X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=425f7105c3dd48acfc671a525308c013ff3b37eb;hb=e67a74ee1dac618d941fce0fc5ef4561f76380b1;hp=a1bcebd25a43917bf7d0561cc58889ee4219638b;hpb=8fbc01654883e68f8843ad6632efaabfaf21692e;p=jalview.git diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index a1bcebd..425f710 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -36,6 +36,9 @@ import java.awt.print.PageFormat; 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; @@ -50,7 +53,12 @@ import javax.swing.ToolTipManager; 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; @@ -60,6 +68,7 @@ import jalview.schemes.ColourSchemeI; import jalview.structure.SelectionSource; import jalview.util.Format; import jalview.util.MessageManager; +import jalview.ws.datamodel.MappableContactMatrixI; /** * DOCUMENT ME! @@ -182,7 +191,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, { BinaryNode lf = leaves.elementAt(i); - if (lf instanceof SequenceNode && ((SequenceNode)lf).isPlaceholder()) + if (lf instanceof SequenceNode && ((SequenceNode) lf).isPlaceholder()) { has_placeholders = true; } @@ -278,9 +287,10 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, g.drawString(nodeLabel, xstart + 2, ypos - 2); } - String name = (markPlaceholders && ((node instanceof SequenceNode && ((SequenceNode)node).isPlaceholder()))) - ? (PLACEHOLDER + node.getName()) - : node.getName(); + String name = (markPlaceholders && ((node instanceof SequenceNode + && ((SequenceNode) node).isPlaceholder()))) + ? (PLACEHOLDER + node.getName()) + : node.getName(); int charWidth = fm.stringWidth(name) + 3; int charHeight = font.getSize(); @@ -291,10 +301,22 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, 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); @@ -335,8 +357,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, int ystart = (node.left() == null ? 0 : (int) (((BinaryNode) node.left()).ycount * chunk)) + offy; int yend = (node.right() == null ? 0 - : (int) (((BinaryNode) node.right()).ycount * chunk)) - + offy; + : (int) (((BinaryNode) node.right()).ycount * chunk)) + offy; Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5); nodeHash.put(node, pos); @@ -704,6 +725,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (longestName == null || tree == null) { g2.drawString("Calculating tree.", 20, 20); + return; } offy = font.getSize() + 10; @@ -806,11 +828,17 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, else { Vector leaves = tree.findLeaves(highlightNode); - - for (int i = 0; i < leaves.size(); i++) + if (tp.isColumnWise()) { - SequenceI seq = (SequenceI) leaves.elementAt(i).element(); - treeSelectionChanged(seq); + 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(); } @@ -974,6 +1002,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, void colourGroups(List groups) { AlignmentPanel[] aps = getAssociatedPanels(); + List colGroups = new ArrayList<>(); + Map colors = new HashMap(); for (int i = 0; i < groups.size(); i++) { Color col = new Color((int) (Math.random() * 255), @@ -981,54 +1011,67 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, setColor(groups.get(i), col.brighter()); Vector l = tree.findLeaves(groups.get(i)); - - Vector sequences = new Vector<>(); - - for (int j = 0; j < l.size(); j++) + if (!tp.isColumnWise()) { - SequenceI s1 = (SequenceI) l.elementAt(j).element(); - - if (!sequences.contains(s1)) - { - sequences.addElement(s1); - } + createSeqGroupFor(aps, l, col); } - - 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++) + else { - SequenceGroup sg = new SequenceGroup(_sg); - AlignViewport viewport = aps[a].av; + BitSet gp = createColumnGroupFor(l, col); - // Propagate group colours in each view - if (viewport.getGlobalColourScheme() != null) + 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) { - cs = viewport.getGlobalColourScheme().getInstance(viewport, sg); - sg.setColourScheme(cs); - sg.getGroupColourScheme().setThreshold( - viewport.getResidueShading().getThreshold(), - viewport.isIgnoreGapsConsensus()); - - if (viewport.getResidueShading().conservationApplied()) + cm.updateGroups(colGroups); + for (BitSet gp : colors.keySet()) + { + cm.setColorForGroup(gp, colors.get(gp)); + } + } + // 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()) + { + 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); } } @@ -1047,6 +1090,202 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } } + 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(); + AlignmentAnnotation aa = tp.getAssocAnnotation(); + int offp=-1; + if (aa != null) + { + ContactMatrixI cm = av.getContactMatrix(aa); + if (cm instanceof MappableContactMatrixI) + { + MappableContactMatrixI mcm = (MappableContactMatrixI) cm; + int pos[]=mcm.getMappedPositionsFor(rseq, colm); + if (pos!=null) + { + offp=rseq.findIndex(pos[0])-1; + } else { + offp=-2; + } + } + } + if (offp==-1) + { + // assume a direct mapping to reference or column number + offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + colm) + : colm; + } + + if (!av.hasHiddenColumns()) + { + return cs.contains(offp); + } + if (hc.isVisible(offp - 1)) + { + return cs.contains(offp - 1); + // return cs.contains(hc.absoluteToVisibleColumn(offp)); + } + return false; + } + private BitSet createColumnGroupFor(Vector 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 l, + Color col) + { + SequenceI rseq = tp.assocAnnotation.sequenceRef; + if (av == null || av.getAlignment() == null) + { + // alignment is closed + return; + } + + // 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; + } + for (BinaryNode bn : l) + { + int colm = -1; + try + { + colm = Integer.parseInt( + bn.getName().substring(bn.getName().indexOf("c") + 1)); + } catch (Exception e) + { + continue; + } + if (mcm!=null) + { + int[] seqpos = mcm.getMappedPositionsFor( + tp.assocAnnotation.sequenceRef, colm); + if (seqpos == null) + { + // no mapping for this column. + continue; + } + // TODO: handle ranges... + offp = seqpos[0]-1; + } + 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 l, + Color col) + { + + Vector 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! *