3 import jalview.datamodel.*;
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4 import jalview.analysis.PCA;
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5 import jalview.jbgui.*;
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7 import java.awt.event.*;
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11 public class PCAPanel extends GPCAPanel implements Runnable
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23 public PCAPanel(AlignViewport av, SequenceI[] s) {
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26 if(av.getSelectionGroup().getSize()>3)
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28 s = new Sequence[av.getSelectionGroup().getSize()];
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29 for(int i=0; i<s.length; i++)
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30 s[i] = av.getSelectionGroup().getSequenceAt(i);
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36 s = new Sequence[av.getAlignment().getHeight()];
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37 for (int i = 0; i < av.getAlignment().getHeight(); i++)
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38 s[i] = av.getAlignment().getSequenceAt(i);
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41 //////////////////////This part was done in PCATHread originally. Is it too slow???
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45 // Now find the component coordinates
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47 while (ii < s.length && s[ii] != null)
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52 double[][] comps = new double[ii][ii];
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54 for (int i=0; i < ii; i++ )
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56 if (pca.getEigenvalue(i) > 1e-4)
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58 comps[i] = pca.component(i);
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64 xCombobox.setSelectedIndex(0);
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65 yCombobox.setSelectedIndex(1);
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66 zCombobox.setSelectedIndex(2);
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68 top = pca.getM().rows-1;
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70 Vector points = new Vector();
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71 float[][] scores = pca.getComponents(top-1,top-2,top-3,100);
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73 for (int i =0; i < pca.getM().rows; i++ )
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75 SequencePoint sp = new SequencePoint(s[i],scores[i]);
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76 points.addElement(sp);
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79 rc = new RotatableCanvas(av,points,pca.getM().rows);
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83 add(rc, BorderLayout.CENTER);
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87 void doDimensionChange()
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92 int dim1 = top - xCombobox.getSelectedIndex();
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93 int dim2 = top - yCombobox.getSelectedIndex();
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94 int dim3 = top - zCombobox.getSelectedIndex();
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96 float[][] scores = pca.getComponents(dim1,dim2,dim3,100);
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97 for (int i=0; i < pca.getM().rows; i++) {
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98 ((SequencePoint)rc.points.elementAt(i)).coord = scores[i];
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102 rc.rotmat.setIdentity();
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104 rc.paint(rc.getGraphics());
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107 protected void xCombobox_actionPerformed(ActionEvent e)
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109 doDimensionChange();
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112 protected void yCombobox_actionPerformed(ActionEvent e)
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114 doDimensionChange();
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117 protected void zCombobox_actionPerformed(ActionEvent e)
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119 doDimensionChange();
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