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
  54   @Override
  55   public void mouseClicked(MouseEvent e)
  56   {
  57
  58   }
  59
  60   @Override
  61   public void mousePressed(MouseEvent e)
  62   {
  63     showNodeSelectionOnAlign(e);
  64
  65   }
  66
  67   @Override
  68   public void mouseReleased(MouseEvent e)
  69   {
  70   }
  71
  72   @Override
  73   public void mouseEntered(MouseEvent e)
  74   {
  75
  76   }
  77
  78   @Override
  79   public void mouseExited(MouseEvent e)
  80   {
  81
  82   }
  83
  84   @Override
  85   public void selection(SequenceGroup seqsel, ColumnSelection colsel,
  86           HiddenColumns hidden, SelectionSource source)
  87   {
  88     if (source == parentAvport) // check if source is alignment from where the
  89                                 // tree originates
  90     {
  91       treeView.setFoundNodes0(
  92               new HashSet<Long>(seqsel.getSequences().size()));
  93
  94       for (SequenceI sequence : seqsel.getSequences())
  95       {
  96         PhylogenyNode matchingNode = sequencesBoundToNodes.get(sequence);
  97         if (matchingNode != null)
  98         {
  99           treeView.getFoundNodes0().add(matchingNode.getId());
 100         }
 101
 102       }
 103       PaintRefresher.Refresh(treeView, parentAvport.getSequenceSetId());
 104
 105     }
 106
 107
 108   }
 109
 110   @Override
 111   public void showNodeSelectionOnAlign(MouseEvent e)
 112   {
 113     final PhylogenyNode node = treeView.findNode(e.getX(), e.getY());
 114     if (node != null && node.isExternal())
 115     {
 116       SequenceI matchingSequence = nodesBoundToSequences.get(node);
 117
 118       if ((e.getModifiers() & InputEvent.SHIFT_MASK) != 0) // shift is pressed
 119       // (so multiple nodes
 120       // can be selected)
 121       {
 122
 123       }
 124       else
 125       {
 126         parentAvport.setSelectionGroup(null); // reset selection if shift isn't
 127                                               // pressed
 128       }
 129
 130       treeSelectionChanged(matchingSequence);
 131       parentAvport.sendSelection(); // not actually needed?
 132
 133       PaintRefresher.Refresh(treeView, parentAvport.getSequenceSetId());
 134     }
 135
 136     }
 137
 138   /**
 139    * Refactored from TreeCanvas
 140    *
 141    * @param sequence
 142    */
 143   public void treeSelectionChanged(SequenceI sequence)
 144   {
 145     SequenceGroup selected = parentAvport.getSelectionGroup();
 146
 147     if (selected == null)
 148     {
 149       selected = new SequenceGroup();
 150       parentAvport.setSelectionGroup(selected);
 151     }
 152
 153     selected.setEndRes(parentAvport.getAlignment().getWidth() - 1);
 154     selected.addOrRemove(sequence, true);
 155
 156   }
 157
 158   public AlignmentViewport getParentAvport()
 159   {
 160     return parentAvport;
 161   }
 162
 163   public void setParentAvport(AlignmentViewport parentAvport)
 164   {
 165     this.parentAvport = parentAvport;
 166   }
 167
 168 }
 169
 170
 171