package jalview.ext.archaeopteryx;
+import jalview.analysis.Conservation;
+import jalview.api.AlignViewportI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.ext.treeviewer.ExternalTreeViewerBindingI;
+import jalview.gui.AlignViewport;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.gui.PaintRefresher;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
+import jalview.util.MappingUtils;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
+import java.awt.Color;
import java.awt.Graphics;
import java.awt.event.ActionEvent;
import java.awt.event.InputEvent;
import java.awt.event.MouseEvent;
+import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import javax.swing.event.ChangeListener;
import org.forester.archaeopteryx.MainFrame;
+import org.forester.archaeopteryx.TreePanelUtil;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.BranchColor;
/**
* Class for binding the Archaeopteryx tree viewer to the Jalview alignment that
private Map<PhylogenyNode, SequenceI> nodesBoundToSequences;
+ private float rootX;
+
+ private float furthestNodeX;
+
/**
*
* @param archaeopteryx
treeView.addMouseListener(this);
PaintRefresher.Register(treeView, parentAvport.getSequenceSetId());
+
treeTabs.addChangeListener(new ChangeListener()
{
}
else
{
- partitionTree(e.getX());
+ partitionTree(e.getX());
}
-
PaintRefresher.Refresh(treeView, parentAvport.getSequenceSetId());
+
+
+
}
});
if (matchingNode != null)
{
treeView.getFoundNodes0().add(matchingNode.getId());
+
+
+ if (!matchingNode.getBranchData().isHasBranchColor())
+ {
+ Color foundNodesColour = treeView.getTreeColorSet()
+ .getFoundColor0();
+ matchingNode.getBranchData()
+ .setBranchColor(new BranchColor(foundNodesColour));
+
+ }
+
}
}
- treeView.repaint();
+ treeView.repaint();
}
if (!tree.isEmpty())
{
- double treeDepth = tree.calculateHeight(true);
- if (treeDepth != 0)
+ // should be calculated on each partition as the tree can theoretically
+ // change in the meantime
+ PhylogenyNode furthestNode = PhylogenyMethods
+ .calculateNodeWithMaxDistanceToRoot(tree);
+ furthestNodeX = furthestNode.getXcoord();
+ rootX = tree.getRoot().getXcoord();
+
+ if (furthestNodeX != rootX && x < furthestNodeX) // don't bother if 0
+ // distance tree or
+ // clicked x lies outside
+ // of tree
{
Graphics g = treeView.getGraphics();
int panelHeight = treeView.getHeight();
g.drawLine(x, 0, x, panelHeight);
- int viewWidth = treeView.getWidth();
- float threshold = (float) x / (float) viewWidth;
+ float threshold = (x - rootX) / (furthestNodeX - rootX);
+ List<PhylogenyNode> foundNodes = getNodesAboveThreshold(threshold,
+ tree.getRoot());
}
}
}
-
+
+ public List<PhylogenyNode> getNodesAboveThreshold(double threshold,
+ PhylogenyNode node)
+ {
+
+ List<PhylogenyNode> nodesAboveThreshold = new ArrayList<>();
+
+ parentAvport.setSelectionGroup(null);
+ parentAvport.getAlignment().deleteAllGroups();
+ parentAvport.clearSequenceColours();
+ if (parentAvport.getCodingComplement() != null)
+ {
+ parentAvport.getCodingComplement().setSelectionGroup(null);
+ parentAvport.getCodingComplement().getAlignment().deleteAllGroups();
+ parentAvport.getCodingComplement().clearSequenceColours();
+ }
+
+
+ colourNodesAboveThreshold(nodesAboveThreshold, threshold,
+ node);
+ return nodesAboveThreshold;
+
+ }
+
+ /**
+ * Partially refactored from TreeCanvas colourGroups (can be made nicer).
+ *
+ * @param nodeList
+ * @param threshold
+ * @param treeLength
+ * @param node
+ * @return
+ */
+ private List<PhylogenyNode> colourNodesAboveThreshold(
+ List<PhylogenyNode> nodeList, double threshold,
+ PhylogenyNode node)
+ {
+ // could also use PhylogenyMethods.getAllDescendants
+ for (PhylogenyNode childNode : node.getDescendants())
+ {
+ childNode.getBranchData()
+ .setBranchColor(new BranchColor(Color.black));
+ float nodeCutoff = (childNode.getXcoord() - rootX)
+ / (furthestNodeX - rootX);
+
+ if (nodeCutoff > threshold)
+ {
+ nodeList.add(childNode);
+
+ Color randomColor = new Color((int) (Math.random() * 255),
+ (int) (Math.random() * 255), (int) (Math.random() * 255));
+ TreePanelUtil.colorizeSubtree(childNode,
+ new BranchColor(randomColor));
+ List<PhylogenyNode> descendantNodes = childNode
+ .getAllExternalDescendants();
+ List<SequenceI> descendantSeqs = new ArrayList<>(); // .forEach instead?
+ for (PhylogenyNode descNode : descendantNodes)
+ {
+ descendantSeqs.add(nodesBoundToSequences.get(descNode));
+ }
+
+ SequenceGroup sg = new SequenceGroup(descendantSeqs, null, null,
+ true, true, false, 0,
+ parentAvport.getAlignment().getWidth() - 1);
+
+ ColourSchemeI cs = null;
+ if (parentAvport.getGlobalColourScheme() != null)
+ {
+ if (parentAvport.getGlobalColourScheme() instanceof UserColourScheme)
+ {
+ cs = new UserColourScheme(
+ ((UserColourScheme) parentAvport.getGlobalColourScheme())
+ .getColours());
+ }
+ else
+ {
+ cs = ColourSchemeProperty.getColourScheme(sg, ColourSchemeProperty
+ .getColourName(parentAvport.getGlobalColourScheme()));
+ }
+ }
+ sg.setColourScheme(cs);
+ sg.getGroupColourScheme().setThreshold(
+ parentAvport.getResidueShading().getThreshold(),
+ parentAvport.isIgnoreGapsConsensus());
+ // sg.recalcConservation();
+ sg.setName("Tree Group:" + sg.hashCode());
+ sg.setIdColour(randomColor);
+
+ if (parentAvport.getGlobalColourScheme() != null
+ && parentAvport.getResidueShading().conservationApplied())
+ {
+ Conservation c = new Conservation("Group", sg.getSequences(null),
+ sg.getStartRes(), sg.getEndRes());
+ c.calculate();
+ c.verdict(false, parentAvport.getConsPercGaps());
+ sg.cs.setConservation(c);
+ }
+
+ parentAvport.getAlignment().addGroup(new SequenceGroup(sg));
+ // TODO can we push all of the below into AlignViewportI?
+ final AlignViewportI codingComplement = parentAvport
+ .getCodingComplement();
+ if (codingComplement != null)
+ {
+ SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg,
+ parentAvport,
+ codingComplement);
+ if (mappedGroup.getSequences().size() > 0)
+ {
+ codingComplement.getAlignment().addGroup(mappedGroup);
+ for (SequenceI seq : mappedGroup.getSequences())
+ {
+ codingComplement.setSequenceColour(seq,
+ randomColor.brighter());
+ }
+ }
+ }
+
+
+ }
+
+ else
+ {
+ colourNodesAboveThreshold(nodeList, threshold,
+ childNode);
+ }
+ }
+
+ // GROSS
+ ((AlignViewport) parentAvport).getAlignPanel().updateAnnotation();
+
+ final AlignViewportI codingComplement = parentAvport
+ .getCodingComplement();
+ if (codingComplement != null)
+ {
+ ((AlignViewport) codingComplement).getAlignPanel().updateAnnotation();
+ }
+
+ return nodeList;
+ }
+
+
+
+
+ // public List<PhylogenyNode> groupNodes(float threshold, PhylogenyNode root,
+ // double treeHeight)
+ // {
+ // List<PhylogenyNode> groups = new ArrayList<>();
+ // _groupNodes(groups, root, threshold, treeHeight);
+ // System.out.println(groups);
+ // return groups;
+ // }
+ //
+ // protected void _groupNodes(List<PhylogenyNode> groups, PhylogenyNode nd,
+ // float threshold, double treeHeight)
+ // {
+ // if (nd == null)
+ // {
+ // return;
+ // }
+ //
+ // if ((nd.calculateDistanceToRoot() / treeHeight) > threshold)
+ // {
+ // groups.add(nd);
+ // }
+ // else
+ // {
+ // for (PhylogenyNode childNode : nd.getDescendants())
+ // {
+ // _groupNodes(groups, childNode, threshold, treeHeight);
+ // }
+ // }
+ // }
+ //
+
/**
* may or may not need an extra repaint on the alignment view (check what kira
// for (AlignmentPanel ap : PaintRefresher
// .getAssociatedPanels(parentAvport.getSequenceSetId()))
// {
- // commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
+ // commands.add(sortAlignmentIn(ap.parentAvport.getAlignPanel()));
// }
- // av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
+ // parentAvport.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
// {
//
// @Override
// }
// });
// for (AlignmentPanel ap : PaintRefresher
- // .getAssociatedPanels(av.getSequenceSetId()))
+ // .getAssociatedPanels(parentAvport.getSequenceSetId()))
// {
// // ensure all the alignFrames refresh their GI after adding an undo item
// ap.alignFrame.updateEditMenuBar();
git://source.jalview.org / jalview.git / blobdiff