1 package jalview.appletgui;
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3 import jalview.datamodel.*;
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4 import jalview.analysis.*;
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5 import jalview.jbappletgui.GTreePanel;
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6 import java.awt.event.*;
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8 import jalview.io.NewickFile;
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11 public class TreePanel extends GTreePanel
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19 TreeCanvas treeCanvas;
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22 public NJTree getTree()
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27 public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)
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32 this.pwtype = pwtype;
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37 String longestName = "";
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38 seq = new Sequence [seqVector.size()];
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39 for (int i=0;i < seqVector.size();i++)
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41 seq[i] = (Sequence) seqVector.elementAt(i);
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42 if(seq[i].getName().length()>longestName.length())
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43 longestName = seq[i].getName();
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46 tree = new NJTree(seq, type, pwtype, start, end);
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48 treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
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50 tree.reCount(tree.getTopNode());
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51 tree.findHeight(tree.getTopNode());
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52 scrollPane.add(treeCanvas);
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56 public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
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57 String type, String pwtype)
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60 // These are probably only arbitrary strings reflecting source of tree
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62 this.pwtype = pwtype;
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65 end = seqVector.size();
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67 String longestName = "";
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68 seq = new Sequence [seqVector.size()];
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69 for (int i=0;i < seqVector.size();i++)
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71 seq[i] = (Sequence) seqVector.elementAt(i);
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72 if(seq[i].getName().length()>longestName.length())
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73 longestName = seq[i].getName();
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75 // This constructor matches sequence names to treenodes and sets up the tree layouts.
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76 tree = new NJTree(seq, newtree);
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78 tree.reCount(tree.getTopNode());
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79 tree.findHeight(tree.getTopNode());
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81 treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
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82 treeCanvas.setShowBootstrap(newtree.HasBootstrap());
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83 bootstrapMenu.setState(newtree.HasBootstrap());
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84 treeCanvas.setShowDistances(newtree.HasDistances());
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85 distanceMenu.setState(newtree.HasDistances());
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86 scrollPane.add(treeCanvas);
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92 public String getText(String format) {
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96 protected void fitToWindow_actionPerformed(ActionEvent e)
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98 treeCanvas.fitToWindow = fitToWindow.getState();
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102 public void newickOutput_actionPerformed(ActionEvent actionEvent)
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104 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
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105 String output = fout.print(false, true);
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106 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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107 cap.setText(output);
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108 java.awt.Frame frame = new java.awt.Frame();
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110 jalview.bin.JalviewLite.addFrame(frame, type+" "+pwtype, 500,500);
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115 protected void fontSize_actionPerformed(ActionEvent e)
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117 /* if( treeCanvas==null )
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120 String size = fontSize.getLabel().substring( fontSize.getLabel().indexOf("-")+1);
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122 Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,
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123 "Select font size",
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125 JOptionPane.QUESTION_MESSAGE,
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126 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
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127 ,"Font Size - "+size);
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128 if(selection!=null)
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130 fontSize.setText("Font Size - " + selection);
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132 int i = Integer.parseInt(selection.toString());
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133 treeCanvas.setFontSize(i);
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135 scrollPane.setViewportView(treeCanvas);
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139 protected void distanceMenu_actionPerformed(ActionEvent e)
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141 treeCanvas.setShowDistances(distanceMenu.getState());
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144 protected void bootstrapMenu_actionPerformed(ActionEvent e)
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146 treeCanvas.setShowBootstrap(bootstrapMenu.getState());
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