X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=9180d52269a0dc660e80e4ef8639742bf384919c;hb=0ebbad305e982eeda562a1842362dc415c36cc8d;hp=3a055ae44cab8ac696fc7c2c9c006214195521dc;hpb=fdde9a078d7bdb46ed9fb7fe115ea83c84a19c81;p=jalview.git diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index 3a055ae..9180d52 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -53,7 +53,9 @@ 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; @@ -65,8 +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! @@ -141,9 +145,44 @@ 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! * @@ -185,6 +224,13 @@ 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); @@ -200,6 +246,18 @@ 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); @@ -223,7 +281,7 @@ 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) @@ -353,9 +411,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } int ystart = (node.left() == null ? 0 - : (int) (((BinaryNode) node.left()).ycount * chunk)) + offy; + : (int) (node.left().ycount * chunk)) + offy; int yend = (node.right() == null ? 0 - : (int) (((BinaryNode) node.right()).ycount * chunk)) + offy; + : (int) (node.right().ycount * chunk)) + offy; Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5); nodeHash.put(node, pos); @@ -738,8 +796,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (top.count == 0) { - top.count = ((BinaryNode) top.left()).count - + ((BinaryNode) top.right()).count; + top.count = top.left().count + top.right().count; } float chunk = (float) (height - (offy)) / top.count; @@ -828,7 +885,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Vector leaves = tree.findLeaves(highlightNode); if (tp.isColumnWise()) { - markColumnsFor(getAssociatedPanels(), leaves, Color.red); + markColumnsFor(getAssociatedPanels(), leaves, Color.red, false); } else { @@ -989,7 +1046,7 @@ 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(); @@ -1004,8 +1061,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, 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)); @@ -1035,6 +1092,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, cm.setColorForGroup(gp, colors.get(gp)); } } + cm.transferGroupColorsTo(aa); } } @@ -1053,14 +1111,19 @@ 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; @@ -1071,18 +1134,46 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, return false; } ColumnSelection cs = av.getColumnSelection(); - HiddenColumns hc = av.getAlignment().getHiddenColumns(); - int offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + 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; + } + offp -= 2; if (!av.hasHiddenColumns()) { - return cs.contains(offp - 1); + return cs.contains(offp); } - if (hc.isVisible(offp - 1)) + if (hc.isVisible(offp)) { - return cs.contains(offp - 1); + return cs.contains(offp); // return cs.contains(hc.absoluteToVisibleColumn(offp)); } return false; @@ -1103,8 +1194,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, // parse out from nodename try { - colm = Integer.parseInt( - bn.getName().substring(bn.getName().indexOf("c") + 1)); + colm = parseColumnNode(bn); } catch (Exception e) { continue; @@ -1116,7 +1206,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } private void markColumnsFor(AlignmentPanel[] aps, Vector l, - Color col) + Color col, boolean clearSelected) { SequenceI rseq = tp.assocAnnotation.sequenceRef; if (av == null || av.getAlignment() == null) @@ -1125,6 +1215,16 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, 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; @@ -1136,25 +1236,35 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, { continue; } - ColumnSelection cs = av.getColumnSelection(); - HiddenColumns hc = av.getAlignment().getHiddenColumns(); + if (mcm != null) { - int offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + colm) + 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 - 1)) + } + if (!av.hasHiddenColumns() || hc.isVisible(offp)) + { + if (clearSelected || cs.contains(offp)) { - if (cs.contains(offp - 1)) - { - cs.removeElement(offp - 1); - } - else - { - cs.addElement(offp - 1); - } + cs.removeElement(offp); + } + else + { + cs.addElement(offp); } } } + PaintRefresher.Refresh(tp, av.getSequenceSetId()); } public void createSeqGroupFor(AlignmentPanel[] aps, Vector l,