X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=45def89ebb7c1ffb82707cc6b3b1a6569b5313e7;hb=7e82e1fed011077e5cd4cc40ac8ad3519d7c47a8;hp=ead2a71a94ed067a42434217930e76d494ecdcf3;hpb=8ea2930d1b4a23415ec924674d043999d3d6f2ce;p=jalview.git diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index ead2a71..45def89 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -1,85 +1,136 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program 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 2 + * 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. - * - * This program 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. - * + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * 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 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; +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.Enumeration; +import java.util.Hashtable; +import java.util.List; +import java.util.Vector; + +import javax.swing.JColorChooser; +import javax.swing.JPanel; +import javax.swing.JScrollPane; +import javax.swing.SwingUtilities; +import javax.swing.ToolTipManager; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ -public class TreeCanvas - extends JPanel implements MouseListener, Runnable, - Printable, MouseMotionListener +public class TreeCanvas extends JPanel implements MouseListener, Runnable, + Printable, MouseMotionListener, SelectionSource { /** DOCUMENT ME!! */ public static final String PLACEHOLDER = " * "; - NJTree tree; + + TreeModel tree; + JScrollPane scrollPane; + TreePanel tp; - AlignViewport av; - AlignmentPanel ap; + + private AlignViewport av; + + private AlignmentPanel ap; + Font font; + FontMetrics fm; + boolean fitToWindow = true; + boolean showDistances = false; + boolean showBootstrap = false; + boolean markPlaceholders = false; + int offx = 20; + int offy; - float threshold; + + private float threshold; + String longestName; + int labelLength = -1; Hashtable nameHash = new Hashtable(); + Hashtable nodeHash = new Hashtable(); + SequenceNode highlightNode; boolean applyToAllViews = false; /** * Creates a new TreeCanvas object. - * - * @param av DOCUMENT ME! - * @param tree DOCUMENT ME! - * @param scroller DOCUMENT ME! - * @param label DOCUMENT ME! + * + * @param av + * DOCUMENT ME! + * @param tree + * DOCUMENT ME! + * @param scroller + * DOCUMENT ME! + * @param label + * DOCUMENT ME! */ - public TreeCanvas(TreePanel tp, - AlignmentPanel ap, - JScrollPane scroller) + public TreeCanvas(TreePanel tp, AlignmentPanel ap, JScrollPane scroller) { this.tp = tp; this.av = ap.av; - this.ap = ap; + this.setAssociatedPanel(ap); font = av.getFont(); scrollPane = scroller; addMouseListener(this); @@ -89,8 +140,9 @@ public class TreeCanvas /** * DOCUMENT ME! - * - * @param sequence DOCUMENT ME! + * + * @param sequence + * DOCUMENT ME! */ public void treeSelectionChanged(SequenceI sequence) { @@ -106,40 +158,41 @@ public class TreeCanvas aps[a].av.setSelectionGroup(selected); } - selected.setEndRes(aps[a].av.alignment.getWidth() - 1); + selected.setEndRes(aps[a].av.getAlignment().getWidth() - 1); selected.addOrRemove(sequence, true); } } /** * DOCUMENT ME! - * - * @param tree DOCUMENT ME! + * + * @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()) { has_placeholders = true; } - if (longestName.length() < ( (Sequence) lf.element()).getName() - .length()) + if (longestName.length() < ((Sequence) lf.element()).getName() + .length()) { - longestName = TreeCanvas.PLACEHOLDER + - ( (Sequence) lf.element()).getName(); + longestName = TreeCanvas.PLACEHOLDER + + ((Sequence) lf.element()).getName(); } } @@ -148,37 +201,44 @@ public class TreeCanvas /** * DOCUMENT ME! - * - * @param g DOCUMENT ME! - * @param node DOCUMENT ME! - * @param chunk DOCUMENT ME! - * @param scale DOCUMENT ME! - * @param width DOCUMENT ME! - * @param offx DOCUMENT ME! - * @param offy DOCUMENT ME! + * + * @param g + * DOCUMENT ME! + * @param node + * DOCUMENT ME! + * @param chunk + * DOCUMENT ME! + * @param wscale + * DOCUMENT ME! + * @param width + * DOCUMENT ME! + * @param offx + * DOCUMENT ME! + * @param offy + * 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) { return; } - if ( (node.left() == null) && (node.right() == null)) + 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) { @@ -204,7 +264,7 @@ public class TreeCanvas nodeLabel = new Format("%-.2f").form(node.dist); } - if (showBootstrap) + if (showBootstrap && node.bootstrap > -1) { if (showDistances) { @@ -220,26 +280,26 @@ public class TreeCanvas } String name = (markPlaceholders && node.isPlaceholder()) - ? (PLACEHOLDER + node.getName()) : node.getName(); + ? (PLACEHOLDER + node.getName()) + : node.getName(); int charWidth = fm.stringWidth(name) + 3; int charHeight = font.getSize(); Rectangle rect = new Rectangle(xend + 10, ypos - charHeight / 2, - charWidth, charHeight); + 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())) + if ((selected != null) + && selected.getSequences(null).contains(node.element())) { g.setColor(Color.gray); - g.fillRect(xend + 10, ypos - charHeight / 2, charWidth, - charHeight); + g.fillRect(xend + 10, ypos - charHeight / 2, charWidth, charHeight); g.setColor(Color.white); } @@ -248,19 +308,19 @@ public class TreeCanvas } else { - drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx, - offy); - drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx, - offy); + drawNode(g, (SequenceNode) node.left(), chunk, wscale, width, offx, + offy); + 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); @@ -273,16 +333,17 @@ public class TreeCanvas 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) (((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 = ""; @@ -291,7 +352,7 @@ public class TreeCanvas nodeLabel = new Format("%-.2f").form(node.dist); } - if (showBootstrap) + if (showBootstrap && node.bootstrap > -1) { if (showDistances) { @@ -310,10 +371,12 @@ public class TreeCanvas /** * DOCUMENT ME! - * - * @param x DOCUMENT ME! - * @param y DOCUMENT ME! - * + * + * @param x + * DOCUMENT ME! + * @param y + * DOCUMENT ME! + * * @return DOCUMENT ME! */ public Object findElement(int x, int y) @@ -325,8 +388,8 @@ public class TreeCanvas Object ob = keys.nextElement(); Rectangle rect = (Rectangle) nameHash.get(ob); - if ( (x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) && - (y <= (rect.y + rect.height))) + if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) + && (y <= (rect.y + rect.height))) { return ob; } @@ -339,8 +402,8 @@ public class TreeCanvas Object ob = keys.nextElement(); Rectangle rect = (Rectangle) nodeHash.get(ob); - if ( (x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) && - (y <= (rect.y + rect.height))) + if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) + && (y <= (rect.y + rect.height))) { return ob; } @@ -351,8 +414,9 @@ public class TreeCanvas /** * DOCUMENT ME! - * - * @param pickBox DOCUMENT ME! + * + * @param pickBox + * DOCUMENT ME! */ public void pickNodes(Rectangle pickBox) { @@ -361,12 +425,12 @@ public class TreeCanvas 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) { - top.count = ( (SequenceNode) top.left()).count + - ( (SequenceNode) top.right()).count; + top.count = ((SequenceNode) top.left()).count + + ((SequenceNode) top.right()).count; } float chunk = (float) (height - (offy)) / top.count; @@ -376,30 +440,37 @@ public class TreeCanvas /** * DOCUMENT ME! - * - * @param pickBox DOCUMENT ME! - * @param node DOCUMENT ME! - * @param chunk DOCUMENT ME! - * @param scale DOCUMENT ME! - * @param width DOCUMENT ME! - * @param offx DOCUMENT ME! - * @param offy DOCUMENT ME! + * + * @param pickBox + * DOCUMENT ME! + * @param node + * DOCUMENT ME! + * @param chunk + * DOCUMENT ME! + * @param wscale + * DOCUMENT ME! + * @param width + * DOCUMENT ME! + * @param offx + * DOCUMENT ME! + * @param offy + * 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) { return; } - if ( (node.left() == null) && (node.right() == null)) + if ((node.left() == null) && (node.right() == null)) { - 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; @@ -419,18 +490,20 @@ public class TreeCanvas } else { - pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width, - offx, offy); - pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width, - offx, offy); + pickNode(pickBox, (SequenceNode) node.left(), chunk, wscale, width, + offx, offy); + pickNode(pickBox, (SequenceNode) node.right(), chunk, wscale, width, + offx, offy); } } /** * DOCUMENT ME! - * - * @param node DOCUMENT ME! - * @param c DOCUMENT ME! + * + * @param node + * DOCUMENT ME! + * @param c + * DOCUMENT ME! */ public void setColor(SequenceNode node, Color c) { @@ -439,24 +512,28 @@ public class TreeCanvas return; } - if ( (node.left() == null) && (node.right() == null)) // TODO: internal node + if ((node.left() == null) && (node.right() == null)) // TODO: internal node { node.color = c; if (node.element() instanceof SequenceI) { AlignmentPanel[] aps = getAssociatedPanels(); - for (int a = 0; a < aps.length; a++) + if (aps != null) { - aps[a].av.setSequenceColour( (SequenceI) node.element(), c); + for (int a = 0; a < aps.length; a++) + { + final SequenceI seq = (SequenceI) node.element(); + 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); } } @@ -470,10 +547,20 @@ public class TreeCanvas } // 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); @@ -482,8 +569,7 @@ public class TreeCanvas try { printJob.print(); - } - catch (Exception PrintException) + } catch (Exception PrintException) { PrintException.printStackTrace(); } @@ -492,20 +578,25 @@ public class TreeCanvas /** * DOCUMENT ME! - * - * @param pg DOCUMENT ME! - * @param pf DOCUMENT ME! - * @param pi DOCUMENT ME! - * + * + * @param pg + * DOCUMENT ME! + * @param pf + * DOCUMENT ME! + * @param pi + * DOCUMENT ME! + * * @return DOCUMENT ME! - * - * @throws PrinterException DOCUMENT ME! + * + * @throws PrinterException + * DOCUMENT ME! */ + @Override public int print(Graphics pg, PageFormat pf, int pi) - throws PrinterException + throws PrinterException { pg.setFont(font); - pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY()); + pg.translate((int) pf.getImageableX(), (int) pf.getImageableY()); int pwidth = (int) pf.getImageableWidth(); int pheight = (int) pf.getImageableHeight(); @@ -551,9 +642,11 @@ public class TreeCanvas /** * DOCUMENT ME! - * - * @param g DOCUMENT ME! + * + * @param g + * DOCUMENT ME! */ + @Override public void paintComponent(Graphics g) { super.paintComponent(g); @@ -561,7 +654,9 @@ public class TreeCanvas if (tree == null) { - g.drawString("Calculating tree....", 20, getHeight() / 2); + g.drawString( + MessageManager.getString("label.calculating_tree") + "....", + 20, getHeight() / 2); } else { @@ -572,10 +667,8 @@ public class TreeCanvas repaint(); } - if (fitToWindow || - (!fitToWindow && - (scrollPane.getHeight() > ( (fm.getHeight() * nameHash.size()) + - offy)))) + if (fitToWindow || (!fitToWindow && (scrollPane + .getHeight() > ((fm.getHeight() * nameHash.size()) + offy)))) { draw(g, scrollPane.getWidth(), scrollPane.getHeight()); setPreferredSize(null); @@ -583,7 +676,7 @@ public class TreeCanvas else { setPreferredSize(new Dimension(scrollPane.getWidth(), - fm.getHeight() * nameHash.size())); + fm.getHeight() * nameHash.size())); draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size()); } @@ -593,9 +686,11 @@ public class TreeCanvas /** * DOCUMENT ME! - * - * @param fontSize DOCUMENT ME! + * + * @param fontSize + * DOCUMENT ME! */ + @Override public void setFont(Font font) { this.font = font; @@ -604,36 +699,42 @@ public class TreeCanvas /** * DOCUMENT ME! - * - * @param g1 DOCUMENT ME! - * @param width DOCUMENT ME! - * @param height DOCUMENT ME! + * + * @param g1 + * DOCUMENT ME! + * @param width + * DOCUMENT ME! + * @param height + * DOCUMENT ME! */ public void draw(Graphics g1, int width, int height) { Graphics2D g2 = (Graphics2D) g1; g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, - RenderingHints.VALUE_ANTIALIAS_ON); + RenderingHints.VALUE_ANTIALIAS_ON); g2.setColor(Color.white); g2.fillRect(0, 0, width, height); - g2.setFont(font); + if (longestName == null || tree == null) + { + g2.drawString("Calculating tree.", 20, 20); + } offy = font.getSize() + 10; fm = g2.getFontMetrics(font); - labelLength = fm.stringWidth(longestName) + 20; //20 allows for scrollbar + labelLength = fm.stringWidth(longestName) + 20; // 20 allows for scrollbar - float wscale = (float) (width - labelLength - (offx * 2)) / - tree.getMaxHeight(); + double wscale = (width - labelLength - (offx * 2)) + / tree.getMaxHeight(); SequenceNode top = tree.getTopNode(); if (top.count == 0) { - top.count = ( (SequenceNode) top.left()).count + - ( (SequenceNode) top.right()).count; + top.count = ((SequenceNode) top.left()).count + + ((SequenceNode) top.right()).count; } float chunk = (float) (height - (offy)) / top.count; @@ -651,83 +752,107 @@ public class TreeCanvas 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! - * - * @param e DOCUMENT ME! + * Empty method to satisfy the MouseListener interface + * + * @param e */ + @Override public void mouseReleased(MouseEvent e) { + /* + * isPopupTrigger is set on mouseReleased on Windows + */ + if (e.isPopupTrigger()) + { + chooseSubtreeColour(); + e.consume(); // prevent mouseClicked happening + } } /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * Empty method to satisfy the MouseListener interface + * + * @param e */ + @Override public void mouseEntered(MouseEvent e) { } /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * Empty method to satisfy the MouseListener interface + * + * @param e */ + @Override public void mouseExited(MouseEvent e) { } /** - * DOCUMENT ME! - * - * @param 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 */ + @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); - } - } + PaintRefresher.Refresh(tp, av.getSequenceSetId()); + repaint(); + } - PaintRefresher.Refresh(tp, av.getSequenceSetId()); + /** + * 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() + { + Color col = JColorChooser.showDialog(this, + MessageManager.getString("label.select_subtree_colour"), + highlightNode.color); + if (col != null) + { + setColor(highlightNode, col); + PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId()); repaint(); } } + @Override public void mouseMoved(MouseEvent evt) { av.setCurrentTree(tree); @@ -738,9 +863,7 @@ public class TreeCanvas { highlightNode = (SequenceNode) ob; this.setToolTipText( - "Left click to select leaves" - + "
Double-click to invert leaves" - + "
Right click to change colour"); + "" + MessageManager.getString("label.highlightnode")); repaint(); } @@ -755,18 +878,48 @@ public class TreeCanvas } } + @Override public void mouseDragged(MouseEvent ect) - {} + { + } /** - * DOCUMENT ME! - * - * @param e 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 */ + @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(); @@ -774,59 +927,74 @@ public class TreeCanvas if (ob instanceof SequenceI) { - treeSelectionChanged( (Sequence) ob); - PaintRefresher.Refresh(tp, ap.av.getSequenceSetId()); + treeSelectionChanged((Sequence) ob); + PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId()); repaint(); + av.sendSelection(); return; } - else if (! (ob instanceof SequenceNode)) + else if (!(ob instanceof SequenceNode)) { // Find threshold if (tree.getMaxHeight() != 0) { - threshold = (float) (x - offx) / (float) (getWidth() - - labelLength - (2 * offx)); + 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.alignment.deleteAllGroups(); - aps[a].av.sequenceColours = 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(); + } + } + 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) { - for (int i = 0; i < tree.getGroups().size(); i++) + AlignmentPanel[] aps = getAssociatedPanels(); + 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()); + Color col = new Color((int) (Math.random() * 255), + (int) (Math.random() * 255), (int) (Math.random() * 255)); + 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)) { @@ -835,61 +1003,91 @@ public class TreeCanvas } ColourSchemeI cs = null; + 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()); + ((UserColourScheme) av.getGlobalColourScheme()) + .getColours()); } else { - cs = ColourSchemeProperty.getColour(sequences, - av.alignment.getWidth(), - ColourSchemeProperty. - getColourName( - av.getGlobalColourScheme())); + cs = ColourSchemeProperty.getColourScheme(sg, ColourSchemeProperty + .getColourName(av.getGlobalColourScheme())); } - - cs.setThreshold(av.getGlobalColourScheme().getThreshold(), - av.getIgnoreGapsConsensus()); + // cs is null if shading is an annotationColourGradient + // if (cs != null) + // { + // cs.setThreshold(av.getViewportColourScheme().getThreshold(), + // av.isIgnoreGapsConsensus()); + // } } - - SequenceGroup sg = new SequenceGroup(sequences, - null, cs, true, true, false, - 0, - av.alignment.getWidth() - 1); - + sg.setColourScheme(cs); + sg.getGroupColourScheme().setThreshold( + av.getResidueShading().getThreshold(), + av.isIgnoreGapsConsensus()); + // sg.recalcConservation(); sg.setName("JTreeGroup:" + sg.hashCode()); + sg.setIdColour(col); - AlignmentPanel[] aps = getAssociatedPanels(); for (int a = 0; a < aps.length; a++) { if (aps[a].av.getGlobalColourScheme() != null - && aps[a].av.getGlobalColourScheme().conservationApplied()) + && aps[a].av.getResidueShading().conservationApplied()) { - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, - sg.getSequences(null), - sg.getStartRes(), sg.getEndRes()); - + Conservation c = new Conservation("Group", sg.getSequences(null), + sg.getStartRes(), sg.getEndRes()); c.calculate(); - c.verdict(false, aps[a].av.ConsPercGaps); + c.verdict(false, aps[a].av.getConsPercGaps()); sg.cs.setConservation(c); } - aps[a].av.alignment.addGroup(sg); + 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) + { + 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()); + } + } + } } } + // 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) + { + ((AlignViewport) codingComplement).getAlignPanel() + .updateAnnotation(); + } + } } /** * DOCUMENT ME! - * - * @param state DOCUMENT ME! + * + * @param state + * DOCUMENT ME! */ public void setShowDistances(boolean state) { @@ -899,8 +1097,9 @@ public class TreeCanvas /** * DOCUMENT ME! - * - * @param state DOCUMENT ME! + * + * @param state + * DOCUMENT ME! */ public void setShowBootstrap(boolean state) { @@ -910,8 +1109,9 @@ public class TreeCanvas /** * DOCUMENT ME! - * - * @param state DOCUMENT ME! + * + * @param state + * DOCUMENT ME! */ public void setMarkPlaceholders(boolean state) { @@ -927,9 +1127,37 @@ public class TreeCanvas } 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; + } }