src/jalview/gui/TreePanel.java

   1 /*\r
   2 * Jalview - A Sequence Alignment Editor and Viewer\r
   3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4 *\r
   5 * This program is free software; you can redistribute it and/or\r
   6 * modify it under the terms of the GNU General Public License\r
   7 * as published by the Free Software Foundation; either version 2\r
   8 * of the License, or (at your option) any later version.\r
   9 *\r
  10 * This program is distributed in the hope that it will be useful,\r
  11 * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13 * GNU General Public License for more details.\r
  14 *\r
  15 * You should have received a copy of the GNU General Public License\r
  16 * along with this program; if not, write to the Free Software\r
  17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18 */\r
  19 \r
  20 package jalview.gui;\r
  21 \r
  22 import jalview.datamodel.*;\r
  23 import jalview.analysis.*;\r
  24 import jalview.jbgui.GTreePanel;\r
  25 import jalview.io.*;\r
  26 import java.awt.event.*;\r
  27 import java.util.*;\r
  28 import java.io.*;\r
  29 import javax.swing.*;\r
  30 import java.awt.*;\r
  31 import java.awt.image.*;\r
  32 import org.jibble.epsgraphics.*;\r
  33 import javax.imageio.*;\r
  34 \r
  35 \r
  36 \r
  37 public class TreePanel extends GTreePanel\r
  38 {\r
  39   SequenceI[] seq;\r
  40   String type;\r
  41   String pwtype;\r
  42   AlignViewport av;\r
  43   int start;\r
  44   int end;\r
  45   TreeCanvas treeCanvas;\r
  46   NJTree tree;\r
  47 \r
  48   public NJTree getTree()\r
  49   {\r
  50     return tree;\r
  51   }\r
  52 \r
  53   public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)\r
  54   {\r
  55     super();\r
  56 \r
  57     this.type = type;\r
  58     this.pwtype = pwtype;\r
  59 \r
  60     start = s;\r
  61     end = e;\r
  62 \r
  63     String longestName = "";\r
  64     seq = new Sequence [seqVector.size()];\r
  65     for (int i=0;i < seqVector.size();i++)\r
  66     {\r
  67       seq[i] = (Sequence) seqVector.elementAt(i);\r
  68       if(seq[i].getName().length()>longestName.length())\r
  69         longestName = seq[i].getName();\r
  70     }\r
  71 \r
  72     tree = new NJTree(seq, type, pwtype, start, end);\r
  73 \r
  74     treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
  75     treeCanvas.setShowDistances(true); // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default\r
  76     setViewStateFromTreeCanvas(treeCanvas);\r
  77     tree.reCount(tree.getTopNode());\r
  78     tree.findHeight(tree.getTopNode());\r
  79     scrollPane.setViewportView(treeCanvas);\r
  80 \r
  81   }\r
  82   private void setViewStateFromTreeCanvas(TreeCanvas tree) {\r
  83     // update view menu state from treeCanvas render state\r
  84     distanceMenu.setSelected(tree.showDistances);\r
  85     bootstrapMenu.setSelected(tree.showBootstrap);\r
  86     placeholdersMenu.setSelected(tree.markPlaceholders);\r
  87   }\r
  88 \r
  89   private void setTreeCanvasFromViewState(TreeCanvas tree) {\r
  90       // update view menu state from treeCanvas render state\r
  91       tree.showDistances = distanceMenu.isSelected();\r
  92       tree.showBootstrap = bootstrapMenu.isSelected();\r
  93       tree.markPlaceholders = placeholdersMenu.isSelected();\r
  94     }\r
  95 \r
  96 \r
  97   public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,\r
  98                    String type, String pwtype)\r
  99     {\r
 100       super();\r
 101       // These are probably only  arbitrary strings reflecting source of tree\r
 102       this.type = type;\r
 103       this.pwtype = pwtype;\r
 104 \r
 105       start = 0;\r
 106       end = seqVector.size();\r
 107 \r
 108       String longestName = "";\r
 109       seq = new Sequence [seqVector.size()];\r
 110       for (int i=0;i < seqVector.size();i++)\r
 111       {\r
 112         seq[i] = (Sequence) seqVector.elementAt(i);\r
 113       }\r
 114       // This constructor matches sequence names to treenodes and sets up the tree layouts.\r
 115       tree = new NJTree(seq, newtree);\r
 116       // Now have to calculate longest name based on the leaves\r
 117       Vector leaves = tree.findLeaves(tree.getTopNode(),new Vector());\r
 118       boolean has_placeholders = false;\r
 119       for (int i=0;i < leaves.size();i++) {\r
 120         SequenceNode lf = (SequenceNode) leaves.elementAt(i);\r
 121         if (lf.isPlaceholder())\r
 122           has_placeholders = true;\r
 123         if (longestName.length()<((Sequence) lf.element()).getName().length())\r
 124           longestName = TreeCanvas.PLACEHOLDER+((Sequence) lf.element()).getName();\r
 125       }\r
 126       tree.reCount(tree.getTopNode());\r
 127       tree.findHeight(tree.getTopNode());\r
 128 \r
 129       treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
 130       treeCanvas.setShowBootstrap(newtree.HasBootstrap());\r
 131       treeCanvas.setShowDistances(newtree.HasDistances());\r
 132       scrollPane.setViewportView(treeCanvas);\r
 133       treeCanvas.setMarkPlaceholders(has_placeholders);\r
 134       setViewStateFromTreeCanvas(treeCanvas);\r
 135       // JBPNote TODO: preference for always marking placeholders in new associated tree\r
 136     }\r
 137 \r
 138 \r
 139     public void textbox_actionPerformed(ActionEvent e)\r
 140     {\r
 141       CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
 142 \r
 143       StringBuffer buffer = new StringBuffer();\r
 144 \r
 145       if(type.equals("AV"))\r
 146         buffer.append("Average distance tree using ");\r
 147       else\r
 148         buffer.append("Neighbour joining tree using ");\r
 149 \r
 150       if(pwtype.equals("BL"))\r
 151        buffer.append("BLOSUM62");\r
 152       else\r
 153         buffer.append("PID");\r
 154 \r
 155       Desktop.addInternalFrame(cap,buffer.toString(), 500, 100);\r
 156       jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
 157       cap.setText(  fout.print(false,true) );\r
 158 \r
 159     }\r
 160 \r
 161 \r
 162     public void saveAsNewick_actionPerformed(ActionEvent e)\r
 163     {\r
 164 \r
 165   JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
 166         getProperty("LAST_DIRECTORY"));\r
 167     chooser.setFileView(new JalviewFileView());\r
 168     chooser.setDialogTitle("Save tree as newick file");\r
 169     chooser.setToolTipText("Save");\r
 170     int value = chooser.showSaveDialog(null);\r
 171     if (value == JalviewFileChooser.APPROVE_OPTION) {\r
 172       String choice =  chooser.getSelectedFile().getPath();\r
 173       jalview.bin.Cache.setProperty("LAST_DIRECTORY",  chooser.getSelectedFile().getParent());\r
 174       try{\r
 175         jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
 176         String output = fout.print(false,true); // distances only\r
 177         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );\r
 178         out.println(output);\r
 179         out.close();\r
 180       }\r
 181       catch (Exception ex) {\r
 182         ex.printStackTrace();\r
 183       }\r
 184     }\r
 185   }\r
 186 \r
 187   protected void printMenu_actionPerformed(ActionEvent e)\r
 188   {\r
 189 \r
 190     //Putting in a thread avoids Swing painting problems\r
 191     treeCanvas.startPrinting();\r
 192   }\r
 193 \r
 194   protected void fitToWindow_actionPerformed(ActionEvent e)\r
 195   {\r
 196     treeCanvas.fitToWindow = fitToWindow.isSelected();\r
 197     repaint();\r
 198   }\r
 199 \r
 200 \r
 201   protected void fontSize_actionPerformed(ActionEvent e)\r
 202   {\r
 203     if( treeCanvas==null )\r
 204      return;\r
 205 \r
 206    String size = fontSize.getText().substring( fontSize.getText().indexOf("-")+1);\r
 207 \r
 208    Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
 209                                "Select font size",\r
 210                                "Font size",\r
 211                                JOptionPane.QUESTION_MESSAGE,\r
 212                                null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
 213                                ,"Font Size - "+size);\r
 214    if(selection!=null)\r
 215    {\r
 216      fontSize.setText("Font Size - " + selection);\r
 217 \r
 218      int i = Integer.parseInt(selection.toString());\r
 219      treeCanvas.setFontSize(i);\r
 220    }\r
 221     scrollPane.setViewportView(treeCanvas);\r
 222 \r
 223   }\r
 224 \r
 225   protected void distanceMenu_actionPerformed(ActionEvent e)\r
 226   {\r
 227     treeCanvas.setShowDistances(distanceMenu.isSelected());\r
 228   }\r
 229 \r
 230   protected void bootstrapMenu_actionPerformed(ActionEvent e)\r
 231   {\r
 232     treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());\r
 233   }\r
 234 \r
 235   protected void placeholdersMenu_actionPerformed(ActionEvent e)\r
 236     {\r
 237       treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());\r
 238   }\r
 239 \r
 240   protected void epsTree_actionPerformed(ActionEvent e)\r
 241   {\r
 242     int width = treeCanvas.getWidth(), height=treeCanvas.getHeight();\r
 243     try\r
 244     {\r
 245       jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 246           "LAST_DIRECTORY"),\r
 247               new String[]{"eps"},\r
 248               new String[]{"Encapsulated Postscript"},\r
 249               "Encapsulated Postscript");\r
 250       chooser.setFileView(new jalview.io.JalviewFileView());\r
 251       chooser.setDialogTitle("Create EPS file from tree");\r
 252       chooser.setToolTipText("Save");\r
 253 \r
 254       int value = chooser.showSaveDialog(this);\r
 255       if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
 256         return;\r
 257 \r
 258       jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getParent());\r
 259       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
 260       EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);\r
 261 \r
 262 \r
 263       treeCanvas.draw(pg, width, height);\r
 264 \r
 265         pg.flush();\r
 266         pg.close();\r
 267     }\r
 268     catch (Exception ex)\r
 269     {\r
 270       ex.printStackTrace();\r
 271     }\r
 272   }\r
 273 \r
 274   protected void pngTree_actionPerformed(ActionEvent e)\r
 275  {\r
 276   int width = treeCanvas.getWidth(), height = treeCanvas.getHeight();\r
 277     try\r
 278     {\r
 279       jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
 280           jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
 281           new String[] {"png"},\r
 282           new String[] {"Portable network graphics"},\r
 283           "Portable network graphics");\r
 284 \r
 285       chooser.setFileView(new jalview.io.JalviewFileView());\r
 286       chooser.setDialogTitle("Create PNG image from tree");\r
 287       chooser.setToolTipText("Save");\r
 288 \r
 289       int value = chooser.showSaveDialog(this);\r
 290       if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
 291         return;\r
 292 \r
 293       jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getParent());\r
 294       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
 295 \r
 296       BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);\r
 297       Graphics png = bi.getGraphics();\r
 298 \r
 299       treeCanvas.draw(png, width, height);\r
 300 \r
 301         ImageIO.write(bi, "png", out);\r
 302         out.close();\r
 303     }\r
 304     catch (Exception ex)\r
 305     {\r
 306       ex.printStackTrace();\r
 307     }\r
 308   }\r
 309 \r
 310 }\r