src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java

   1 package jalview.ext.archaeopteryx;
   2
   3 import jalview.analysis.TreeBuilder;
   4 import jalview.datamodel.SequenceI;
   5 import jalview.gui.Desktop;
   6 import jalview.viewmodel.AlignmentViewport;
   7
   8 import java.awt.Dimension;
   9 import java.util.Map;
  10
  11 import org.forester.archaeopteryx.Archaeopteryx;
  12 import org.forester.archaeopteryx.MainFrame;
  13 import org.forester.phylogeny.Phylogeny;
  14 import org.forester.phylogeny.PhylogenyNode;
  15
  16 public final class ArchaeopteryxInit
  17 {
  18   /**
  19    * This method should generally not be used as it does not bind the tree to
  20    * its alignment
  21    *
  22    * @param aptxTrees
  23    * @return
  24    */
  25   public static MainFrame createUnboundInstance(Phylogeny aptxTree)
  26   {
  27     Phylogeny[] aptxTrees = { aptxTree };
  28     return createBoundAptxFrame(aptxTrees, null);
  29   }
  30
  31   public static MainFrame createInstance(Phylogeny[] aptxTrees,
  32           AlignmentViewport jalviewAlignmentView)
  33   {
  34     return createBoundAptxFrame(aptxTrees, jalviewAlignmentView);
  35
  36   }
  37
  38   public static MainFrame createInstance(Phylogeny aptxTree,
  39           AlignmentViewport jalviewAlignmentView)
  40   {
  41     Phylogeny[] aptxTrees = { aptxTree }; // future possibility to load in
  42     // several trees simultaneously
  43     return createBoundAptxFrame(aptxTrees, jalviewAlignmentView);
  44
  45   }
  46
  47   public static MainFrame createInstance(
  48           TreeBuilder calculatedTree) // very dense method, to be split up
  49   {
  50     ArchaeopteryxTreeConverter aptxTreeBuilder = new ArchaeopteryxTreeConverter(
  51             calculatedTree);
  52
  53     Phylogeny aptxTree = aptxTreeBuilder.buildAptxTree();
  54     Phylogeny[] aptxTrees = { aptxTree }; // future possibility to load in
  55                                           // several trees simultaneously
  56
  57     MainFrame aptxApp = createBoundAptxFrame(aptxTrees,
  58             calculatedTree.getAvport());
  59     bindNodesToJalviewSequences(aptxApp, calculatedTree.getAvport(),
  60             aptxTreeBuilder.getAlignmentBoundNodes());
  61     return bindFrameToJalview(aptxApp);
  62
  63   }
  64
  65
  66
  67
  68   private static MainFrame createBoundAptxFrame(Phylogeny[] aptxTrees,
  69           AlignmentViewport jalviewAlignmentView)
  70   {
  71     MainFrame aptxApp = Archaeopteryx.createApplication(aptxTrees,
  72             "_aptx_jalview_configuration_file", null);
  73
  74     return aptxApp;
  75   }
  76
  77   private static void bindNodesToJalviewSequences(MainFrame aptxApp,
  78           AlignmentViewport jalviewAlignViewport,
  79           Map<SequenceI, PhylogenyNode> alignMappedToNodes)
  80   {
  81     new JalviewAptxBinding(aptxApp, jalviewAlignViewport,
  82             alignMappedToNodes);
  83   }
  84
  85
  86   private static MainFrame bindFrameToJalview(MainFrame aptxApp)
  87   {
  88     int width = 400;
  89     int height = 550;
  90     aptxApp.setMinimumSize(new Dimension(width, height));
  91
  92     Desktop.addInternalFrame(aptxApp, "Archaeopteryx Tree View", true,
  93             width, height, true, true);
  94
  95     return aptxApp;
  96
  97   }
  98
  99
 100 }