src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java

   1 package jalview.ext.archaeopteryx;
   2
   3 import jalview.analysis.TreeBuilder;
   4 import jalview.gui.Desktop;
   5
   6 import java.awt.Dimension;
   7
   8 import org.forester.archaeopteryx.Archaeopteryx;
   9 import org.forester.archaeopteryx.MainFrame;
  10 import org.forester.phylogeny.Phylogeny;
  11
  12 public final class ArchaeopteryxInit
  13 {
  14   public static MainFrame createInstance(Phylogeny[] aptxTrees)
  15   {
  16     return createBoundAptxFrame(aptxTrees);
  17
  18   }
  19
  20   public static MainFrame createInstance(Phylogeny aptxTree)
  21   {
  22     Phylogeny[] aptxTrees = { aptxTree }; // future possibility to load in
  23     // several trees simultaneously
  24     return createBoundAptxFrame(aptxTrees);
  25
  26   }
  27
  28   public static MainFrame createInstance(
  29           TreeBuilder calculatedTree)
  30   {
  31     ArchaeopteryxTreeConverter aptxTreeBuilder = new ArchaeopteryxTreeConverter(
  32             calculatedTree);
  33     Phylogeny aptxTree = aptxTreeBuilder.buildAptxTree();
  34     Phylogeny[] aptxTrees = { aptxTree }; // future possibility to load in
  35                                           // several trees simultaneously
  36
  37     return createBoundAptxFrame(aptxTrees);
  38
  39   }
  40
  41
  42   private static MainFrame createBoundAptxFrame(Phylogeny[] aptxTrees)
  43   {
  44     MainFrame aptxApp = Archaeopteryx.createApplication(aptxTrees,
  45             "_aptx_jalview_configuration_file", null);
  46     return bindFrameToJalview(aptxApp);
  47   }
  48
  49
  50
  51   private static MainFrame bindFrameToJalview(MainFrame aptxApp)
  52   {
  53     int width = 400;
  54     int height = 550;
  55     aptxApp.setMinimumSize(new Dimension(width, height));
  56
  57     Desktop.addInternalFrame(aptxApp, "Archaeopteryx Tree View", true,
  58             width, height, true, true);
  59
  60     return aptxApp;
  61
  62   }
  63
  64
  65 }