2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.gui;
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21 import jalview.analysis.*;
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23 import jalview.datamodel.*;
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25 import jalview.jbgui.*;
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28 import java.awt.event.*;
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31 import javax.swing.JOptionPane;
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38 * @version $Revision$
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40 public class PCAPanel extends GPCAPanel implements Runnable
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49 * Creates a new PCAPanel object.
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51 * @param av DOCUMENT ME!
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52 * @param s DOCUMENT ME!
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54 public PCAPanel(AlignViewport av, SequenceI[] s)
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58 if ((av.getSelectionGroup() != null) &&
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59 (av.getSelectionGroup().getSize() > 3))
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61 seqs = new Sequence[av.getSelectionGroup().getSize()];
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63 for (int i = 0; i < s.length; i++)
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65 seqs[i] = av.getSelectionGroup().getSequenceAt(i);
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71 seqs = new Sequence[av.getAlignment().getHeight()];
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73 for (int i = 0; i < av.getAlignment().getHeight(); i++)
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75 seqs[i] = av.getAlignment().getSequenceAt(i);
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80 rc = new RotatableCanvas(av);
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81 add(rc, BorderLayout.CENTER);
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82 Thread worker = new Thread(this);
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94 pca = new PCA(seqs);
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97 // Now find the component coordinates
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100 while ( (ii < seqs.length) && (seqs[ii] != null))
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105 double[][] comps = new double[ii][ii];
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107 for (int i = 0; i < ii; i++)
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109 if (pca.getEigenvalue(i) > 1e-4)
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111 comps[i] = pca.component(i);
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116 xCombobox.setSelectedIndex(0);
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117 yCombobox.setSelectedIndex(1);
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118 zCombobox.setSelectedIndex(2);
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120 top = pca.getM().rows - 1;
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122 Vector points = new Vector();
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123 float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
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125 for (int i = 0; i < pca.getM().rows; i++)
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127 SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
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128 points.addElement(sp);
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131 rc.setPoints(points, pca.getM().rows);
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135 catch(OutOfMemoryError er)
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136 { JOptionPane.showInternalMessageDialog(Desktop.desktop,
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137 "Out of memory calculating PCA!!"
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139 "\nSee help files for increasing Java Virtual Machine memory."
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141 JOptionPane.WARNING_MESSAGE);
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142 System.out.println("PCAPanel: "+er);
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152 void doDimensionChange()
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159 int dim1 = top - xCombobox.getSelectedIndex();
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160 int dim2 = top - yCombobox.getSelectedIndex();
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161 int dim3 = top - zCombobox.getSelectedIndex();
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163 float[][] scores = pca.getComponents(dim1, dim2, dim3, 100);
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165 for (int i = 0; i < pca.getM().rows; i++)
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167 ((SequencePoint) rc.points.elementAt(i)).coord = scores[i];
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171 rc.rotmat.setIdentity();
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173 rc.paint(rc.getGraphics());
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179 * @param e DOCUMENT ME!
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181 protected void xCombobox_actionPerformed(ActionEvent e)
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183 doDimensionChange();
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189 * @param e DOCUMENT ME!
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191 protected void yCombobox_actionPerformed(ActionEvent e)
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193 doDimensionChange();
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199 * @param e DOCUMENT ME!
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201 protected void zCombobox_actionPerformed(ActionEvent e)
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203 doDimensionChange();
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