X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=6fbd4225fd3688742083d4ed93afa52106874982;hb=fa48c836ad6e85a9e8146177cc865f4a061dc1a4;hp=3730b566ebe936d355bde47af1c3577bbadfd3e1;hpb=be27d7b3cadbfb5c488066034c48b1735799b429;p=jalview.git diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index 3730b56..6fbd422 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -20,21 +20,6 @@ */ package jalview.gui; -import jalview.analysis.Conservation; -import jalview.analysis.TreeModel; -import jalview.api.AlignViewportI; -import jalview.datamodel.Sequence; -import jalview.datamodel.SequenceGroup; -import jalview.datamodel.SequenceI; -import jalview.datamodel.SequenceNode; -import jalview.schemes.ColourSchemeI; -import jalview.schemes.ColourSchemeProperty; -import jalview.schemes.UserColourScheme; -import jalview.structure.SelectionSource; -import jalview.util.Format; -import jalview.util.MappingUtils; -import jalview.util.MessageManager; - import java.awt.Color; import java.awt.Dimension; import java.awt.Font; @@ -51,17 +36,42 @@ import java.awt.print.PageFormat; import java.awt.print.Printable; import java.awt.print.PrinterException; import java.awt.print.PrinterJob; -import java.util.Enumeration; +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 java.util.Map.Entry; import java.util.Vector; -import javax.swing.JColorChooser; import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.SwingUtilities; 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; +import jalview.datamodel.SequenceI; +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! * @@ -80,9 +90,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, TreePanel tp; - AlignViewport av; + private AlignViewport av; - AlignmentPanel ap; + private AlignmentPanel ap; Font font; @@ -100,17 +110,17 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, int offy; - float threshold; + private float threshold; String longestName; int labelLength = -1; - Hashtable nameHash = new Hashtable(); + Map nameHash = new Hashtable<>(); - Hashtable nodeHash = new Hashtable(); + Map nodeHash = new Hashtable<>(); - SequenceNode highlightNode; + BinaryNode highlightNode; boolean applyToAllViews = false; @@ -130,14 +140,48 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, { this.tp = tp; this.av = ap.av; - this.ap = ap; + this.setAssociatedPanel(ap); font = av.getFont(); 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! * @@ -175,15 +219,22 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, tree.findHeight(tree.getTopNode()); // Now have to calculate longest name based on the leaves - Vector leaves = tree.findLeaves(tree.getTopNode()); + Vector leaves = tree.findLeaves(tree.getTopNode()); 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++) { - SequenceNode lf = leaves.elementAt(i); + BinaryNode lf = leaves.elementAt(i); - if (lf.isPlaceholder()) + if (lf instanceof SequenceNode && ((SequenceNode) lf).isPlaceholder()) { has_placeholders = true; } @@ -194,6 +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); @@ -217,7 +276,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * @param offy * DOCUMENT ME! */ - public void drawNode(Graphics g, SequenceNode node, float chunk, + public void drawNode(Graphics g, BinaryNode node, double chunk, double wscale, int width, int offx, int offy) { if (node == null) @@ -261,7 +320,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (showDistances && (node.dist > 0)) { - nodeLabel = new Format("%-.2f").form(node.dist); + nodeLabel = new Format("%g").form(node.dist); } if (showBootstrap && node.bootstrap > -1) @@ -279,8 +338,10 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, g.drawString(nodeLabel, xstart + 2, ypos - 2); } - String name = (markPlaceholders && 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 +352,22 @@ 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); @@ -307,9 +380,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } 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; @@ -332,10 +405,10 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, g.fillRect(xend - 2, ypos - 2, 4, 4); } - int ystart = (int) (((SequenceNode) node.left()).ycount * chunk) - + offy; - int yend = (int) (((SequenceNode) node.right()).ycount * chunk) - + offy; + 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; Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5); nodeHash.put(node, pos); @@ -347,7 +420,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (showDistances && (node.dist > 0)) { - nodeLabel = new Format("%-.2f").form(node.dist); + nodeLabel = new Format("%g").form(node.dist); } if (showBootstrap && node.bootstrap > -1) @@ -379,31 +452,25 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, */ public Object findElement(int x, int y) { - Enumeration keys = nameHash.keys(); - - while (keys.hasMoreElements()) + for (Entry entry : nameHash.entrySet()) { - Object ob = keys.nextElement(); - Rectangle rect = (Rectangle) nameHash.get(ob); + Rectangle rect = entry.getValue(); if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) && (y <= (rect.y + rect.height))) { - return ob; + return entry.getKey(); } } - keys = nodeHash.keys(); - - while (keys.hasMoreElements()) + for (Entry entry : nodeHash.entrySet()) { - Object ob = keys.nextElement(); - Rectangle rect = (Rectangle) nodeHash.get(ob); + Rectangle rect = entry.getValue(); if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) && (y <= (rect.y + rect.height))) { - return ob; + return entry.getKey(); } } @@ -421,15 +488,14 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, int width = getWidth(); int height = getHeight(); - SequenceNode top = tree.getTopNode(); + BinaryNode top = tree.getTopNode(); - double wscale = ((width * .8) - (offx * 2)) - / tree.getMaxHeight(); + double wscale = ((width * .8) - (offx * 2)) / tree.getMaxHeight(); if (top.count == 0) { - top.count = ((SequenceNode) top.left()).count - + ((SequenceNode) top.right()).count; + top.count = ((BinaryNode) top.left()).count + + ((BinaryNode) top.right()).count; } float chunk = (float) (height - (offy)) / top.count; @@ -455,7 +521,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * @param offy * DOCUMENT ME! */ - public void pickNode(Rectangle pickBox, SequenceNode node, float chunk, + public void pickNode(Rectangle pickBox, BinaryNode node, float chunk, double wscale, int width, int offx, int offy) { if (node == null) @@ -466,9 +532,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if ((node.left() == null) && (node.right() == null)) { double height = node.height; - double dist = node.dist; - - int xstart = (int) ((height - dist) * wscale) + offx; + // double dist = node.dist; + // int xstart = (int) ((height - dist) * wscale) + offx; int xend = (int) (height * wscale) + offx; int ypos = (int) (node.ycount * chunk) + offy; @@ -489,9 +554,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } else { - pickNode(pickBox, (SequenceNode) node.left(), chunk, wscale, width, + pickNode(pickBox, (BinaryNode) node.left(), chunk, wscale, width, offx, offy); - pickNode(pickBox, (SequenceNode) node.right(), chunk, wscale, width, + pickNode(pickBox, (BinaryNode) node.right(), chunk, wscale, width, offx, offy); } } @@ -504,36 +569,28 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * @param c * DOCUMENT ME! */ - public void setColor(SequenceNode node, Color c) + public void setColor(BinaryNode node, Color c) { if (node == null) { return; } - if ((node.left() == null) && (node.right() == null)) // TODO: internal node + node.color = c; + if (node.element() instanceof SequenceI) { - node.color = c; - - if (node.element() instanceof SequenceI) + final SequenceI seq = (SequenceI) node.element(); + AlignmentPanel[] aps = getAssociatedPanels(); + if (aps != null) { - AlignmentPanel[] aps = getAssociatedPanels(); - if (aps != null) + for (int a = 0; a < aps.length; a++) { - for (int a = 0; a < aps.length; a++) - { - final SequenceI seq = (SequenceI) node.element(); - aps[a].av.setSequenceColour(seq, c); - } + aps[a].av.setSequenceColour(seq, c); } } } - else - { - node.color = c; - setColor((SequenceNode) node.left(), c); - setColor((SequenceNode) node.right(), c); - } + setColor((BinaryNode) node.left(), c); + setColor((BinaryNode) node.right(), c); } /** @@ -550,7 +607,16 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, public void run() { PrinterJob printJob = PrinterJob.getPrinterJob(); - PageFormat pf = printJob.pageDialog(printJob.defaultPage()); + PageFormat defaultPage = printJob.defaultPage(); + PageFormat pf = printJob.pageDialog(defaultPage); + + if (defaultPage == pf) + { + /* + * user cancelled + */ + return; + } printJob.setPrintable(this, pf); @@ -644,21 +710,22 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (tree == null) { - g.drawString(MessageManager.getString("label.calculating_tree") - + "....", 20, getHeight() / 2); + g.drawString( + MessageManager.getString("label.calculating_tree") + "....", + 20, getHeight() / 2); } else { fm = g.getFontMetrics(font); - if (nameHash.size() == 0) + int nameCount = nameHash.size(); + if (nameCount == 0) { repaint(); } - if (fitToWindow - || (!fitToWindow && (scrollPane.getHeight() > ((fm - .getHeight() * nameHash.size()) + offy)))) + if (fitToWindow || (!fitToWindow && (scrollPane + .getHeight() > ((fm.getHeight() * nameCount) + offy)))) { draw(g, scrollPane.getWidth(), scrollPane.getHeight()); setPreferredSize(null); @@ -666,8 +733,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, else { setPreferredSize(new Dimension(scrollPane.getWidth(), - fm.getHeight() * nameHash.size())); - draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size()); + fm.getHeight() * nameCount)); + draw(g, scrollPane.getWidth(), fm.getHeight() * nameCount); } scrollPane.revalidate(); @@ -709,6 +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; @@ -719,15 +787,15 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, double wscale = (width - labelLength - (offx * 2)) / tree.getMaxHeight(); - SequenceNode top = tree.getTopNode(); + BinaryNode top = tree.getTopNode(); if (top.count == 0) { - top.count = ((SequenceNode) top.left()).count - + ((SequenceNode) top.right()).count; + top.count = ((BinaryNode) top.left()).count + + ((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); @@ -742,7 +810,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, g2.setColor(Color.gray); } - int x = (int) ((threshold * (getWidth() - labelLength - (2 * offx))) + offx); + int x = (int) ((threshold * (getWidth() - labelLength - (2 * offx))) + + offx); g2.drawLine(x, 0, x, getHeight()); } @@ -809,12 +878,18 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } else { - Vector leaves = tree.findLeaves(highlightNode); - - for (int i = 0; i < leaves.size(); i++) + Vector leaves = tree.findLeaves(highlightNode); + if (tp.isColumnWise()) + { + markColumnsFor(getAssociatedPanels(), leaves, Color.red,false); + } + else { - SequenceI seq = (SequenceI) leaves.elementAt(i).element(); - treeSelectionChanged(seq); + for (int i = 0; i < leaves.size(); i++) + { + SequenceI seq = (SequenceI) leaves.elementAt(i).element(); + treeSelectionChanged(seq); + } } av.sendSelection(); } @@ -830,15 +905,19 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, */ void chooseSubtreeColour() { - Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_subtree_colour"), - highlightNode.color); - if (col != null) + String ttl = MessageManager.getString("label.select_subtree_colour"); + ColourChooserListener listener = new ColourChooserListener() { - setColor(highlightNode, col); - PaintRefresher.Refresh(tp, ap.av.getSequenceSetId()); - repaint(); - } + @Override + public void colourSelected(Color c) + { + setColor(highlightNode, c); + PaintRefresher.Refresh(tp, ap.av.getSequenceSetId()); + repaint(); + } + }; + JalviewColourChooser.showColourChooser(this, ttl, highlightNode.color, + listener); } @Override @@ -848,11 +927,11 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Object ob = findElement(evt.getX(), evt.getY()); - if (ob instanceof SequenceNode) + if (ob instanceof BinaryNode) { - highlightNode = (SequenceNode) ob; - this.setToolTipText("" - + MessageManager.getString("label.highlightnode")); + highlightNode = (BinaryNode) ob; + this.setToolTipText( + "" + MessageManager.getString("label.highlightnode")); repaint(); } @@ -917,12 +996,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (ob instanceof SequenceI) { treeSelectionChanged((Sequence) ob); - PaintRefresher.Refresh(tp, ap.av.getSequenceSetId()); + PaintRefresher.Refresh(tp, + getAssociatedPanel().av.getSequenceSetId()); repaint(); av.sendSelection(); return; } - else if (!(ob instanceof SequenceNode)) + else if (!(ob instanceof BinaryNode)) { // Find threshold if (tree.getMaxHeight() != 0) @@ -930,7 +1010,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, threshold = (float) (x - offx) / (float) (getWidth() - labelLength - (2 * offx)); - List groups = tree.groupNodes(threshold); + List groups = tree.groupNodes(threshold); setColor(tree.getTopNode(), Color.black); AlignmentPanel[] aps = getAssociatedPanels(); @@ -949,119 +1029,285 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, .deleteAllGroups(); aps[a].av.getCodingComplement().clearSequenceColours(); } + aps[a].av.setUpdateStructures(true); } colourGroups(groups); - } - PaintRefresher.Refresh(tp, ap.av.getSequenceSetId()); + /* + * clear partition (don't show vertical line) if + * it is to the right of all nodes + */ + if (groups.isEmpty()) + { + threshold = 0f; + } + } + Console.log.debug("Tree cut threshold set at:" + threshold); + PaintRefresher.Refresh(tp, + getAssociatedPanel().av.getSequenceSetId()); repaint(); } } - void colourGroups(List groups) + 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)); - - Vector sequences = new Vector(); - - for (int j = 0; j < l.size(); j++) + Vector l = tree.findLeaves(groups.get(i)); + if (!tp.isColumnWise()) { - SequenceI s1 = (SequenceI) l.elementAt(j).element(); + 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)); + } } + cm.transferGroupColorsTo(aa); } + } - ColourSchemeI cs = null; - SequenceGroup sg = new SequenceGroup(sequences, null, cs, true, true, - false, 0, av.getAlignment().getWidth() - 1); - - if (av.getGlobalColourScheme() != null) + // 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) + { + ((AlignViewport) codingComplement).getAlignPanel() + .updateAnnotation(); + } + } + } + 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 = 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(); + 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) { - if (av.getGlobalColourScheme() instanceof UserColourScheme) + 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) { - cs = new UserColourScheme( - ((UserColourScheme) av.getGlobalColourScheme()) - .getColours()); + offp = rseq.findIndex(pos[0]); + } + } else { + offp = colm; + } + } + if (offp<=0) + { + return false; + } + 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; } - else + } + gp.set(colm); + } + return gp; + } + + private void markColumnsFor(AlignmentPanel[] aps, Vector l, + Color col, boolean clearSelected) + { + 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( + rseq, colm); + if (seqpos == null) { - cs = ColourSchemeProperty.getColourScheme(sg, - ColourSchemeProperty.getColourName(av - .getGlobalColourScheme())); + // no mapping for this column. + continue; } - // cs is null if shading is an annotationColourGradient - // if (cs != null) - // { - // cs.setThreshold(av.getViewportColourScheme().getThreshold(), - // av.isIgnoreGapsConsensus()); - // } + // TODO: handle ranges... + offp = rseq.findIndex(seqpos[0])-1; + } + else + { + offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + colm) + : colm; } - sg.setColourScheme(cs); - sg.getGroupColourScheme().setThreshold( - av.getResidueShading().getThreshold(), - av.isIgnoreGapsConsensus()); - // sg.recalcConservation(); - sg.setName("JTreeGroup:" + sg.hashCode()); - sg.setIdColour(col); - - for (int a = 0; a < aps.length; a++) + if (!av.hasHiddenColumns() || hc.isVisible(offp)) { - if (aps[a].av.getGlobalColourScheme() != null - && aps[a].av.getResidueShading() - .conservationApplied()) + if (clearSelected || cs.contains(offp)) { - Conservation c = new Conservation("Group", sg.getSequences(null), - sg.getStartRes(), sg.getEndRes()); - c.calculate(); - c.verdict(false, aps[a].av.getConsPercGaps()); - sg.cs.setConservation(c); + cs.removeElement(offp); } - - aps[a].av.getAlignment().addGroup(new SequenceGroup(sg)); - // TODO can we push all of the below into AlignViewportI? - final AlignViewportI codingComplement = aps[a].av - .getCodingComplement(); - if (codingComplement != null) + else { - SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, av, - codingComplement); - if (mappedGroup.getSequences().size() > 0) - { - codingComplement.getAlignment().addGroup(mappedGroup); - for (SequenceI seq : mappedGroup.getSequences()) - { - codingComplement.setSequenceColour(seq, col.brighter()); - } - } + cs.addElement(offp); } } } + PaintRefresher.Refresh(tp, av.getSequenceSetId()); + } + + 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); - // notify the panel(s) to redo any group specific stuff. for (int a = 0; a < aps.length; a++) { - aps[a].updateAnnotation(); - // TODO: JAL-868 - need to ensure view colour change message is broadcast - // to any Jmols listening in - 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); } } @@ -1109,7 +1355,47 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } else { - return new AlignmentPanel[] { ap }; + return new AlignmentPanel[] { getAssociatedPanel() }; } } + + public AlignmentPanel getAssociatedPanel() + { + return ap; + } + + public void setAssociatedPanel(AlignmentPanel ap) + { + this.ap = ap; + } + + public AlignViewport getViewport() + { + return av; + } + + public void setViewport(AlignViewport av) + { + this.av = av; + } + + public float getThreshold() + { + return threshold; + } + + public void setThreshold(float threshold) + { + this.threshold = threshold; + } + + public boolean isApplyToAllViews() + { + return this.applyToAllViews; + } + + public void setApplyToAllViews(boolean applyToAllViews) + { + this.applyToAllViews = applyToAllViews; + } }