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         if(seq[i].getName().length()>longestName.length())\r
  82           longestName = seq[i].getName();\r
  83       }\r
  84       // This constructor matches sequence names to treenodes and sets up the tree layouts.\r
  85       tree = new NJTree(seq, newtree);\r
  86 \r
  87       tree.reCount(tree.getTopNode());\r
  88       tree.findHeight(tree.getTopNode());\r
  89 \r
  90       treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
  91       treeCanvas.setShowBootstrap(newtree.HasBootstrap());\r
  92       treeCanvas.setShowDistances(newtree.HasDistances());\r
  93       scrollPane.setViewportView(treeCanvas);\r
  94 \r
  95     }\r
  96 \r
  97     public String getText(String format)\r
  98     {\r
  99       return null;\r
 100     }\r
 101 \r
 102     public void saveAsNewick_actionPerformed(ActionEvent e)\r
 103     {\r
 104 \r
 105   JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
 106         getProperty("LAST_DIRECTORY"));\r
 107     chooser.setFileView(new JalviewFileView());\r
 108     chooser.setDialogTitle("Save tree as newick file");\r
 109     chooser.setToolTipText("Save");\r
 110     int value = chooser.showSaveDialog(null);\r
 111     if (value == JalviewFileChooser.APPROVE_OPTION) {\r
 112       String choice =  chooser.getSelectedFile().getPath();\r
 113       jalview.bin.Cache.setProperty("LAST_DIRECTORY",  chooser.getSelectedFile().getParent());\r
 114       try{\r
 115         jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
 116         String output = fout.print(false,true); // distances only\r
 117         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );\r
 118         out.println(output);\r
 119         out.close();\r
 120       }\r
 121       catch (Exception ex) {\r
 122         ex.printStackTrace();\r
 123       }\r
 124     }\r
 125   }\r
 126 \r
 127   protected void printMenu_actionPerformed(ActionEvent e)\r
 128   {\r
 129 \r
 130     //Putting in a thread avoids Swing painting problems\r
 131     treeCanvas.startPrinting();\r
 132   }\r
 133 \r
 134   protected void fitToWindow_actionPerformed(ActionEvent e)\r
 135   {\r
 136     treeCanvas.fitToWindow = fitToWindow.isSelected();\r
 137     repaint();\r
 138   }\r
 139 \r
 140 \r
 141   protected void fontSize_actionPerformed(ActionEvent e)\r
 142   {\r
 143     if( treeCanvas==null )\r
 144      return;\r
 145 \r
 146    String size = fontSize.getText().substring( fontSize.getText().indexOf("-")+1);\r
 147 \r
 148    Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
 149                                "Select font size",\r
 150                                "Font size",\r
 151                                JOptionPane.QUESTION_MESSAGE,\r
 152                                null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
 153                                ,"Font Size - "+size);\r
 154    if(selection!=null)\r
 155    {\r
 156      fontSize.setText("Font Size - " + selection);\r
 157 \r
 158      int i = Integer.parseInt(selection.toString());\r
 159      treeCanvas.setFontSize(i);\r
 160    }\r
 161     scrollPane.setViewportView(treeCanvas);\r
 162 \r
 163   }\r
 164 \r
 165   protected void distanceMenu_actionPerformed(ActionEvent e)\r
 166   {\r
 167     treeCanvas.setShowDistances(distanceMenu.isSelected());\r
 168   }\r
 169 \r
 170   protected void bootstrapMenu_actionPerformed(ActionEvent e)\r
 171   {\r
 172     treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());\r
 173   }\r
 174 \r
 175 \r
 176   protected void epsTree_actionPerformed(ActionEvent e)\r
 177   {\r
 178     int width = treeCanvas.getWidth(), height=treeCanvas.getHeight();\r
 179     try\r
 180     {\r
 181       jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 182           "LAST_DIRECTORY"),\r
 183               new String[]{"eps"},\r
 184               new String[]{"Encapsulated Postscript"},\r
 185               "Encapsulated Postscript");\r
 186       chooser.setFileView(new jalview.io.JalviewFileView());\r
 187       chooser.setDialogTitle("Create EPS file from tree");\r
 188       chooser.setToolTipText("Save");\r
 189 \r
 190       int value = chooser.showSaveDialog(this);\r
 191       if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
 192         return;\r
 193 \r
 194       jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getParent());\r
 195       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
 196       EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);\r
 197 \r
 198 \r
 199       treeCanvas.draw(pg, width, height);\r
 200 \r
 201         pg.flush();\r
 202         pg.close();\r
 203     }\r
 204     catch (Exception ex)\r
 205     {\r
 206       ex.printStackTrace();\r
 207     }\r
 208   }\r
 209 \r
 210   protected void pngTree_actionPerformed(ActionEvent e)\r
 211  {\r
 212   int width = treeCanvas.getWidth(), height = treeCanvas.getHeight();\r
 213     try\r
 214     {\r
 215       jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
 216           jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
 217           new String[] {"png"},\r
 218           new String[] {"Portable network graphics"},\r
 219           "Portable network graphics");\r
 220 \r
 221       chooser.setFileView(new jalview.io.JalviewFileView());\r
 222       chooser.setDialogTitle("Create PNG image from tree");\r
 223       chooser.setToolTipText("Save");\r
 224 \r
 225       int value = chooser.showSaveDialog(this);\r
 226       if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
 227         return;\r
 228 \r
 229       jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getParent());\r
 230       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
 231 \r
 232       BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);\r
 233       Graphics png = bi.getGraphics();\r
 234 \r
 235       treeCanvas.draw(png, width, height);\r
 236 \r
 237         ImageIO.write(bi, "png", out);\r
 238         out.close();\r
 239     }\r
 240     catch (Exception ex)\r
 241     {\r
 242       ex.printStackTrace();\r
 243     }\r
 244   }\r
 245 \r
 246 }\r