src/jalview/gui/TreePanel.java

   1 package jalview.gui;\r
   2 \r
   3 import jalview.datamodel.*;\r
   4 import jalview.analysis.*;\r
   5 import jalview.jbgui.GTreePanel;\r
   6 import jalview.io.*;\r
   7 import java.awt.event.*;\r
   8 import java.util.*;\r
   9 import java.io.*;\r
  10 import jalview.util.*;\r
  11 import javax.swing.*;\r
  12 import java.awt.print.*;\r
  13 import java.awt.*;\r
  14 import java.awt.image.*;\r
  15 import org.jibble.epsgraphics.*;\r
  16 import javax.imageio.*;\r
  17 \r
  18 \r
  19 \r
  20 \r
  21 public class TreePanel extends GTreePanel\r
  22 {\r
  23   SequenceI[] seq;\r
  24   String type;\r
  25   String pwtype;\r
  26   AlignViewport av;\r
  27   int start;\r
  28   int end;\r
  29   TreeCanvas treeCanvas;\r
  30   NJTree tree;\r
  31 \r
  32   public NJTree getTree()\r
  33   {\r
  34     return tree;\r
  35   }\r
  36 \r
  37   public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)\r
  38   {\r
  39     super();\r
  40 \r
  41     this.type = type;\r
  42     this.pwtype = pwtype;\r
  43 \r
  44     start = s;\r
  45     end = e;\r
  46 \r
  47     String longestName = "";\r
  48     seq = new Sequence [seqVector.size()];\r
  49     for (int i=0;i < seqVector.size();i++)\r
  50     {\r
  51       seq[i] = (Sequence) seqVector.elementAt(i);\r
  52       if(seq[i].getName().length()>longestName.length())\r
  53         longestName = seq[i].getName();\r
  54     }\r
  55 \r
  56     tree = new NJTree(seq, type, pwtype, start, end);\r
  57 \r
  58     treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
  59 \r
  60     tree.reCount(tree.getTopNode());\r
  61     tree.findHeight(tree.getTopNode());\r
  62     scrollPane.setViewportView(treeCanvas);\r
  63 \r
  64   }\r
  65   public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,\r
  66                    String type, String pwtype)\r
  67     {\r
  68       super();\r
  69       // These are probably only  arbitrary strings reflecting source of tree\r
  70       this.type = type;\r
  71       this.pwtype = pwtype;\r
  72 \r
  73       start = 0;\r
  74       end = seqVector.size();\r
  75 \r
  76       String longestName = "";\r
  77       seq = new Sequence [seqVector.size()];\r
  78       for (int i=0;i < seqVector.size();i++)\r
  79       {\r
  80         seq[i] = (Sequence) seqVector.elementAt(i);\r
  81       }\r
  82       // This constructor matches sequence names to treenodes and sets up the tree layouts.\r
  83       tree = new NJTree(seq, newtree);\r
  84       // Now have to calculate longest name based on the leaves\r
  85       Vector leaves = tree.findLeaves(tree.getTopNode(),new Vector());\r
  86 \r
  87       for (int i=0;i < leaves.size();i++)\r
  88         if (longestName.length()<((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName().length())\r
  89           longestName = TreeCanvas.PLACEHOLDER+((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName();\r
  90 \r
  91       tree.reCount(tree.getTopNode());\r
  92       tree.findHeight(tree.getTopNode());\r
  93 \r
  94       treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
  95       treeCanvas.setShowBootstrap(newtree.HasBootstrap());\r
  96       treeCanvas.setShowDistances(newtree.HasDistances());\r
  97       scrollPane.setViewportView(treeCanvas);\r
  98       distanceMenu.setSelected(newtree.HasDistances());\r
  99       bootstrapMenu.setSelected(newtree.HasBootstrap());\r
 100       if (true) // JBPNote TODO: preference for always marking placeholders in new associated tree\r
 101         placeholdersMenu.setSelected(treeCanvas.markPlaceholders);\r
 102 \r
 103     }\r
 104 \r
 105     public String getText(String format)\r
 106     {\r
 107       return null;\r
 108     }\r
 109 \r
 110     public void saveAsNewick_actionPerformed(ActionEvent e)\r
 111     {\r
 112 \r
 113   JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
 114         getProperty("LAST_DIRECTORY"));\r
 115     chooser.setFileView(new JalviewFileView());\r
 116     chooser.setDialogTitle("Save tree as newick file");\r
 117     chooser.setToolTipText("Save");\r
 118     int value = chooser.showSaveDialog(null);\r
 119     if (value == JalviewFileChooser.APPROVE_OPTION) {\r
 120       String choice =  chooser.getSelectedFile().getPath();\r
 121       jalview.bin.Cache.setProperty("LAST_DIRECTORY",  chooser.getSelectedFile().getParent());\r
 122       try{\r
 123         jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
 124         String output = fout.print(false,true); // distances only\r
 125         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );\r
 126         out.println(output);\r
 127         out.close();\r
 128       }\r
 129       catch (Exception ex) {\r
 130         ex.printStackTrace();\r
 131       }\r
 132     }\r
 133   }\r
 134 \r
 135   protected void printMenu_actionPerformed(ActionEvent e)\r
 136   {\r
 137 \r
 138     //Putting in a thread avoids Swing painting problems\r
 139     treeCanvas.startPrinting();\r
 140   }\r
 141 \r
 142   protected void fitToWindow_actionPerformed(ActionEvent e)\r
 143   {\r
 144     treeCanvas.fitToWindow = fitToWindow.isSelected();\r
 145     repaint();\r
 146   }\r
 147 \r
 148 \r
 149   protected void fontSize_actionPerformed(ActionEvent e)\r
 150   {\r
 151     if( treeCanvas==null )\r
 152      return;\r
 153 \r
 154    String size = fontSize.getText().substring( fontSize.getText().indexOf("-")+1);\r
 155 \r
 156    Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
 157                                "Select font size",\r
 158                                "Font size",\r
 159                                JOptionPane.QUESTION_MESSAGE,\r
 160                                null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
 161                                ,"Font Size - "+size);\r
 162    if(selection!=null)\r
 163    {\r
 164      fontSize.setText("Font Size - " + selection);\r
 165 \r
 166      int i = Integer.parseInt(selection.toString());\r
 167      treeCanvas.setFontSize(i);\r
 168    }\r
 169     scrollPane.setViewportView(treeCanvas);\r
 170 \r
 171   }\r
 172 \r
 173   protected void distanceMenu_actionPerformed(ActionEvent e)\r
 174   {\r
 175     treeCanvas.setShowDistances(distanceMenu.isSelected());\r
 176   }\r
 177 \r
 178   protected void bootstrapMenu_actionPerformed(ActionEvent e)\r
 179   {\r
 180     treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());\r
 181   }\r
 182 \r
 183   protected void placeholdersMenu_actionPerformed(ActionEvent e)\r
 184     {\r
 185       treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());\r
 186   }\r
 187 \r
 188   protected void epsTree_actionPerformed(ActionEvent e)\r
 189   {\r
 190     int width = treeCanvas.getWidth(), height=treeCanvas.getHeight();\r
 191     try\r
 192     {\r
 193       jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 194           "LAST_DIRECTORY"),\r
 195               new String[]{"eps"},\r
 196               new String[]{"Encapsulated Postscript"},\r
 197               "Encapsulated Postscript");\r
 198       chooser.setFileView(new jalview.io.JalviewFileView());\r
 199       chooser.setDialogTitle("Create EPS file from tree");\r
 200       chooser.setToolTipText("Save");\r
 201 \r
 202       int value = chooser.showSaveDialog(this);\r
 203       if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
 204         return;\r
 205 \r
 206       jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getParent());\r
 207       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
 208       EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);\r
 209 \r
 210 \r
 211       treeCanvas.draw(pg, width, height);\r
 212 \r
 213         pg.flush();\r
 214         pg.close();\r
 215     }\r
 216     catch (Exception ex)\r
 217     {\r
 218       ex.printStackTrace();\r
 219     }\r
 220   }\r
 221 \r
 222   protected void pngTree_actionPerformed(ActionEvent e)\r
 223  {\r
 224   int width = treeCanvas.getWidth(), height = treeCanvas.getHeight();\r
 225     try\r
 226     {\r
 227       jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
 228           jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
 229           new String[] {"png"},\r
 230           new String[] {"Portable network graphics"},\r
 231           "Portable network graphics");\r
 232 \r
 233       chooser.setFileView(new jalview.io.JalviewFileView());\r
 234       chooser.setDialogTitle("Create PNG image from tree");\r
 235       chooser.setToolTipText("Save");\r
 236 \r
 237       int value = chooser.showSaveDialog(this);\r
 238       if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
 239         return;\r
 240 \r
 241       jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getParent());\r
 242       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
 243 \r
 244       BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);\r
 245       Graphics png = bi.getGraphics();\r
 246 \r
 247       treeCanvas.draw(png, width, height);\r
 248 \r
 249         ImageIO.write(bi, "png", out);\r
 250         out.close();\r
 251     }\r
 252     catch (Exception ex)\r
 253     {\r
 254       ex.printStackTrace();\r
 255     }\r
 256   }\r
 257 \r
 258 }\r