X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=6f143dbb5b54f24342db1cc7c355d17558822b99;hp=97cca4b34536c105a3a43e78c75ee3f2412ab71c;hb=20b5e49eaffdbc56b9d0274200a12204e362d5b1;hpb=d919b93d3c0a57e36c2a90a34a6788bca86bfe81 diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index 97cca4b..6f143db 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -1,34 +1,64 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; -import java.awt.print.*; -import javax.swing.*; - -import jalview.analysis.*; -import jalview.datamodel.*; -import jalview.schemes.*; -import jalview.util.*; +import java.awt.Color; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.FontMetrics; +import java.awt.Graphics; +import java.awt.Graphics2D; +import java.awt.Point; +import java.awt.Rectangle; +import java.awt.RenderingHints; +import java.awt.event.MouseEvent; +import java.awt.event.MouseListener; +import java.awt.event.MouseMotionListener; +import java.awt.print.PageFormat; +import java.awt.print.Printable; +import java.awt.print.PrinterException; +import java.awt.print.PrinterJob; +import java.util.Hashtable; +import java.util.List; +import java.util.Map; +import java.util.Map.Entry; +import java.util.Vector; + +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.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.Format; +import jalview.util.MessageManager; /** * DOCUMENT ME! @@ -37,20 +67,20 @@ import jalview.util.*; * @version $Revision$ */ public class TreeCanvas extends JPanel implements MouseListener, Runnable, - Printable, MouseMotionListener + Printable, MouseMotionListener, SelectionSource { /** DOCUMENT ME!! */ public static final String PLACEHOLDER = " * "; - NJTree tree; + TreeModel tree; JScrollPane scrollPane; TreePanel tp; - AlignViewport av; + private AlignViewport av; - AlignmentPanel ap; + private AlignmentPanel ap; Font font; @@ -68,15 +98,15 @@ 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; @@ -98,7 +128,7 @@ 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); @@ -137,19 +167,19 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * @param tree * DOCUMENT ME! */ - public void setTree(NJTree tree) + public void setTree(TreeModel tree) { this.tree = tree; tree.findHeight(tree.getTopNode()); // Now have to calculate longest name based on the leaves - Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector()); + Vector leaves = tree.findLeaves(tree.getTopNode()); boolean has_placeholders = false; longestName = ""; for (int i = 0; i < leaves.size(); i++) { - SequenceNode lf = (SequenceNode) leaves.elementAt(i); + SequenceNode lf = leaves.elementAt(i); if (lf.isPlaceholder()) { @@ -176,7 +206,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * DOCUMENT ME! * @param chunk * DOCUMENT ME! - * @param scale + * @param wscale * DOCUMENT ME! * @param width * DOCUMENT ME! @@ -186,7 +216,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * DOCUMENT ME! */ public void drawNode(Graphics g, SequenceNode node, float chunk, - float scale, int width, int offx, int offy) + double wscale, int width, int offx, int offy) { if (node == null) { @@ -196,17 +226,17 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if ((node.left() == null) && (node.right() == null)) { // Drawing leaf node - float height = node.height; - float dist = node.dist; + double height = node.height; + double dist = node.dist; - int xstart = (int) ((height - dist) * scale) + offx; - int xend = (int) (height * scale) + offx; + int xstart = (int) ((height - dist) * wscale) + offx; + int xend = (int) (height * wscale) + offx; int ypos = (int) (node.ycount * chunk) + offy; if (node.element() instanceof SequenceI) { - SequenceI seq = (SequenceI) ((SequenceNode) node).element(); + SequenceI seq = (SequenceI) node.element(); if (av.getSequenceColour(seq) == Color.white) { @@ -229,7 +259,7 @@ 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) @@ -247,8 +277,9 @@ 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.isPlaceholder()) + ? (PLACEHOLDER + node.getName()) + : node.getName(); int charWidth = fm.stringWidth(name) + 3; int charHeight = font.getSize(); @@ -256,14 +287,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Rectangle rect = new Rectangle(xend + 10, ypos - charHeight / 2, charWidth, charHeight); - nameHash.put((SequenceI) node.element(), rect); + nameHash.put(node.element(), rect); // Colour selected leaves differently SequenceGroup selected = av.getSelectionGroup(); if ((selected != null) - && selected.getSequences(null).contains( - (SequenceI) node.element())) + && selected.getSequences(null).contains(node.element())) { g.setColor(Color.gray); @@ -276,19 +306,19 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } else { - drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx, + drawNode(g, (SequenceNode) node.left(), chunk, wscale, width, offx, offy); - drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx, + drawNode(g, (SequenceNode) node.right(), chunk, wscale, width, offx, offy); - float height = node.height; - float dist = node.dist; + double height = node.height; + double dist = node.dist; - int xstart = (int) ((height - dist) * scale) + offx; - int xend = (int) (height * scale) + offx; + int xstart = (int) ((height - dist) * wscale) + offx; + int xend = (int) (height * wscale) + offx; int ypos = (int) (node.ycount * chunk) + offy; - g.setColor(((SequenceNode) node).color.darker()); + g.setColor(node.color.darker()); // Draw horizontal line g.drawLine(xstart, ypos, xend, ypos); @@ -301,22 +331,23 @@ 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) + int ystart = (node.left() == null ? 0 + : (int) (((SequenceNode) node.left()).ycount * chunk)) + offy; + int yend = (node.right() == null ? 0 + : (int) (((SequenceNode) node.right()).ycount * chunk)) + offy; Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5); nodeHash.put(node, pos); - g.drawLine((int) (height * scale) + offx, ystart, - (int) (height * scale) + offx, yend); + g.drawLine((int) (height * wscale) + offx, ystart, + (int) (height * wscale) + offx, yend); String nodeLabel = ""; if (showDistances && (node.dist > 0)) { - nodeLabel = new Format("%-.2f").form(node.dist); + nodeLabel = new Format("%g").form(node.dist); } if (showBootstrap && node.bootstrap > -1) @@ -348,31 +379,25 @@ 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(); } } @@ -392,8 +417,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, SequenceNode top = tree.getTopNode(); - float wscale = (float) ((width * .8) - (offx * 2)) - / tree.getMaxHeight(); + double wscale = ((width * .8) - (offx * 2)) / tree.getMaxHeight(); if (top.count == 0) { @@ -415,7 +439,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * DOCUMENT ME! * @param chunk * DOCUMENT ME! - * @param scale + * @param wscale * DOCUMENT ME! * @param width * DOCUMENT ME! @@ -425,7 +449,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * DOCUMENT ME! */ public void pickNode(Rectangle pickBox, SequenceNode node, float chunk, - float scale, int width, int offx, int offy) + double wscale, int width, int offx, int offy) { if (node == null) { @@ -434,11 +458,10 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if ((node.left() == null) && (node.right() == null)) { - float height = node.height; - float dist = node.dist; - - int xstart = (int) ((height - dist) * scale) + offx; - int xend = (int) (height * scale) + offx; + double height = node.height; + // double dist = node.dist; + // int xstart = (int) ((height - dist) * wscale) + offx; + int xend = (int) (height * wscale) + offx; int ypos = (int) (node.ycount * chunk) + offy; @@ -458,9 +481,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } else { - pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width, + pickNode(pickBox, (SequenceNode) node.left(), chunk, wscale, width, offx, offy); - pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width, + pickNode(pickBox, (SequenceNode) node.right(), chunk, wscale, width, offx, offy); } } @@ -480,28 +503,21 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, 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++) - { - aps[a].av.setSequenceColour((SequenceI) node.element(), c); - } + aps[a].av.setSequenceColour(seq, c); } } } - else - { - node.color = c; - setColor((SequenceNode) node.left(), c); - setColor((SequenceNode) node.right(), c); - } + setColor((SequenceNode) node.left(), c); + setColor((SequenceNode) node.right(), c); } /** @@ -514,10 +530,20 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } // put printing in a thread to avoid painting problems + @Override 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); @@ -548,6 +574,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * @throws PrinterException * DOCUMENT ME! */ + @Override public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException { @@ -602,6 +629,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * @param g * DOCUMENT ME! */ + @Override public void paintComponent(Graphics g) { super.paintComponent(g); @@ -609,20 +637,22 @@ 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); @@ -630,8 +660,8 @@ 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(); @@ -644,6 +674,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * @param fontSize * DOCUMENT ME! */ + @Override public void setFont(Font font) { this.font = font; @@ -669,9 +700,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, g2.fillRect(0, 0, width, height); g2.setFont(font); - if (longestName==null || tree ==null) + if (longestName == null || tree == null) { - g2.drawString("Calculating tree.",20,20); + g2.drawString("Calculating tree.", 20, 20); } offy = font.getSize() + 10; @@ -679,7 +710,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, labelLength = fm.stringWidth(longestName) + 20; // 20 allows for scrollbar - float wscale = (float) (width - labelLength - (offx * 2)) + double wscale = (width - labelLength - (offx * 2)) / tree.getMaxHeight(); SequenceNode top = tree.getTopNode(); @@ -705,86 +736,111 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, g2.setColor(Color.gray); } - int x = (int) ((threshold * (float) (getWidth() - labelLength - (2 * offx))) + offx); + int x = (int) ((threshold * (getWidth() - labelLength - (2 * offx))) + + offx); g2.drawLine(x, 0, x, getHeight()); } } /** - * DOCUMENT ME! + * Empty method to satisfy the MouseListener interface * * @param e - * DOCUMENT ME! */ + @Override public void mouseReleased(MouseEvent e) { + /* + * isPopupTrigger is set on mouseReleased on Windows + */ + if (e.isPopupTrigger()) + { + chooseSubtreeColour(); + e.consume(); // prevent mouseClicked happening + } } /** - * DOCUMENT ME! + * Empty method to satisfy the MouseListener interface * * @param e - * DOCUMENT ME! */ + @Override public void mouseEntered(MouseEvent e) { } /** - * DOCUMENT ME! + * Empty method to satisfy the MouseListener interface * * @param e - * DOCUMENT ME! */ + @Override public void mouseExited(MouseEvent e) { } /** - * DOCUMENT ME! + * Handles a mouse click on a tree node (clicks elsewhere are handled in + * mousePressed). Click selects the sub-tree, double-click swaps leaf nodes + * order, right-click opens a dialogue to choose colour for the sub-tree. * * @param e - * DOCUMENT ME! */ + @Override public void mouseClicked(MouseEvent evt) { - if (highlightNode != null) + if (highlightNode == null) { - if (SwingUtilities.isRightMouseButton(evt)) - { - Color col = JColorChooser.showDialog(this, - "Select Sub-Tree Colour", highlightNode.color); - if (col != null) - { - setColor(highlightNode, col); - } - } - else if (evt.getClickCount() > 1) + return; + } + + if (evt.getClickCount() > 1) + { + tree.swapNodes(highlightNode); + tree.reCount(tree.getTopNode()); + tree.findHeight(tree.getTopNode()); + } + else + { + Vector leaves = tree.findLeaves(highlightNode); + + for (int i = 0; i < leaves.size(); i++) { - tree.swapNodes(highlightNode); - tree.reCount(tree.getTopNode()); - tree.findHeight(tree.getTopNode()); + SequenceI seq = (SequenceI) leaves.elementAt(i).element(); + treeSelectionChanged(seq); } - else - { - Vector leaves = new Vector(); - tree.findLeaves(highlightNode, leaves); + av.sendSelection(); + } - for (int i = 0; i < leaves.size(); i++) - { - SequenceI seq = (SequenceI) ((SequenceNode) leaves.elementAt(i)) - .element(); - treeSelectionChanged(seq); - } - av.sendSelection(); - } + PaintRefresher.Refresh(tp, av.getSequenceSetId()); + repaint(); + } - PaintRefresher.Refresh(tp, av.getSequenceSetId()); - repaint(); - } + /** + * Offer the user the option to choose a colour for the highlighted node and + * its children; this colour is also applied to the corresponding sequence ids + * in the alignment + */ + void chooseSubtreeColour() + { + String ttl = MessageManager.getString("label.select_subtree_colour"); + ColourChooserListener listener = new ColourChooserListener() + { + @Override + public void colourSelected(Color c) + { + setColor(highlightNode, c); + PaintRefresher.Refresh(tp, ap.av.getSequenceSetId()); + repaint(); + } + }; + JalviewColourChooser.showColourChooser(this, ttl, highlightNode.color, + listener); } + @Override public void mouseMoved(MouseEvent evt) { av.setCurrentTree(tree); @@ -794,7 +850,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (ob instanceof SequenceNode) { highlightNode = (SequenceNode) ob; - this.setToolTipText("" + MessageManager.getString("label.highlightnode")); + this.setToolTipText( + "" + MessageManager.getString("label.highlightnode")); repaint(); } @@ -809,20 +866,48 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } } + @Override public void mouseDragged(MouseEvent ect) { } /** - * DOCUMENT ME! + * Handles a mouse press on a sequence name or the tree background canvas + * (click on a node is handled in mouseClicked). The action is to create + * groups by partitioning the tree at the mouse position. Colours for the + * groups (and sequence names) are generated randomly. * * @param e - * DOCUMENT ME! */ + @Override public void mousePressed(MouseEvent e) { av.setCurrentTree(tree); + /* + * isPopupTrigger is set for mousePressed (Mac) + * or mouseReleased (Windows) + */ + if (e.isPopupTrigger()) + { + if (highlightNode != null) + { + chooseSubtreeColour(); + } + return; + } + + /* + * defer right-click handling on Windows to + * mouseClicked; note isRightMouseButton + * also matches Cmd-click on Mac which should do + * nothing here + */ + if (SwingUtilities.isRightMouseButton(e)) + { + return; + } + int x = e.getX(); int y = e.getY(); @@ -831,7 +916,8 @@ 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; @@ -844,45 +930,62 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, threshold = (float) (x - offx) / (float) (getWidth() - labelLength - (2 * offx)); - tree.getGroups().removeAllElements(); - tree.groupNodes(tree.getTopNode(), threshold); + List groups = tree.groupNodes(threshold); setColor(tree.getTopNode(), Color.black); AlignmentPanel[] aps = getAssociatedPanels(); + // TODO push calls below into a single AlignViewportI method? + // see also AlignViewController.deleteGroups for (int a = 0; a < aps.length; a++) { aps[a].av.setSelectionGroup(null); aps[a].av.getAlignment().deleteAllGroups(); aps[a].av.clearSequenceColours(); + if (aps[a].av.getCodingComplement() != null) + { + aps[a].av.getCodingComplement().setSelectionGroup(null); + aps[a].av.getCodingComplement().getAlignment() + .deleteAllGroups(); + aps[a].av.getCodingComplement().clearSequenceColours(); + } + aps[a].av.setUpdateStructures(true); + } + colourGroups(groups); + + /* + * clear partition (don't show vertical line) if + * it is to the right of all nodes + */ + if (groups.isEmpty()) + { + threshold = 0f; } - colourGroups(); } - PaintRefresher.Refresh(tp, ap.av.getSequenceSetId()); + PaintRefresher.Refresh(tp, + getAssociatedPanel().av.getSequenceSetId()); repaint(); } } - void colourGroups() + void colourGroups(List groups) { AlignmentPanel[] aps = getAssociatedPanels(); - for (int i = 0; i < tree.getGroups().size(); i++) + for (int i = 0; i < groups.size(); i++) { Color col = new Color((int) (Math.random() * 255), (int) (Math.random() * 255), (int) (Math.random() * 255)); - setColor((SequenceNode) tree.getGroups().elementAt(i), col.brighter()); + setColor(groups.get(i), col.brighter()); - Vector l = tree.findLeaves( - (SequenceNode) tree.getGroups().elementAt(i), new Vector()); + Vector l = tree.findLeaves(groups.get(i)); - Vector sequences = new Vector(); + Vector sequences = new Vector<>(); for (int j = 0; j < l.size(); j++) { - SequenceI s1 = (SequenceI) ((SequenceNode) l.elementAt(j)) - .element(); + SequenceI s1 = (SequenceI) l.elementAt(j).element(); if (!sequences.contains(s1)) { @@ -891,59 +994,56 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } ColourSchemeI cs = null; - SequenceGroup sg = new SequenceGroup(sequences, null, cs, true, true, + SequenceGroup _sg = new SequenceGroup(sequences, null, cs, true, true, false, 0, av.getAlignment().getWidth() - 1); - if (av.getGlobalColourScheme() != null) - { - if (av.getGlobalColourScheme() instanceof UserColourScheme) - { - cs = new UserColourScheme( - ((UserColourScheme) av.getGlobalColourScheme()) - .getColours()); + _sg.setName("JTreeGroup:" + _sg.hashCode()); + _sg.setIdColour(col); - } - else - { - cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty - .getColourName(av.getGlobalColourScheme())); - } - // cs is null if shading is an annotationColourGradient - if (cs != null) - { - cs.setThreshold(av.getGlobalColourScheme().getThreshold(), - av.getIgnoreGapsConsensus()); - } - } - sg.cs = cs; - // sg.recalcConservation(); - sg.setName("JTreeGroup:" + sg.hashCode()); - sg.setIdColour(col); for (int a = 0; a < aps.length; a++) { - if (aps[a].av.getGlobalColourScheme() != null - && aps[a].av.getGlobalColourScheme().conservationApplied()) + SequenceGroup sg = new SequenceGroup(_sg); + AlignViewport viewport = aps[a].av; + + // Propagate group colours in each view + if (viewport.getGlobalColourScheme() != null) { - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg.getSequences(null), - sg.getStartRes(), sg.getEndRes()); + cs = viewport.getGlobalColourScheme().getInstance(viewport, sg); + sg.setColourScheme(cs); + sg.getGroupColourScheme().setThreshold( + viewport.getResidueShading().getThreshold(), + viewport.isIgnoreGapsConsensus()); - c.calculate(); - c.verdict(false, aps[a].av.getConsPercGaps()); - sg.cs.setConservation(c); + 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); + } } - - aps[a].av.getAlignment().addGroup(new SequenceGroup(sg)); + // 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); } } - // notify the panel to redo any group specific stuff. + + // 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(); - // 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) + { + ((AlignViewport) codingComplement).getAlignPanel() + .updateAnnotation(); + } } - } /** @@ -990,8 +1090,47 @@ 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; + } }