src/jalview/appletgui/TreePanel.java

   1 package jalview.appletgui;\r
   2 \r
   3 import jalview.datamodel.*;\r
   4 import jalview.io.NewickFile;\r
   5 import jalview.analysis.*;\r
   6 import jalview.jbappletgui.GTreePanel;\r
   7 import java.awt.event.*;\r
   8 import java.util.*;\r
   9 import jalview.io.NewickFile;\r
  10 \r
  11 \r
  12 public class TreePanel extends GTreePanel\r
  13 {\r
  14   SequenceI[] seq;\r
  15   String type;\r
  16   String pwtype;\r
  17   AlignViewport av;\r
  18   int start;\r
  19   int end;\r
  20   TreeCanvas treeCanvas;\r
  21   NJTree tree;\r
  22 \r
  23   public NJTree getTree()\r
  24   {\r
  25     return tree;\r
  26   }\r
  27 \r
  28   public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)\r
  29   {\r
  30     super();\r
  31 \r
  32     this.type = type;\r
  33     this.pwtype = pwtype;\r
  34 \r
  35     start = s;\r
  36     end = e;\r
  37 \r
  38     String longestName = "";\r
  39     seq = new Sequence [seqVector.size()];\r
  40     for (int i=0;i < seqVector.size();i++)\r
  41     {\r
  42       seq[i] = (Sequence) seqVector.elementAt(i);\r
  43       if(seq[i].getName().length()>longestName.length())\r
  44         longestName = seq[i].getName();\r
  45     }\r
  46 \r
  47     tree = new NJTree(seq, type, pwtype, start, end);\r
  48 \r
  49     treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
  50 \r
  51     tree.reCount(tree.getTopNode());\r
  52     tree.findHeight(tree.getTopNode());\r
  53     scrollPane.add(treeCanvas);\r
  54 \r
  55   }\r
  56   public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,\r
  57                    String type, String pwtype)\r
  58     {\r
  59       super();\r
  60       // These are probably only  arbitrary strings reflecting source of tree\r
  61       this.type = type;\r
  62       this.pwtype = pwtype;\r
  63 \r
  64       start = 0;\r
  65       end = seqVector.size();\r
  66 \r
  67       String longestName = "";\r
  68       seq = new Sequence [seqVector.size()];\r
  69       for (int i=0;i < seqVector.size();i++)\r
  70       {\r
  71         seq[i] = (Sequence) seqVector.elementAt(i);\r
  72       }\r
  73       // This constructor matches sequence names to treenodes and sets up the tree layouts.\r
  74       tree = new NJTree(seq, newtree);\r
  75       // Now have to calculate longest name based on the leaves\r
  76       Vector leaves = tree.findLeaves(tree.getTopNode(),new Vector());\r
  77 \r
  78       for (int i=0;i < leaves.size();i++)\r
  79         if (longestName.length()<((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName().length())\r
  80           longestName = TreeCanvas.PLACEHOLDER+((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName();\r
  81 \r
  82       tree.reCount(tree.getTopNode());\r
  83       tree.findHeight(tree.getTopNode());\r
  84 \r
  85       treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
  86       treeCanvas.setShowBootstrap(newtree.HasBootstrap());\r
  87       treeCanvas.setShowDistances(newtree.HasDistances());\r
  88       distanceMenu.setState(newtree.HasDistances());\r
  89       bootstrapMenu.setState(newtree.HasBootstrap());\r
  90       if (true) // JBPNote TODO: preference for always marking placeholders in new associated tree\r
  91         placeholdersMenu.setState(treeCanvas.markPlaceholders);\r
  92       scrollPane.add(treeCanvas);\r
  93 \r
  94     }\r
  95 \r
  96 public String getText(String format) {\r
  97   return null;\r
  98 }\r
  99 \r
 100   protected void fitToWindow_actionPerformed(ActionEvent e)\r
 101   {\r
 102     treeCanvas.fitToWindow = fitToWindow.getState();\r
 103     repaint();\r
 104   }\r
 105 \r
 106   public void newickOutput_actionPerformed(ActionEvent actionEvent)\r
 107   {\r
 108     jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
 109     String output = fout.print(false, true);\r
 110     CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
 111     cap.setText(output);\r
 112     java.awt.Frame frame = new java.awt.Frame();\r
 113     frame.add(cap);\r
 114     jalview.bin.JalviewLite.addFrame(frame, type+" "+pwtype, 500,100);\r
 115   }\r
 116 \r
 117 \r
 118 \r
 119   protected void fontSize_actionPerformed(ActionEvent e)\r
 120   {\r
 121  /*   if( treeCanvas==null )\r
 122      return;\r
 123 \r
 124    String size = fontSize.getLabel().substring( fontSize.getLabel().indexOf("-")+1);\r
 125 \r
 126    Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
 127                                "Select font size",\r
 128                                "Font size",\r
 129                                JOptionPane.QUESTION_MESSAGE,\r
 130                                null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
 131                                ,"Font Size - "+size);\r
 132    if(selection!=null)\r
 133    {\r
 134      fontSize.setText("Font Size - " + selection);\r
 135 \r
 136      int i = Integer.parseInt(selection.toString());\r
 137      treeCanvas.setFontSize(i);\r
 138    }\r
 139     scrollPane.setViewportView(treeCanvas);\r
 140 */\r
 141   }\r
 142 \r
 143   protected void distanceMenu_actionPerformed(ActionEvent e)\r
 144   {\r
 145     treeCanvas.setShowDistances(distanceMenu.getState());\r
 146   }\r
 147 \r
 148   protected void bootstrapMenu_actionPerformed(ActionEvent e)\r
 149   {\r
 150     treeCanvas.setShowBootstrap(bootstrapMenu.getState());\r
 151   }\r
 152 \r
 153   protected void placeholdersMenu_actionPerformed(ActionEvent e)\r
 154   {\r
 155       treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());\r
 156   }\r
 157 \r
 158 }\r