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 \r
  33   public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)\r
  34   {\r
  35     super();\r
  36 \r
  37     this.type = type;\r
  38     this.pwtype = pwtype;\r
  39 \r
  40     start = s;\r
  41     end = e;\r
  42 \r
  43     String longestName = "";\r
  44     seq = new Sequence [seqVector.size()];\r
  45     for (int i=0;i < seqVector.size();i++)\r
  46     {\r
  47       seq[i] = (Sequence) seqVector.elementAt(i);\r
  48       if(seq[i].getName().length()>longestName.length())\r
  49         longestName = seq[i].getName();\r
  50     }\r
  51 \r
  52     tree = new NJTree(seq, type, pwtype, start, end);\r
  53     av.setCurrentTree(tree);\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         if(seq[i].getName().length()>longestName.length())\r
  79           longestName = seq[i].getName();\r
  80       }\r
  81       // This constructor matches sequence names to treenodes and sets up the tree layouts.\r
  82       tree = new NJTree(seq, newtree);\r
  83       av.setCurrentTree(tree);\r
  84 \r
  85 \r
  86       tree.reCount(tree.getTopNode());\r
  87       tree.findHeight(tree.getTopNode());\r
  88 \r
  89       treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
  90       treeCanvas.setShowBootstrap(newtree.HasBootstrap());\r
  91       treeCanvas.setShowDistances(newtree.HasDistances());\r
  92       scrollPane.setViewportView(treeCanvas);\r
  93 \r
  94     }\r
  95 \r
  96 \r
  97 \r
  98 public String getText(String format) {\r
  99   return null;\r
 100 }\r
 101 \r
 102 \r
 103   protected void saveMenu_actionPerformed(ActionEvent e)\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",  choice);\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"), new String[]{"eps"}, "Encapsulated Postscript");\r
 183       chooser.setFileView(new jalview.io.JalviewFileView());\r
 184       chooser.setDialogTitle("Create EPS file from tree");\r
 185       chooser.setToolTipText("Save");\r
 186 \r
 187       int value = chooser.showSaveDialog(this);\r
 188       if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
 189         return;\r
 190 \r
 191       jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());\r
 192       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
 193       EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);\r
 194 \r
 195 \r
 196       treeCanvas.draw(pg, width, height);\r
 197 \r
 198         pg.flush();\r
 199         pg.close();\r
 200     }\r
 201     catch (Exception ex)\r
 202     {\r
 203       ex.printStackTrace();\r
 204     }\r
 205   }\r
 206 \r
 207   protected void pngTree_actionPerformed(ActionEvent e)\r
 208  {\r
 209   int width = treeCanvas.getWidth(), height = treeCanvas.getHeight();\r
 210     try\r
 211     {\r
 212       jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 213           "LAST_DIRECTORY"), new String[]{"png"}, "Portable network graphics");\r
 214       chooser.setFileView(new jalview.io.JalviewFileView());\r
 215       chooser.setDialogTitle("Create PNG image from tree");\r
 216       chooser.setToolTipText("Save");\r
 217 \r
 218       int value = chooser.showSaveDialog(this);\r
 219       if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
 220         return;\r
 221 \r
 222       jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());\r
 223       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
 224 \r
 225       BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);\r
 226       Graphics png = bi.getGraphics();\r
 227 \r
 228       treeCanvas.draw(png, width, height);\r
 229 \r
 230         ImageIO.write(bi, "png", out);\r
 231         out.close();\r
 232     }\r
 233     catch (Exception ex)\r
 234     {\r
 235       ex.printStackTrace();\r
 236     }\r
 237   }\r
 238 \r
 239 }\r