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 \r
 124       StringBuffer buffer = new StringBuffer();\r
 125 \r
 126       if(type.equals("AV"))\r
 127         buffer.append("Average distance tree using ");\r
 128       else\r
 129         buffer.append("Neighbour joining tree using ");\r
 130 \r
 131       if(pwtype.equals("BL"))\r
 132        buffer.append("BLOSUM62");\r
 133       else\r
 134         buffer.append("PID");\r
 135 \r
 136       Desktop.addInternalFrame(cap,buffer.toString(), 500, 100);\r
 137       jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
 138       cap.setText(  fout.print(false,true) );\r
 139 \r
 140     }\r
 141 \r
 142 \r
 143     public void saveAsNewick_actionPerformed(ActionEvent e)\r
 144     {\r
 145 \r
 146   JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
 147         getProperty("LAST_DIRECTORY"));\r
 148     chooser.setFileView(new JalviewFileView());\r
 149     chooser.setDialogTitle("Save tree as newick file");\r
 150     chooser.setToolTipText("Save");\r
 151     int value = chooser.showSaveDialog(null);\r
 152     if (value == JalviewFileChooser.APPROVE_OPTION) {\r
 153       String choice =  chooser.getSelectedFile().getPath();\r
 154       jalview.bin.Cache.setProperty("LAST_DIRECTORY",  chooser.getSelectedFile().getParent());\r
 155       try{\r
 156         jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
 157         String output = fout.print(false,true); // distances only\r
 158         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );\r
 159         out.println(output);\r
 160         out.close();\r
 161       }\r
 162       catch (Exception ex) {\r
 163         ex.printStackTrace();\r
 164       }\r
 165     }\r
 166   }\r
 167 \r
 168   protected void printMenu_actionPerformed(ActionEvent e)\r
 169   {\r
 170 \r
 171     //Putting in a thread avoids Swing painting problems\r
 172     treeCanvas.startPrinting();\r
 173   }\r
 174 \r
 175   protected void fitToWindow_actionPerformed(ActionEvent e)\r
 176   {\r
 177     treeCanvas.fitToWindow = fitToWindow.isSelected();\r
 178     repaint();\r
 179   }\r
 180 \r
 181 \r
 182   protected void fontSize_actionPerformed(ActionEvent e)\r
 183   {\r
 184     if( treeCanvas==null )\r
 185      return;\r
 186 \r
 187    String size = fontSize.getText().substring( fontSize.getText().indexOf("-")+1);\r
 188 \r
 189    Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
 190                                "Select font size",\r
 191                                "Font size",\r
 192                                JOptionPane.QUESTION_MESSAGE,\r
 193                                null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
 194                                ,"Font Size - "+size);\r
 195    if(selection!=null)\r
 196    {\r
 197      fontSize.setText("Font Size - " + selection);\r
 198 \r
 199      int i = Integer.parseInt(selection.toString());\r
 200      treeCanvas.setFontSize(i);\r
 201    }\r
 202     scrollPane.setViewportView(treeCanvas);\r
 203 \r
 204   }\r
 205 \r
 206   protected void distanceMenu_actionPerformed(ActionEvent e)\r
 207   {\r
 208     treeCanvas.setShowDistances(distanceMenu.isSelected());\r
 209   }\r
 210 \r
 211   protected void bootstrapMenu_actionPerformed(ActionEvent e)\r
 212   {\r
 213     treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());\r
 214   }\r
 215 \r
 216   protected void placeholdersMenu_actionPerformed(ActionEvent e)\r
 217     {\r
 218       treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());\r
 219   }\r
 220 \r
 221   protected void epsTree_actionPerformed(ActionEvent e)\r
 222   {\r
 223     int width = treeCanvas.getWidth(), height=treeCanvas.getHeight();\r
 224     try\r
 225     {\r
 226       jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 227           "LAST_DIRECTORY"),\r
 228               new String[]{"eps"},\r
 229               new String[]{"Encapsulated Postscript"},\r
 230               "Encapsulated Postscript");\r
 231       chooser.setFileView(new jalview.io.JalviewFileView());\r
 232       chooser.setDialogTitle("Create EPS file from tree");\r
 233       chooser.setToolTipText("Save");\r
 234 \r
 235       int value = chooser.showSaveDialog(this);\r
 236       if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
 237         return;\r
 238 \r
 239       jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getParent());\r
 240       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
 241       EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);\r
 242 \r
 243 \r
 244       treeCanvas.draw(pg, width, height);\r
 245 \r
 246         pg.flush();\r
 247         pg.close();\r
 248     }\r
 249     catch (Exception ex)\r
 250     {\r
 251       ex.printStackTrace();\r
 252     }\r
 253   }\r
 254 \r
 255   protected void pngTree_actionPerformed(ActionEvent e)\r
 256  {\r
 257   int width = treeCanvas.getWidth(), height = treeCanvas.getHeight();\r
 258     try\r
 259     {\r
 260       jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
 261           jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
 262           new String[] {"png"},\r
 263           new String[] {"Portable network graphics"},\r
 264           "Portable network graphics");\r
 265 \r
 266       chooser.setFileView(new jalview.io.JalviewFileView());\r
 267       chooser.setDialogTitle("Create PNG image from tree");\r
 268       chooser.setToolTipText("Save");\r
 269 \r
 270       int value = chooser.showSaveDialog(this);\r
 271       if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
 272         return;\r
 273 \r
 274       jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getParent());\r
 275       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
 276 \r
 277       BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);\r
 278       Graphics png = bi.getGraphics();\r
 279 \r
 280       treeCanvas.draw(png, width, height);\r
 281 \r
 282         ImageIO.write(bi, "png", out);\r
 283         out.close();\r
 284     }\r
 285     catch (Exception ex)\r
 286     {\r
 287       ex.printStackTrace();\r
 288     }\r
 289   }\r
 290 \r
 291 }\r