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