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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28 s = new Sequence[av.getAlignment().getHeight()];
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29 for (int i = 0; i < av.getAlignment().getHeight(); i++)
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30 s[i] = av.getAlignment().getSequenceAt(i);
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33 //////////////////////This part was done in PCATHread originally. Is it too slow???
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37 // Now find the component coordinates
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39 while (ii < s.length && s[ii] != null)
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44 double[][] comps = new double[ii][ii];
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46 for (int i=0; i < ii; i++ )
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48 if (pca.getEigenvalue(i) > 1e-4)
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50 comps[i] = pca.component(i);
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56 xCombobox.setSelectedIndex(0);
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57 yCombobox.setSelectedIndex(1);
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58 zCombobox.setSelectedIndex(2);
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60 top = pca.getM().rows-1;
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62 Vector points = new Vector();
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63 float[][] scores = pca.getComponents(top-1,top-2,top-3,100);
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65 for (int i =0; i < pca.getM().rows; i++ ) {
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66 SequencePoint sp = new SequencePoint(s[i],scores[i]);
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67 points.addElement(sp);
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69 rc = new RotatableCanvas(av,points,pca.getM().rows);
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73 add(rc, BorderLayout.CENTER);
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77 void doDimensionChange()
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82 int dim1 = top - xCombobox.getSelectedIndex();
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83 int dim2 = top - yCombobox.getSelectedIndex();
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84 int dim3 = top - zCombobox.getSelectedIndex();
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86 float[][] scores = pca.getComponents(dim1,dim2,dim3,100);
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87 for (int i=0; i < pca.getM().rows; i++) {
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88 ((SequencePoint)rc.points.elementAt(i)).coord = scores[i];
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92 rc.rotmat.setIdentity();
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94 rc.paint(rc.getGraphics());
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97 protected void xCombobox_actionPerformed(ActionEvent e)
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99 doDimensionChange();
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102 protected void yCombobox_actionPerformed(ActionEvent e)
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104 doDimensionChange();
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107 protected void zCombobox_actionPerformed(ActionEvent e)
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109 doDimensionChange();
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