X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=6fbd4225fd3688742083d4ed93afa52106874982;hb=fa48c836ad6e85a9e8146177cc865f4a061dc1a4;hp=7bdb673028cd6f9f31f3211fb96fd36184d09392;hpb=581a86ef3fc695b8a906bc6d1746cc5f39fcba35;p=jalview.git diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index 7bdb673..6fbd422 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -36,7 +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; @@ -51,8 +53,12 @@ import javax.swing.ToolTipManager; import jalview.analysis.Conservation; import jalview.analysis.TreeModel; import jalview.api.AlignViewportI; +import jalview.bin.Console; +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; @@ -61,8 +67,10 @@ import jalview.datamodel.SequenceNode; import jalview.gui.JalviewColourChooser.ColourChooserListener; import jalview.schemes.ColourSchemeI; import jalview.structure.SelectionSource; +import jalview.util.ColorUtils; import jalview.util.Format; import jalview.util.MessageManager; +import jalview.ws.datamodel.MappableContactMatrixI; /** * DOCUMENT ME! @@ -137,9 +145,43 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, scrollPane = scroller; addMouseListener(this); addMouseMotionListener(this); + ToolTipManager.sharedInstance().registerComponent(this); } + public void clearSelectedLeaves() + { + Vector leaves = tp.getTree() + .findLeaves(tp.getTree().getTopNode()); + if (tp.isColumnWise()) + { + markColumnsFor(getAssociatedPanels(), leaves, Color.white, true); + } + else + { + for (AlignmentPanel ap : getAssociatedPanels()) + { + SequenceGroup selected = ap.av.getSelectionGroup(); + if (selected != null) + { + { + for (int i = 0; i < leaves.size(); i++) + { + SequenceI seq = (SequenceI) leaves.elementAt(i).element(); + if (selected.contains(seq)) + { + selected.addOrRemove(seq, false); + } + } + selected.recalcConservation(); + } + } + ap.av.sendSelection(); + } + } + PaintRefresher.Refresh(tp, av.getSequenceSetId()); + repaint(); + } /** * DOCUMENT ME! * @@ -181,11 +223,18 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, boolean has_placeholders = false; longestName = ""; + AlignmentAnnotation aa = tp.getAssocAnnotation(); + ContactMatrixI cm = (aa!=null) ? av.getContactMatrix(aa) : null; + if (cm!=null && cm.hasCutHeight()) + { + threshold=(float) cm.getCutHeight(); + } + for (int i = 0; i < leaves.size(); i++) { BinaryNode lf = leaves.elementAt(i); - if (lf instanceof SequenceNode && ((SequenceNode)lf).isPlaceholder()) + if (lf instanceof SequenceNode && ((SequenceNode) lf).isPlaceholder()) { has_placeholders = true; } @@ -196,6 +245,14 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, longestName = TreeCanvas.PLACEHOLDER + ((Sequence) lf.element()).getName(); } + if (tp.isColumnWise() && cm!=null) + { + // get color from group colours, if they are set for the matrix + try { + Color col = cm.getGroupColorForPosition(parseColumnNode(lf)); + setColor(lf,col.brighter()); + } catch (NumberFormatException ex) {}; + } } setMarkPlaceholders(has_placeholders); @@ -219,7 +276,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * @param offy * DOCUMENT ME! */ - public void drawNode(Graphics g, BinaryNode node, float chunk, + public void drawNode(Graphics g, BinaryNode node, double chunk, double wscale, int width, int offx, int offy) { if (node == null) @@ -281,9 +338,10 @@ 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(); @@ -295,7 +353,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, // Colour selected leaves differently boolean isSelected = false; - if (tp.getColumnWise()) + if (tp.isColumnWise()) { isSelected = isColumnForNodeSelected(node); } @@ -350,8 +408,7 @@ 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); @@ -719,6 +776,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (longestName == null || tree == null) { g2.drawString("Calculating tree.", 20, 20); + return; } offy = font.getSize() + 10; @@ -737,7 +795,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, + ((BinaryNode) top.right()).count; } - float chunk = (float) (height - (offy)) / top.count; + double chunk = (double) (height - (offy)) / (double)top.count; drawNode(g2, tree.getTopNode(), chunk, wscale, width, offx, offy); @@ -821,14 +879,17 @@ 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++) + if (tp.isColumnWise()) { - SequenceI seq = (SequenceI) leaves.elementAt(i).element(); - treeSelectionChanged(seq); + markColumnsFor(getAssociatedPanels(), leaves, Color.red,false); } + else + { + for (int i = 0; i < leaves.size(); i++) + { + SequenceI seq = (SequenceI) leaves.elementAt(i).element(); + treeSelectionChanged(seq); + } } av.sendSelection(); } @@ -981,7 +1042,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, threshold = 0f; } } - + Console.log.debug("Tree cut threshold set at:" + threshold); PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId()); repaint(); @@ -992,17 +1053,42 @@ 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), - (int) (Math.random() * 255), (int) (Math.random() * 255)); + Color col = ColorUtils.getARandomColor(); + setColor(groups.get(i), col.brighter()); Vector l = tree.findLeaves(groups.get(i)); - if (!tp.getColumnWise()) { + if (!tp.isColumnWise()) + { createSeqGroupFor(aps, l, col); - } else { - markColumnsFor(aps,l,col); + } + else + { + BitSet gp = createColumnGroupFor(l, col); + + 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) + { + cm.updateGroups(colGroups); + for (BitSet gp : colors.keySet()) + { + cm.setColorForGroup(gp, colors.get(gp)); + } + } + cm.transferGroupColorsTo(aa); } } @@ -1020,60 +1106,156 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } } } - + private int parseColumnNode(BinaryNode bn) throws NumberFormatException + { + return Integer.parseInt( + bn.getName().substring(bn.getName().indexOf("c") + 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)); + colm = parseColumnNode(bn); } 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() - 1 + colm) - : colm; + AlignmentAnnotation aa = tp.getAssocAnnotation(); + int offp=-1; + if (aa != null) + { + ContactMatrixI cm = av.getContactMatrix(aa); + // generally, we assume cm has 1:1 mapping to annotation row - probably wrong + // but.. if + if (cm instanceof MappableContactMatrixI) + { + int[] pos; + // use the mappable's mapping - always the case for PAE Matrices so good + // for 2.11.3 + MappableContactMatrixI mcm = (MappableContactMatrixI) cm; + pos = mcm.getMappedPositionsFor(rseq, colm + 1); + // finally, look up the position of the column + if (pos != null) + { + offp = rseq.findIndex(pos[0]); + } + } else { + offp = colm; + } + } + if (offp<=0) + { + return false; + } - if (!av.hasHiddenColumns() || hc.isVisible(offp)) + offp-=2; + if (!av.hasHiddenColumns()) + { + return cs.contains(offp); + } + if (hc.isVisible(offp)) { return cs.contains(offp); + // 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 = parseColumnNode(bn); + } catch (Exception e) + { + continue; + } + } + gp.set(colm); + } + return gp; + } private void markColumnsFor(AlignmentPanel[] aps, Vector l, - Color col) + Color col, boolean clearSelected) { SequenceI rseq = tp.assocAnnotation.sequenceRef; - for (BinaryNode bn:l) + if (av == null || av.getAlignment() == null) { - int colm=-1; - try { - colm = Integer.parseInt(bn.getName().substring(bn.getName().indexOf("c")+1)); + // 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; } - ColumnSelection cs = av.getColumnSelection(); - HiddenColumns hc = av.getAlignment().getHiddenColumns(); + if (mcm!=null) { - int offp = (rseq!=null) ? rseq.findIndex(rseq.getStart()-1+colm) : colm; - - if (!av.hasHiddenColumns() || hc.isVisible(offp)) - { - if (cs.contains(offp)) - { - cs.removeElement(offp); - } else { - cs.addElement(offp); - } + int[] seqpos = mcm.getMappedPositionsFor( + rseq, colm); + if (seqpos == null) + { + // no mapping for this column. + continue; } + // TODO: handle ranges... + offp = rseq.findIndex(seqpos[0])-1; } - } + else + { + offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + colm) + : colm; + } + if (!av.hasHiddenColumns() || hc.isVisible(offp)) + { + if (clearSelected || cs.contains(offp)) + { + cs.removeElement(offp); + } + else + { + cs.addElement(offp); + } + } + } + PaintRefresher.Refresh(tp, av.getSequenceSetId()); } public void createSeqGroupFor(AlignmentPanel[] aps, Vector l,