecalc").start(); + } + } } protected void xCombobox_actionPerformed() @@ -208,29 +255,41 @@ public class PCAPanel CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "PCA details", 500, 500); + jalview.bin.JalviewLite.addFrame(frame, + MessageManager.getString("label.pca_details"), 500, 500); - cap.setText(pca.getDetails()); + cap.setText(pcaModel.getDetails()); } void showOriginalData() { - // decide if av alignment is sufficiently different to original data to warrant a new window to be created - // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs) + // decide if av alignment is sufficiently different to original data to + // warrant a new window to be created + // create new alignmnt window with hidden regions (unhiding hidden regions + // yields unaligned seqs) // or create a selection box around columns in alignment view // test Alignment(SeqCigar[]) - Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(av. - getGapCharacter()); + char gc = '-'; + try + { + // we try to get the associated view's gap character + // but this may fail if the view was closed... + gc = av.getGapCharacter(); + } catch (Exception ex) + { + } + ; + Object[] alAndColsel = pcaModel.getInputData() + .getAlignmentAndHiddenColumns(gc); if (alAndColsel != null && alAndColsel[0] != null) { - Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]); - AlignFrame af = new AlignFrame(al, - av.applet, - "Original Data for PCA", - false); + Alignment al = new Alignment((SequenceI[]) alAndColsel[0]); + AlignFrame af = new AlignFrame(al, av.applet, "Original Data for PCA", + false); - af.viewport.setHiddenColumns( (ColumnSelection) alAndColsel[1]); + af.viewport.getAlignment() + .setHiddenColumns((HiddenColumns) alAndColsel[1]); } } @@ -240,23 +299,44 @@ public class PCAPanel } Panel jPanel2 = new Panel(); + Label jLabel1 = new Label(); + Label jLabel2 = new Label(); + Label jLabel3 = new Label(); + protected Choice xCombobox = new Choice(); + protected Choice yCombobox = new Choice(); + protected Choice zCombobox = new Choice(); + + protected Button resetButton = new Button(); + FlowLayout flowLayout1 = new FlowLayout(); + BorderLayout borderLayout1 = new BorderLayout(); + MenuBar menuBar1 = new MenuBar(); + Menu menu1 = new Menu(); + 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(); - private void jbInit() - throws Exception + private void jbInit() throws Exception { this.setLayout(borderLayout1); jPanel2.setLayout(flowLayout1); @@ -273,14 +353,23 @@ public class PCAPanel 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(MessageManager.getString("action.reset")); + resetButton.addActionListener(this); this.setMenuBar(menuBar1); - menu1.setLabel("File"); - menu2.setLabel("View"); - labels.setLabel("Labels"); + menu1.setLabel(MessageManager.getString("action.file")); + menu2.setLabel(MessageManager.getString("action.view")); + calcSettings.setLabel(MessageManager.getString("action.change_params")); + labels.setLabel(MessageManager.getString("label.labels")); labels.addItemListener(this); - values.setLabel("Output Values..."); + values.setLabel(MessageManager.getString("label.output_values")); values.addActionListener(this); - inputData.setLabel("Input Data..."); + inputData.setLabel(MessageManager.getString("label.input_data")); + nuclSetting + .setLabel(MessageManager.getString("label.nucleotide_matrix")); + nuclSetting.addItemListener(this); + protSetting.setLabel(MessageManager.getString("label.protein_matrix")); + protSetting.addItemListener(this); this.add(jPanel2, BorderLayout.SOUTH); jPanel2.add(jLabel1, null); jPanel2.add(xCombobox, null); @@ -288,11 +377,15 @@ public class PCAPanel 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); }