X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPCAPanel.java;h=0d607c04809f992ef4484f32c328c5d4418ba9db;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=845e8804b175abf5603dfcc0e865b276e6409fe9;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java old mode 100755 new mode 100644 index 845e880..0d607c0 --- a/src/jalview/appletgui/PCAPanel.java +++ b/src/jalview/appletgui/PCAPanel.java @@ -1,293 +1,376 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 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 - * 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. - * - * 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 - */ - -package jalview.appletgui; - -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import jalview.analysis.*; -import jalview.datamodel.*; - - -public class PCAPanel - extends Frame implements Runnable, ActionListener, ItemListener -{ - PCA pca; - int top; - RotatableCanvas rc; - AlignViewport av; - SequenceI [] seqs; - AlignmentView seqstrings; - - - public PCAPanel(AlignViewport av) - { - try - { - jbInit(); - } - catch (Exception e) - { - e.printStackTrace(); - } - - for (int i = 1; i < 8; i++) - { - xCombobox.addItem("dim " + i); - yCombobox.addItem("dim " + i); - zCombobox.addItem("dim " + i); - } - - this.av = av; - seqstrings = av.getAlignmentView(av.getSelectionGroup()!=null); - if(av.getSelectionGroup()==null) - { - seqs = av.alignment.getSequencesArray(); - } - else - { - seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment); - } - SeqCigar sq[]=seqstrings.getSequences(); - int length = sq[0].getWidth(); - - for (int i = 0; i < seqs.length; i++) - { - if (sq[i].getWidth() != length) - { - System.out.println("Sequences must be equal length for PCA analysis"); - return; - } - } - - - rc = new RotatableCanvas(av); - add(rc, BorderLayout.CENTER); - - jalview.bin.JalviewLite.addFrame(this, "Principal component analysis", - 400, 400); - - - Thread worker = new Thread(this); - worker.start(); - } - - /** - * DOCUMENT ME! - */ - 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++) - { - 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++) - { - SequencePoint sp = new SequencePoint(seqs[i], scores[i]); - points.addElement(sp); - } - - rc.setPoints(points, pca.getM().rows); - rc.repaint(); - seqs = null; - this.repaint(); - } - - void doDimensionChange() - { - if (top == 0) - { - 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]; - } - - rc.img = null; - rc.rotmat.setIdentity(); - rc.initAxes(); - rc.paint(rc.getGraphics()); - } - - public void actionPerformed(ActionEvent evt) - { - if(evt.getSource()==inputData) - showOriginalData(); - else - values_actionPerformed(); - } - - public void itemStateChanged(ItemEvent evt) - { - if(evt.getSource()==xCombobox) - xCombobox_actionPerformed(); - else if(evt.getSource()==yCombobox) - yCombobox_actionPerformed(); - else if(evt.getSource()==zCombobox) - zCombobox_actionPerformed(); - } - - - protected void xCombobox_actionPerformed() - { - doDimensionChange(); - } - - protected void yCombobox_actionPerformed() - { - doDimensionChange(); - } - - protected void zCombobox_actionPerformed() - { - doDimensionChange(); - } - - public void values_actionPerformed() - { - - CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null); - Frame frame = new Frame(); - frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "PCA details", 500, 500); - - cap.setText(pca.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) - // or create a selection box around columns in alignment view - // test Alignment(SeqCigar[]) - Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(av. - getGapCharacter()); - - - 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); - - af.viewport.setHiddenColumns( (ColumnSelection) alAndColsel[1] ); - } - } - - public void labels_itemStateChanged(ItemEvent itemEvent) - { - rc.showLabels( labels.getState() ); - } - 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(); - FlowLayout flowLayout1 = new FlowLayout(); - BorderLayout borderLayout1 = new BorderLayout(); - MenuBar menuBar1 = new MenuBar(); - Menu menu1 = new Menu(); - Menu menu2 = new Menu(); - protected CheckboxMenuItem labels = new CheckboxMenuItem(); - MenuItem values = new MenuItem(); - MenuItem inputData = new MenuItem(); - - private void jbInit() - throws Exception - { - this.setLayout(borderLayout1); - jPanel2.setLayout(flowLayout1); - jLabel1.setFont(new java.awt.Font("Verdana", 0, 12)); - jLabel1.setText("x="); - jLabel2.setFont(new java.awt.Font("Verdana", 0, 12)); - jLabel2.setText("y="); - jLabel3.setFont(new java.awt.Font("Verdana", 0, 12)); - jLabel3.setText("z="); - jPanel2.setBackground(Color.white); - zCombobox.setFont(new java.awt.Font("Verdana", 0, 12)); - zCombobox.addItemListener(this); - yCombobox.setFont(new java.awt.Font("Verdana", 0, 12)); - yCombobox.addItemListener(this); - xCombobox.setFont(new java.awt.Font("Verdana", 0, 12)); - xCombobox.addItemListener(this); - this.setMenuBar(menuBar1); - menu1.setLabel("File"); - menu2.setLabel("View"); - labels.setLabel("Labels"); - labels.addItemListener(this); - values.setLabel("Output Values..."); - values.addActionListener(this); - inputData.setLabel("Input Data..."); - this.add(jPanel2, BorderLayout.SOUTH); - jPanel2.add(jLabel1, null); - jPanel2.add(xCombobox, null); - jPanel2.add(jLabel2, null); - jPanel2.add(yCombobox, null); - jPanel2.add(jLabel3, null); - jPanel2.add(zCombobox, null); - menuBar1.add(menu1); - menuBar1.add(menu2); - menu2.add(labels); - menu1.add(values); - menu1.add(inputData); - inputData.addActionListener(this); - } - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) + * Copyright (C) 2015 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. + * + * 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 Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.appletgui; + +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentView; +import jalview.datamodel.ColumnSelection; +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 +{ + RotatableCanvas rc; + + AlignViewport av; + + PCAModel pcaModel; + + int top = 0; + + public PCAPanel(AlignViewport av) + { + try + { + jbInit(); + } catch (Exception e) + { + e.printStackTrace(); + } + + for (int i = 1; i < 8; i++) + { + xCombobox.addItem("dim " + i); + yCombobox.addItem("dim " + i); + zCombobox.addItem("dim " + i); + } + + this.av = av; + 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(); + } + else + { + seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment()); + } + SeqCigar sq[] = seqstrings.getSequences(); + int length = sq[0].getWidth(); + + for (int i = 0; i < seqs.length; i++) + { + if (sq[i].getWidth() != length) + { + System.out + .println("Sequences must be equal length for PCA analysis"); + return; + } + } + pcaModel = new PCAModel(seqstrings, seqs, nucleotide); + + rc = new RotatableCanvas(av); + embedMenuIfNeeded(rc); + add(rc, BorderLayout.CENTER); + + jalview.bin.JalviewLite.addFrame(this, + MessageManager.getString("label.principal_component_analysis"), + 475, 400); + + Thread worker = new Thread(this); + worker.start(); + } + + /** + * DOCUMENT ME! + */ + public void run() + { + // TODO progress indicator + calcSettings.setEnabled(false); + rc.setEnabled(false); + try + { + 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) + { + System.err.println("Out of memory when calculating PCA."); + return; + } + calcSettings.setEnabled(true); + + // TODO revert progress indicator + rc.setEnabled(true); + rc.repaint(); + this.repaint(); + } + + void doDimensionChange() + { + if (top == 0) + { + return; + } + + int dim1 = top - xCombobox.getSelectedIndex(); + int dim2 = top - yCombobox.getSelectedIndex(); + int dim3 = top - zCombobox.getSelectedIndex(); + pcaModel.updateRcView(dim1, dim2, dim3); + rc.img = null; + rc.rotmat.setIdentity(); + rc.initAxes(); + rc.paint(rc.getGraphics()); + } + + public void actionPerformed(ActionEvent evt) + { + if (evt.getSource() == inputData) + { + showOriginalData(); + } + if (evt.getSource() == resetButton) + { + xCombobox.select(0); + yCombobox.select(1); + zCombobox.select(2); + doDimensionChange(); + } + if (evt.getSource() == values) + { + values_actionPerformed(); + } + } + + public void itemStateChanged(ItemEvent evt) + { + if (evt.getSource() == xCombobox) + { + xCombobox_actionPerformed(); + } + else if (evt.getSource() == yCombobox) + { + yCombobox_actionPerformed(); + } + else if (evt.getSource() == zCombobox) + { + 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() + { + doDimensionChange(); + } + + protected void yCombobox_actionPerformed() + { + doDimensionChange(); + } + + protected void zCombobox_actionPerformed() + { + doDimensionChange(); + } + + public void values_actionPerformed() + { + + CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, + MessageManager.getString("label.pca_details"), 500, 500); + + 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) + // or create a selection box around columns in alignment view + // test Alignment(SeqCigar[]) + 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.getSeqtrings() + .getAlignmentAndColumnSelection(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); + + af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]); + } + } + + public void labels_itemStateChanged(ItemEvent itemEvent) + { + rc.showLabels(labels.getState()); + } + + 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 + { + this.setLayout(borderLayout1); + jPanel2.setLayout(flowLayout1); + jLabel1.setFont(new java.awt.Font("Verdana", 0, 12)); + jLabel1.setText("x="); + jLabel2.setFont(new java.awt.Font("Verdana", 0, 12)); + jLabel2.setText("y="); + jLabel3.setFont(new java.awt.Font("Verdana", 0, 12)); + jLabel3.setText("z="); + jPanel2.setBackground(Color.white); + zCombobox.setFont(new java.awt.Font("Verdana", 0, 12)); + zCombobox.addItemListener(this); + yCombobox.setFont(new java.awt.Font("Verdana", 0, 12)); + 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(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(MessageManager.getString("label.output_values")); + values.addActionListener(this); + 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); + jPanel2.add(jLabel2, null); + 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); + } + +}