X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=354feac25a5fde28c0d08a4327b0c426c111812e;hb=4acbc5576fb42bf6f97202811c92a7cfe9900076;hp=a1bcebd25a43917bf7d0561cc58889ee4219638b;hpb=8fbc01654883e68f8843ad6632efaabfaf21692e;p=jalview.git diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index a1bcebd..354feac 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -36,6 +36,7 @@ import java.awt.print.PageFormat; import java.awt.print.Printable; import java.awt.print.PrinterException; import java.awt.print.PrinterJob; +import java.util.BitSet; import java.util.Hashtable; import java.util.List; import java.util.Map; @@ -51,6 +52,8 @@ import jalview.analysis.Conservation; import jalview.analysis.TreeModel; import jalview.api.AlignViewportI; import jalview.datamodel.BinaryNode; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; @@ -291,10 +294,22 @@ 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.getColumnWise()) + { + 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); @@ -704,6 +719,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (longestName == null || tree == null) { g2.drawString("Calculating tree.", 20, 20); + return; } offy = font.getSize() + 10; @@ -806,12 +822,15 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, else { Vector leaves = tree.findLeaves(highlightNode); - + if (tp.getColumnWise()) { + 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(); } @@ -981,69 +1000,133 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, setColor(groups.get(i), col.brighter()); Vector l = tree.findLeaves(groups.get(i)); + if (!tp.getColumnWise()) { + createSeqGroupFor(aps, l, col); + } else { + markColumnsFor(aps,l,col); + } + } - Vector sequences = new Vector<>(); - - for (int j = 0; j < l.size(); j++) + // notify the panel(s) to redo any group specific stuff + // also updates structure views if necessary + for (int a = 0; a < aps.length; a++) + { + aps[a].updateAnnotation(); + final AlignViewportI codingComplement = aps[a].av + .getCodingComplement(); + if (codingComplement != null) { - SequenceI s1 = (SequenceI) l.elementAt(j).element(); - - if (!sequences.contains(s1)) - { - sequences.addElement(s1); - } + ((AlignViewport) codingComplement).getAlignPanel() + .updateAnnotation(); } + } + } - ColourSchemeI cs = null; - SequenceGroup _sg = new SequenceGroup(sequences, null, cs, true, true, - false, 0, av.getAlignment().getWidth() - 1); + 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; + } + ColumnSelection cs = av.getColumnSelection(); + HiddenColumns hc = av.getAlignment().getHiddenColumns(); + int offp = (rseq != null) ? rseq.findIndex(rseq.getStart() - 1 + colm) + : colm; - _sg.setName("JTreeGroup:" + _sg.hashCode()); - _sg.setIdColour(col); + if (!av.hasHiddenColumns() || hc.isVisible(offp)) + { + return cs.contains(offp); + } + return false; + } - for (int a = 0; a < aps.length; a++) + private void markColumnsFor(AlignmentPanel[] aps, Vector l, + Color col) + { + SequenceI rseq = tp.assocAnnotation.sequenceRef; + for (BinaryNode bn:l) + { + int colm=-1; + try { + colm = Integer.parseInt(bn.getName().substring(bn.getName().indexOf("c")+1)); + } catch (Exception e) { - 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()) + continue; + } + ColumnSelection cs = av.getColumnSelection(); + HiddenColumns hc = av.getAlignment().getHiddenColumns(); + { + int offp = (rseq!=null) ? rseq.findIndex(rseq.getStart()-1+colm) : colm; + + if (!av.hasHiddenColumns() || hc.isVisible(offp)) + { + if (cs.contains(offp)) { - Conservation c = new Conservation("Group", - sg.getSequences(null), sg.getStartRes(), - sg.getEndRes()); - c.calculate(); - c.verdict(false, viewport.getConsPercGaps()); - sg.cs.setConservation(c); + cs.removeElement(offp); + } else { + cs.addElement(offp); } } - // 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); + } + } + } + + 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); } } - // notify the panel(s) to redo any group specific stuff - // also updates structure views if necessary + 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++) { - aps[a].updateAnnotation(); - final AlignViewportI codingComplement = aps[a].av - .getCodingComplement(); - if (codingComplement != null) + SequenceGroup sg = new SequenceGroup(_sg); + AlignViewport viewport = aps[a].av; + + // Propagate group colours in each view + if (viewport.getGlobalColourScheme() != null) { - ((AlignViewport) codingComplement).getAlignPanel() - .updateAnnotation(); + 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); } }