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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82 // This constructor matches sequence names to treenodes and sets up the tree layouts.
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83 tree = new NJTree(seq, newtree);
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84 // Now have to calculate longest name based on the leaves
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85 Vector leaves = tree.findLeaves(tree.getTopNode(),new Vector());
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87 for (int i=0;i < leaves.size();i++)
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88 if (longestName.length()<((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName().length())
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89 longestName = TreeCanvas.PLACEHOLDER+((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName();
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91 tree.reCount(tree.getTopNode());
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92 tree.findHeight(tree.getTopNode());
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94 treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
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95 treeCanvas.setShowBootstrap(newtree.HasBootstrap());
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96 treeCanvas.setShowDistances(newtree.HasDistances());
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97 scrollPane.setViewportView(treeCanvas);
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98 distanceMenu.setSelected(newtree.HasDistances());
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99 bootstrapMenu.setSelected(newtree.HasBootstrap());
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100 if (true) // JBPNote TODO: preference for always marking placeholders in new associated tree
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101 placeholdersMenu.setSelected(treeCanvas.markPlaceholders);
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105 public String getText(String format)
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110 public void saveAsNewick_actionPerformed(ActionEvent e)
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113 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
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114 getProperty("LAST_DIRECTORY"));
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115 chooser.setFileView(new JalviewFileView());
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116 chooser.setDialogTitle("Save tree as newick file");
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117 chooser.setToolTipText("Save");
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118 int value = chooser.showSaveDialog(null);
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119 if (value == JalviewFileChooser.APPROVE_OPTION) {
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120 String choice = chooser.getSelectedFile().getPath();
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121 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent());
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123 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
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124 String output = fout.print(false,true); // distances only
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125 java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
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126 out.println(output);
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129 catch (Exception ex) {
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130 ex.printStackTrace();
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135 protected void printMenu_actionPerformed(ActionEvent e)
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138 //Putting in a thread avoids Swing painting problems
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139 treeCanvas.startPrinting();
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142 protected void fitToWindow_actionPerformed(ActionEvent e)
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144 treeCanvas.fitToWindow = fitToWindow.isSelected();
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149 protected void fontSize_actionPerformed(ActionEvent e)
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151 if( treeCanvas==null )
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154 String size = fontSize.getText().substring( fontSize.getText().indexOf("-")+1);
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156 Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,
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157 "Select font size",
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159 JOptionPane.QUESTION_MESSAGE,
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160 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
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161 ,"Font Size - "+size);
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162 if(selection!=null)
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164 fontSize.setText("Font Size - " + selection);
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166 int i = Integer.parseInt(selection.toString());
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167 treeCanvas.setFontSize(i);
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169 scrollPane.setViewportView(treeCanvas);
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173 protected void distanceMenu_actionPerformed(ActionEvent e)
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175 treeCanvas.setShowDistances(distanceMenu.isSelected());
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178 protected void bootstrapMenu_actionPerformed(ActionEvent e)
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180 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
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183 protected void placeholdersMenu_actionPerformed(ActionEvent e)
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185 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
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188 protected void epsTree_actionPerformed(ActionEvent e)
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190 int width = treeCanvas.getWidth(), height=treeCanvas.getHeight();
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193 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
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195 new String[]{"eps"},
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196 new String[]{"Encapsulated Postscript"},
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197 "Encapsulated Postscript");
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198 chooser.setFileView(new jalview.io.JalviewFileView());
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199 chooser.setDialogTitle("Create EPS file from tree");
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200 chooser.setToolTipText("Save");
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202 int value = chooser.showSaveDialog(this);
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203 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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206 jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getParent());
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207 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
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208 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
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211 treeCanvas.draw(pg, width, height);
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216 catch (Exception ex)
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218 ex.printStackTrace();
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222 protected void pngTree_actionPerformed(ActionEvent e)
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224 int width = treeCanvas.getWidth(), height = treeCanvas.getHeight();
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227 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
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228 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
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229 new String[] {"png"},
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230 new String[] {"Portable network graphics"},
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231 "Portable network graphics");
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233 chooser.setFileView(new jalview.io.JalviewFileView());
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234 chooser.setDialogTitle("Create PNG image from tree");
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235 chooser.setToolTipText("Save");
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237 int value = chooser.showSaveDialog(this);
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238 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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241 jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getParent());
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242 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
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244 BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
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245 Graphics png = bi.getGraphics();
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247 treeCanvas.draw(png, width, height);
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249 ImageIO.write(bi, "png", out);
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252 catch (Exception ex)
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254 ex.printStackTrace();
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