3 import jalview.datamodel.*;
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4 import jalview.analysis.*;
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5 import jalview.jbgui.GTreePanel;
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7 import java.awt.event.*;
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10 import jalview.util.*;
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11 import javax.swing.*;
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12 import java.awt.print.*;
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14 import java.awt.image.*;
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15 import org.jibble.epsgraphics.*;
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16 import javax.imageio.*;
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21 public class TreePanel extends GTreePanel
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29 TreeCanvas treeCanvas;
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32 public NJTree getTree()
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37 public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)
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42 this.pwtype = pwtype;
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47 String longestName = "";
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48 seq = new Sequence [seqVector.size()];
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49 for (int i=0;i < seqVector.size();i++)
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51 seq[i] = (Sequence) seqVector.elementAt(i);
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52 if(seq[i].getName().length()>longestName.length())
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53 longestName = seq[i].getName();
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56 tree = new NJTree(seq, type, pwtype, start, end);
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58 treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
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60 tree.reCount(tree.getTopNode());
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61 tree.findHeight(tree.getTopNode());
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62 scrollPane.setViewportView(treeCanvas);
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65 public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
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66 String type, String pwtype)
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69 // These are probably only arbitrary strings reflecting source of tree
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71 this.pwtype = pwtype;
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74 end = seqVector.size();
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76 String longestName = "";
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77 seq = new Sequence [seqVector.size()];
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78 for (int i=0;i < seqVector.size();i++)
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80 seq[i] = (Sequence) seqVector.elementAt(i);
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81 if(seq[i].getName().length()>longestName.length())
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82 longestName = seq[i].getName();
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84 // This constructor matches sequence names to treenodes and sets up the tree layouts.
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85 tree = new NJTree(seq, newtree);
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87 tree.reCount(tree.getTopNode());
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88 tree.findHeight(tree.getTopNode());
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90 treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
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91 treeCanvas.setShowBootstrap(newtree.HasBootstrap());
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92 treeCanvas.setShowDistances(newtree.HasDistances());
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93 scrollPane.setViewportView(treeCanvas);
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97 public String getText(String format)
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102 public void saveAsNewick_actionPerformed(ActionEvent e)
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105 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
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106 getProperty("LAST_DIRECTORY"));
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107 chooser.setFileView(new JalviewFileView());
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108 chooser.setDialogTitle("Save tree as newick file");
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109 chooser.setToolTipText("Save");
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110 int value = chooser.showSaveDialog(null);
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111 if (value == JalviewFileChooser.APPROVE_OPTION) {
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112 String choice = chooser.getSelectedFile().getPath();
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113 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent());
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115 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
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116 String output = fout.print(false,true); // distances only
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117 java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
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118 out.println(output);
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121 catch (Exception ex) {
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122 ex.printStackTrace();
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127 protected void printMenu_actionPerformed(ActionEvent e)
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130 //Putting in a thread avoids Swing painting problems
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131 treeCanvas.startPrinting();
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134 protected void fitToWindow_actionPerformed(ActionEvent e)
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136 treeCanvas.fitToWindow = fitToWindow.isSelected();
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141 protected void fontSize_actionPerformed(ActionEvent e)
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143 if( treeCanvas==null )
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146 String size = fontSize.getText().substring( fontSize.getText().indexOf("-")+1);
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148 Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,
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149 "Select font size",
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151 JOptionPane.QUESTION_MESSAGE,
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152 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
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153 ,"Font Size - "+size);
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154 if(selection!=null)
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156 fontSize.setText("Font Size - " + selection);
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158 int i = Integer.parseInt(selection.toString());
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159 treeCanvas.setFontSize(i);
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161 scrollPane.setViewportView(treeCanvas);
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165 protected void distanceMenu_actionPerformed(ActionEvent e)
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167 treeCanvas.setShowDistances(distanceMenu.isSelected());
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170 protected void bootstrapMenu_actionPerformed(ActionEvent e)
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172 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
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176 protected void epsTree_actionPerformed(ActionEvent e)
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178 int width = treeCanvas.getWidth(), height=treeCanvas.getHeight();
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181 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
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183 new String[]{"eps"},
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184 new String[]{"Encapsulated Postscript"},
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185 "Encapsulated Postscript");
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186 chooser.setFileView(new jalview.io.JalviewFileView());
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187 chooser.setDialogTitle("Create EPS file from tree");
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188 chooser.setToolTipText("Save");
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190 int value = chooser.showSaveDialog(this);
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191 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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194 jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getParent());
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195 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
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196 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
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199 treeCanvas.draw(pg, width, height);
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204 catch (Exception ex)
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206 ex.printStackTrace();
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210 protected void pngTree_actionPerformed(ActionEvent e)
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212 int width = treeCanvas.getWidth(), height = treeCanvas.getHeight();
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215 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
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216 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
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217 new String[] {"png"},
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218 new String[] {"Portable network graphics"},
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219 "Portable network graphics");
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221 chooser.setFileView(new jalview.io.JalviewFileView());
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222 chooser.setDialogTitle("Create PNG image from tree");
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223 chooser.setToolTipText("Save");
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225 int value = chooser.showSaveDialog(this);
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226 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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229 jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getParent());
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230 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
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232 BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
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233 Graphics png = bi.getGraphics();
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235 treeCanvas.draw(png, width, height);
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237 ImageIO.write(bi, "png", out);
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240 catch (Exception ex)
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242 ex.printStackTrace();
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