1 package jalview.appletgui;
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3 import jalview.datamodel.*;
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4 import jalview.io.NewickFile;
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5 import jalview.analysis.*;
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6 import jalview.jbappletgui.GTreePanel;
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7 import java.awt.event.*;
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9 import jalview.io.NewickFile;
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12 public class TreePanel extends GTreePanel
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20 TreeCanvas treeCanvas;
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23 public NJTree getTree()
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28 public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)
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33 this.pwtype = pwtype;
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38 String longestName = "";
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39 seq = new Sequence [seqVector.size()];
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40 for (int i=0;i < seqVector.size();i++)
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42 seq[i] = (Sequence) seqVector.elementAt(i);
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43 if(seq[i].getName().length()>longestName.length())
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44 longestName = seq[i].getName();
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47 tree = new NJTree(seq, type, pwtype, start, end);
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49 treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
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51 tree.reCount(tree.getTopNode());
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52 tree.findHeight(tree.getTopNode());
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53 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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73 // This constructor matches sequence names to treenodes and sets up the tree layouts.
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74 tree = new NJTree(seq, newtree);
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75 // Now have to calculate longest name based on the leaves
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76 Vector leaves = tree.findLeaves(tree.getTopNode(),new Vector());
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78 for (int i=0;i < leaves.size();i++)
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79 if (longestName.length()<((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName().length())
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80 longestName = TreeCanvas.PLACEHOLDER+((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName();
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82 tree.reCount(tree.getTopNode());
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83 tree.findHeight(tree.getTopNode());
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85 treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
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86 treeCanvas.setShowBootstrap(newtree.HasBootstrap());
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87 treeCanvas.setShowDistances(newtree.HasDistances());
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88 distanceMenu.setState(newtree.HasDistances());
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89 bootstrapMenu.setState(newtree.HasBootstrap());
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90 if (true) // JBPNote TODO: preference for always marking placeholders in new associated tree
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91 placeholdersMenu.setState(treeCanvas.markPlaceholders);
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92 scrollPane.add(treeCanvas);
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96 public String getText(String format) {
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100 protected void fitToWindow_actionPerformed(ActionEvent e)
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102 treeCanvas.fitToWindow = fitToWindow.getState();
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106 public void newickOutput_actionPerformed(ActionEvent actionEvent)
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108 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
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109 String output = fout.print(false, true);
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110 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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111 cap.setText(output);
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112 java.awt.Frame frame = new java.awt.Frame();
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114 jalview.bin.JalviewLite.addFrame(frame, type+" "+pwtype, 500,100);
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119 protected void fontSize_actionPerformed(ActionEvent e)
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121 /* if( treeCanvas==null )
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124 String size = fontSize.getLabel().substring( fontSize.getLabel().indexOf("-")+1);
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126 Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,
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127 "Select font size",
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129 JOptionPane.QUESTION_MESSAGE,
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130 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
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131 ,"Font Size - "+size);
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132 if(selection!=null)
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134 fontSize.setText("Font Size - " + selection);
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136 int i = Integer.parseInt(selection.toString());
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137 treeCanvas.setFontSize(i);
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139 scrollPane.setViewportView(treeCanvas);
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143 protected void distanceMenu_actionPerformed(ActionEvent e)
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145 treeCanvas.setShowDistances(distanceMenu.getState());
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148 protected void bootstrapMenu_actionPerformed(ActionEvent e)
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150 treeCanvas.setShowBootstrap(bootstrapMenu.getState());
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153 protected void placeholdersMenu_actionPerformed(ActionEvent e)
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155 treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
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