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