src/jalview/ext/archaeopteryx/JalviewAptxBinding.java

   1 package jalview.ext.archaeopteryx;
   2
   3 import jalview.datamodel.ColumnSelection;
   4 import jalview.datamodel.HiddenColumns;
   5 import jalview.datamodel.SequenceGroup;
   6 import jalview.datamodel.SequenceI;
   7 import jalview.gui.PaintRefresher;
   8 import jalview.structure.SelectionSource;
   9 import jalview.structure.StructureSelectionManager;
  10 import jalview.viewmodel.AlignmentViewport;
  11
  12 import java.awt.event.ActionEvent;
  13 import java.awt.event.InputEvent;
  14 import java.awt.event.MouseEvent;
  15 import java.util.HashSet;
  16 import java.util.Map;
  17
  18 import org.forester.archaeopteryx.MainFrame;
  19 import org.forester.phylogeny.PhylogenyNode;
  20
  21 public class JalviewAptxBinding implements JalviewTreeViewerBindingI
  22 {
  23   org.forester.archaeopteryx.TreePanel treeView;
  24
  25   AlignmentViewport parentAvport;
  26
  27   StructureSelectionManager ssm;
  28
  29   Map<SequenceI, PhylogenyNode> sequencesBoundToNodes;
  30
  31   Map<PhylogenyNode, SequenceI> nodesBoundToSequences;
  32
  33   public JalviewAptxBinding(MainFrame archaeopteryx,
  34           AlignmentViewport jalviewAlignmentViewport,
  35           Map<SequenceI, PhylogenyNode> alignMappedToNodes,
  36           Map<PhylogenyNode, SequenceI> nodesMappedToAlign)
  37   {
  38     parentAvport = jalviewAlignmentViewport;
  39     sequencesBoundToNodes = alignMappedToNodes;
  40     nodesBoundToSequences = nodesMappedToAlign;
  41     treeView = archaeopteryx.getMainPanel().getCurrentTreePanel();
  42     ssm = parentAvport.getStructureSelectionManager();
  43     ssm.addSelectionListener(this);
  44     treeView.addMouseListener(this);
  45     PaintRefresher.Register(treeView, parentAvport.getSequenceSetId());
  46   }
  47
  48   @Override
  49   public void actionPerformed(ActionEvent e)
  50   {
  51   }
  52
  53   @Override
  54   public void mouseClicked(MouseEvent e)
  55   {
  56   }
  57
  58   @Override
  59   public void mousePressed(MouseEvent e)
  60   {
  61     showNodeSelectionOnAlign(e);
  62   }
  63
  64   @Override
  65   public void mouseReleased(MouseEvent e)
  66   {
  67   }
  68
  69   @Override
  70   public void mouseEntered(MouseEvent e)
  71   {
  72   }
  73
  74   @Override
  75   public void mouseExited(MouseEvent e)
  76   {
  77   }
  78
  79   @Override
  80   public void selection(SequenceGroup seqsel, ColumnSelection colsel,
  81           HiddenColumns hidden, SelectionSource source)
  82   {
  83     if (source == parentAvport) // check if source is alignment from where the
  84                                 // tree originates
  85     {
  86       treeView.setFoundNodes0(
  87               new HashSet<Long>(seqsel.getSequences().size()));
  88
  89       for (SequenceI selectedSequence : seqsel.getSequences())
  90       {
  91         PhylogenyNode matchingNode = sequencesBoundToNodes.get(selectedSequence);
  92         if (matchingNode != null)
  93         {
  94           treeView.getFoundNodes0().add(matchingNode.getId());
  95         }
  96
  97       }
  98       PaintRefresher.Refresh(treeView, parentAvport.getSequenceSetId());
  99
 100     }
 101
 102
 103   }
 104
 105   /**
 106    * Note that this currently only checks external nodes
 107    */
 108   @Override
 109   public void showNodeSelectionOnAlign(MouseEvent e)
 110   {
 111     final PhylogenyNode node = treeView.findNode(e.getX(), e.getY());
 112     if (node != null)
 113     {
 114       SequenceI matchingSequence = nodesBoundToSequences.get(node);
 115       if (matchingSequence != null)
 116       {
 117
 118         if ((e.getModifiers() & InputEvent.SHIFT_MASK) != 0) // shift is pressed
 119         // (so multiple nodes
 120         // can be selected)
 121         {
 122           // something?
 123
 124         }
 125         else
 126         {
 127           parentAvport.setSelectionGroup(null); // reset selection if shift
 128                                                 // isn't
 129           // pressed
 130         }
 131
 132         treeSelectionChanged(matchingSequence);
 133         parentAvport.sendSelection(); // not actually needed?
 134
 135         PaintRefresher.Refresh(treeView, parentAvport.getSequenceSetId());
 136       }
 137     }
 138
 139   }
 140
 141   /**
 142    * Refactored from TreeCanvas
 143    *
 144    * @param sequence
 145    */
 146   public void treeSelectionChanged(SequenceI sequence)
 147   {
 148     SequenceGroup selected = parentAvport.getSelectionGroup();
 149
 150     if (selected == null)
 151     {
 152       selected = new SequenceGroup();
 153       parentAvport.setSelectionGroup(selected);
 154     }
 155
 156     selected.setEndRes(parentAvport.getAlignment().getWidth() - 1);
 157     selected.addOrRemove(sequence, true);
 158
 159   }
 160
 161   public AlignmentViewport getParentAvport()
 162   {
 163     return parentAvport;
 164   }
 165
 166   public void setParentAvport(AlignmentViewport parentAvport)
 167   {
 168     this.parentAvport = parentAvport;
 169   }
 170
 171 }
 172
 173
 174