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   final StructureSelectionManager ssm;
  28
  29   Map<SequenceI, PhylogenyNode> sequencesBoundToNodes;
  30
  31   Map<PhylogenyNode, SequenceI> nodesBoundToSequences;
  32
  33   public JalviewAptxBinding(final MainFrame archaeopteryx,
  34           final AlignmentViewport jalviewAlignmentViewport,
  35           final Map<SequenceI, PhylogenyNode> alignMappedToNodes,
  36           final 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(final 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
  80   @Override
  81   public void selection(final SequenceGroup seqsel,
  82           final ColumnSelection colsel, final HiddenColumns hidden,
  83           final SelectionSource source)
  84   {
  85     if (source == parentAvport) // check if source is alignment from where the
  86     // tree originates
  87     {
  88       treeView.setFoundNodes0(
  89               new HashSet<Long>(seqsel.getSequences().size()));
  90
  91       for (SequenceI selectedSequence : seqsel.getSequences())
  92       {
  93         PhylogenyNode matchingNode = sequencesBoundToNodes.get(selectedSequence);
  94         if (matchingNode != null)
  95         {
  96           treeView.getFoundNodes0().add(matchingNode.getId());
  97         }
  98
  99       }
 100       PaintRefresher.Refresh(treeView, parentAvport.getSequenceSetId());
 101
 102     }
 103
 104
 105   }
 106
 107   /**
 108    * If a node is selected in the tree panel this method highlights the
 109    * corresponding sequence in the Jalview alignment view.
 110    */
 111   @Override
 112   public void showNodeSelectionOnAlign(final MouseEvent e)
 113   {
 114     final PhylogenyNode node = treeView.findNode(e.getX(), e.getY());
 115     if (node != null)
 116     {
 117       SequenceI matchingSequence = nodesBoundToSequences.get(node);
 118       if (matchingSequence != null)
 119       {
 120
 121         if ((e.getModifiers() & InputEvent.SHIFT_MASK) != 0) // shift is pressed
 122         // (so multiple nodes
 123         // can be selected)
 124         {
 125           // something?
 126
 127         }
 128         else
 129         {
 130           parentAvport.setSelectionGroup(null); // reset selection if shift
 131                                                 // isn't
 132           // pressed
 133         }
 134
 135         treeSelectionChanged(matchingSequence);
 136         parentAvport.sendSelection(); // not actually needed?
 137         PaintRefresher.Refresh(treeView, parentAvport.getSequenceSetId());
 138
 139
 140       }
 141     }
 142
 143
 144   }
 145
 146   /**
 147    * Refactored from TreeCanvas
 148    *
 149    * @param sequence
 150    */
 151   public void treeSelectionChanged(final SequenceI sequence)
 152   {
 153     SequenceGroup selected = parentAvport.getSelectionGroup();
 154
 155     if (selected == null)
 156     {
 157       selected = new SequenceGroup();
 158       parentAvport.setSelectionGroup(selected);
 159     }
 160
 161     selected.setEndRes(parentAvport.getAlignment().getWidth() - 1);
 162     selected.addOrRemove(sequence, true);
 163
 164   }
 165
 166   public AlignmentViewport getParentAvport()
 167   {
 168     return parentAvport;
 169   }
 170
 171   public void setParentAvport(final AlignmentViewport parentAvport)
 172   {
 173     this.parentAvport = parentAvport;
 174   }
 175
 176 }
 177
 178
 179