import java.awt.print.Printable;
import java.awt.print.PrinterException;
import java.awt.print.PrinterJob;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.HashMap;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
import jalview.analysis.Conservation;
import jalview.analysis.TreeModel;
import jalview.api.AlignViewportI;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
import jalview.datamodel.BinaryNode;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ContactMatrixI;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.structure.SelectionSource;
import jalview.util.Format;
import jalview.util.MessageManager;
+import jalview.ws.datamodel.MappableContactMatrixI;
/**
* DOCUMENT ME!
Map<Object, Rectangle> nameHash = new Hashtable<>();
- Map<SequenceNode, Rectangle> nodeHash = new Hashtable<>();
+ Map<BinaryNode, Rectangle> nodeHash = new Hashtable<>();
- SequenceNode highlightNode;
+ BinaryNode highlightNode;
boolean applyToAllViews = false;
tree.findHeight(tree.getTopNode());
// Now have to calculate longest name based on the leaves
- Vector<SequenceNode> leaves = tree.findLeaves(tree.getTopNode());
+ Vector<BinaryNode> leaves = tree.findLeaves(tree.getTopNode());
boolean has_placeholders = false;
longestName = "";
for (int i = 0; i < leaves.size(); i++)
{
- SequenceNode lf = leaves.elementAt(i);
+ BinaryNode lf = leaves.elementAt(i);
- if (lf.isPlaceholder())
+ if (lf instanceof SequenceNode && ((SequenceNode)lf).isPlaceholder())
{
has_placeholders = true;
}
* @param offy
* DOCUMENT ME!
*/
- public void drawNode(Graphics g, SequenceNode node, float chunk,
+ public void drawNode(Graphics g, BinaryNode node, float chunk,
double wscale, int width, int offx, int offy)
{
if (node == null)
g.drawString(nodeLabel, xstart + 2, ypos - 2);
}
- String name = (markPlaceholders && node.isPlaceholder())
+ String name = (markPlaceholders && ((node instanceof SequenceNode && ((SequenceNode)node).isPlaceholder())))
? (PLACEHOLDER + node.getName())
: node.getName();
nameHash.put(node.element(), rect);
// Colour selected leaves differently
- SequenceGroup selected = av.getSelectionGroup();
+ boolean isSelected = false;
+ if (tp.isColumnWise())
+ {
+ isSelected = isColumnForNodeSelected(node);
+ }
+ else
+ {
+ SequenceGroup selected = av.getSelectionGroup();
- if ((selected != null)
- && selected.getSequences(null).contains(node.element()))
+ if ((selected != null)
+ && selected.getSequences(null).contains(node.element()))
+ {
+ isSelected = true;
+ }
+ }
+ if (isSelected)
{
g.setColor(Color.gray);
}
else
{
- drawNode(g, (SequenceNode) node.left(), chunk, wscale, width, offx,
+ drawNode(g, (BinaryNode) node.left(), chunk, wscale, width, offx,
offy);
- drawNode(g, (SequenceNode) node.right(), chunk, wscale, width, offx,
+ drawNode(g, (BinaryNode) node.right(), chunk, wscale, width, offx,
offy);
double height = node.height;
}
}
- for (Entry<SequenceNode, Rectangle> entry : nodeHash.entrySet())
+ for (Entry<BinaryNode, Rectangle> entry : nodeHash.entrySet())
{
Rectangle rect = entry.getValue();
if (longestName == null || tree == null)
{
g2.drawString("Calculating tree.", 20, 20);
+ return;
}
offy = font.getSize() + 10;
}
else
{
- Vector<SequenceNode> leaves = tree.findLeaves(highlightNode);
-
+ Vector<BinaryNode> leaves = tree.findLeaves(highlightNode);
+ if (tp.isColumnWise()) {
+ markColumnsFor(getAssociatedPanels(), leaves, Color.red);
+ } else {
for (int i = 0; i < leaves.size(); i++)
{
SequenceI seq = (SequenceI) leaves.elementAt(i).element();
treeSelectionChanged(seq);
}
+ }
av.sendSelection();
}
Object ob = findElement(evt.getX(), evt.getY());
- if (ob instanceof SequenceNode)
+ if (ob instanceof BinaryNode)
{
- highlightNode = (SequenceNode) ob;
+ highlightNode = (BinaryNode) ob;
this.setToolTipText(
"<html>" + MessageManager.getString("label.highlightnode"));
repaint();
av.sendSelection();
return;
}
- else if (!(ob instanceof SequenceNode))
+ else if (!(ob instanceof BinaryNode))
{
// Find threshold
if (tree.getMaxHeight() != 0)
threshold = (float) (x - offx)
/ (float) (getWidth() - labelLength - (2 * offx));
- List<SequenceNode> groups = tree.groupNodes(threshold);
+ List<BinaryNode> groups = tree.groupNodes(threshold);
setColor(tree.getTopNode(), Color.black);
AlignmentPanel[] aps = getAssociatedPanels();
}
- void colourGroups(List<SequenceNode> groups)
+ void colourGroups(List<BinaryNode> groups)
{
AlignmentPanel[] aps = getAssociatedPanels();
+ List<BitSet> colGroups = new ArrayList<>();
+ Map<BitSet,Color> colors=new HashMap();
for (int i = 0; i < groups.size(); i++)
{
Color col = new Color((int) (Math.random() * 255),
(int) (Math.random() * 255), (int) (Math.random() * 255));
setColor(groups.get(i), col.brighter());
- Vector<SequenceNode> l = tree.findLeaves(groups.get(i));
-
- Vector<SequenceI> sequences = new Vector<>();
-
- for (int j = 0; j < l.size(); j++)
- {
- SequenceI s1 = (SequenceI) l.elementAt(j).element();
+ Vector<BinaryNode> l = tree.findLeaves(groups.get(i));
+ if (!tp.isColumnWise()) {
+ createSeqGroupFor(aps, l, col);
+ } else {
+ BitSet gp=createColumnGroupFor(l,col);
- if (!sequences.contains(s1))
+ colGroups.add(gp);
+ colors.put(gp, col);
+ }
+ }
+ if (tp.isColumnWise())
+ {
+ AlignmentAnnotation aa = tp.getAssocAnnotation();
+ if (aa!=null) {
+ ContactMatrixI cm = av.getContactMatrix(aa);
+ if (cm!=null)
{
- sequences.addElement(s1);
+ cm.updateGroups(colGroups);
+ for (BitSet gp:colors.keySet())
+ {
+ cm.setColorForGroup(gp, colors.get(gp));
+ }
}
- }
-
- ColourSchemeI cs = null;
- SequenceGroup _sg = new SequenceGroup(sequences, null, cs, true, true,
- false, 0, av.getAlignment().getWidth() - 1);
-
- _sg.setName("JTreeGroup:" + _sg.hashCode());
- _sg.setIdColour(col);
-
- for (int a = 0; a < aps.length; a++)
- {
- SequenceGroup sg = new SequenceGroup(_sg);
- AlignViewport viewport = aps[a].av;
-
- // Propagate group colours in each view
- if (viewport.getGlobalColourScheme() != null)
+ // stash colors in linked annotation row.
+ // doesn't work yet. TESTS!
+ int sstart=aa.sequenceRef!=null ? aa.sequenceRef.getStart()-1 : 0;
+ Annotation ae;
+ Color gpcol = null;
+ int[] seqpos=null;
+ for (BitSet gp : colors.keySet())
{
- cs = viewport.getGlobalColourScheme().getInstance(viewport, sg);
- sg.setColourScheme(cs);
- sg.getGroupColourScheme().setThreshold(
- viewport.getResidueShading().getThreshold(),
- viewport.isIgnoreGapsConsensus());
-
- if (viewport.getResidueShading().conservationApplied())
+ gpcol = colors.get(gp);
+ for (int p = gp.nextSetBit(0); p >= 0 && p < Integer.MAX_VALUE; p = gp.nextSetBit(p + 1))
{
- Conservation c = new Conservation("Group",
- sg.getSequences(null), sg.getStartRes(),
- sg.getEndRes());
- c.calculate();
- c.verdict(false, viewport.getConsPercGaps());
- sg.cs.setConservation(c);
+ if (cm instanceof MappableContactMatrixI)
+ {
+ MappableContactMatrixI mcm = (MappableContactMatrixI) cm;
+ seqpos = mcm.getMappedPositionsFor(aa.sequenceRef,p);
+ if (seqpos==null)
+ {
+ // no mapping for this column.
+ continue;
+ }
+ // TODO: handle ranges...
+ ae = aa.getAnnotationForPosition(seqpos[0]);
+ } else {
+ ae = aa.getAnnotationForPosition(p+sstart);
+ }
+ if (ae != null)
+ {
+ ae.colour = gpcol.brighter().darker();
+ }
}
}
- // indicate that associated structure views will need an update
- viewport.setUpdateStructures(true);
- // propagate structure view update and sequence group to complement view
- viewport.addSequenceGroup(sg);
}
}
}
}
+ private boolean isColumnForNodeSelected(BinaryNode bn)
+ {
+ SequenceI rseq = tp.assocAnnotation.sequenceRef;
+ int colm = -1;
+ try
+ {
+ colm = Integer.parseInt(
+ bn.getName().substring(bn.getName().indexOf("c") + 1));
+ } catch (Exception e)
+ {
+ return false;
+ }
+ if (av==null||av.getAlignment()==null)
+ {
+ // alignment is closed
+ return false;
+ }
+ ColumnSelection cs = av.getColumnSelection();
+
+ HiddenColumns hc = av.getAlignment().getHiddenColumns();
+ int offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + colm)
+ : colm;
+
+ if (!av.hasHiddenColumns())
+ {
+ return cs.contains(offp-1);
+ }
+ if (hc.isVisible(offp-1))
+ {
+ return cs.contains(offp-1);
+// return cs.contains(hc.absoluteToVisibleColumn(offp));
+ }
+ return false;
+ }
+
+ private BitSet createColumnGroupFor(Vector<BinaryNode> l,
+ Color col)
+ {
+ BitSet gp=new BitSet();
+ for (BinaryNode bn:l)
+ {
+ int colm=-1;
+ if (bn.element()!=null && bn.element()instanceof Integer)
+ { colm = (Integer)bn.element();
+ } else {
+ // parse out from nodename
+ try {
+ colm = Integer.parseInt(bn.getName().substring(bn.getName().indexOf("c")+1));
+ } catch (Exception e)
+ {
+ continue;
+ }
+ }
+ gp.set(colm);
+ }
+ return gp;
+ }
+
+ private void markColumnsFor(AlignmentPanel[] aps, Vector<BinaryNode> l,
+ Color col)
+ {
+ SequenceI rseq = tp.assocAnnotation.sequenceRef;
+
+ if (av == null || av.getAlignment() == null)
+ {
+ // alignment is closed
+ return;
+ }
+
+ for (BinaryNode bn : l)
+ {
+ int colm = -1;
+ try
+ {
+ colm = Integer.parseInt(
+ bn.getName().substring(bn.getName().indexOf("c") + 1));
+ } catch (Exception e)
+ {
+ continue;
+ }
+ // TODO - sort indices for faster lookup
+
+ ColumnSelection cs = av.getColumnSelection();
+ HiddenColumns hc = av.getAlignment().getHiddenColumns();
+ ContactMatrixI cm = av.getContactMatrix(tp.assocAnnotation);
+ MappableContactMatrixI mcm = null;
+ int offp;
+ if (cm instanceof MappableContactMatrixI)
+ {
+ mcm = (MappableContactMatrixI) cm;
+ int[] seqpos = mcm.getMappedPositionsFor(tp.assocAnnotation.sequenceRef,colm);
+ if (seqpos==null)
+ {
+ // no mapping for this column.
+ continue;
+ }
+ // TODO: handle ranges...
+ offp=seqpos[0];
+ }
+ else
+ {
+ offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + colm)
+ : colm;
+ }
+ if (!av.hasHiddenColumns() || hc.isVisible(offp - 1))
+ {
+ if (cs.contains(offp - 1))
+ {
+ cs.removeElement(offp - 1);
+ }
+ else
+ {
+ cs.addElement(offp - 1);
+ }
+ }
+ }
+ }
+
+ public void createSeqGroupFor(AlignmentPanel[] aps, Vector<BinaryNode> l,
+ Color col)
+ {
+
+ Vector<SequenceI> sequences = new Vector<>();
+
+ for (int j = 0; j < l.size(); j++)
+ {
+ SequenceI s1 = (SequenceI) l.elementAt(j).element();
+
+ if (!sequences.contains(s1))
+ {
+ sequences.addElement(s1);
+ }
+ }
+
+ ColourSchemeI cs = null;
+ SequenceGroup _sg = new SequenceGroup(sequences, null, cs, true, true,
+ false, 0, av.getAlignment().getWidth() - 1);
+
+ _sg.setName("JTreeGroup:" + _sg.hashCode());
+ _sg.setIdColour(col);
+
+ for (int a = 0; a < aps.length; a++)
+ {
+ SequenceGroup sg = new SequenceGroup(_sg);
+ AlignViewport viewport = aps[a].av;
+
+ // Propagate group colours in each view
+ if (viewport.getGlobalColourScheme() != null)
+ {
+ cs = viewport.getGlobalColourScheme().getInstance(viewport, sg);
+ sg.setColourScheme(cs);
+ sg.getGroupColourScheme().setThreshold(
+ viewport.getResidueShading().getThreshold(),
+ viewport.isIgnoreGapsConsensus());
+
+ if (viewport.getResidueShading().conservationApplied())
+ {
+ Conservation c = new Conservation("Group", sg.getSequences(null),
+ sg.getStartRes(), sg.getEndRes());
+ c.calculate();
+ c.verdict(false, viewport.getConsPercGaps());
+ sg.cs.setConservation(c);
+ }
+ }
+ // indicate that associated structure views will need an update
+ viewport.setUpdateStructures(true);
+ // propagate structure view update and sequence group to complement view
+ viewport.addSequenceGroup(sg);
+ }
+ }
+
/**
* DOCUMENT ME!
*