X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=0e513f77008dee2bc73b146c90279b8138a4c21c;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=7644673b87c183a8c0c77ea356a13a975cc2774d;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index 7644673..0e513f7 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -1,34 +1,65 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * - * 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 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * 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 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. + * + * 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.NJTree; +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.Vector; + +import javax.swing.JColorChooser; +import javax.swing.JPanel; +import javax.swing.JScrollPane; +import javax.swing.SwingUtilities; +import javax.swing.ToolTipManager; /** * DOCUMENT ME! @@ -37,7 +68,7 @@ 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 = " * "; @@ -86,13 +117,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * Creates a new TreeCanvas object. * * @param av - * DOCUMENT ME! + * DOCUMENT ME! * @param tree - * DOCUMENT ME! + * DOCUMENT ME! * @param scroller - * DOCUMENT ME! + * DOCUMENT ME! * @param label - * DOCUMENT ME! + * DOCUMENT ME! */ public TreeCanvas(TreePanel tp, AlignmentPanel ap, JScrollPane scroller) { @@ -110,7 +141,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * DOCUMENT ME! * * @param sequence - * DOCUMENT ME! + * DOCUMENT ME! */ public void treeSelectionChanged(SequenceI sequence) { @@ -126,7 +157,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, 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); } } @@ -135,7 +166,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * DOCUMENT ME! * * @param tree - * DOCUMENT ME! + * DOCUMENT ME! */ public void setTree(NJTree tree) { @@ -143,13 +174,13 @@ 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(), 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()) { @@ -171,19 +202,19 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * DOCUMENT ME! * * @param g - * DOCUMENT ME! + * DOCUMENT ME! * @param node - * DOCUMENT ME! + * DOCUMENT ME! * @param chunk - * DOCUMENT ME! + * DOCUMENT ME! * @param scale - * DOCUMENT ME! + * DOCUMENT ME! * @param width - * DOCUMENT ME! + * DOCUMENT ME! * @param offx - * DOCUMENT ME! + * DOCUMENT ME! * @param offy - * DOCUMENT ME! + * DOCUMENT ME! */ public void drawNode(Graphics g, SequenceNode node, float chunk, float scale, int width, int offx, int offy) @@ -206,7 +237,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (node.element() instanceof SequenceI) { - SequenceI seq = (SequenceI) ((SequenceNode) node).element(); + SequenceI seq = (SequenceI) node.element(); if (av.getSequenceColour(seq) == Color.white) { @@ -248,8 +279,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node - .getName()) - : node.getName(); + .getName()) : node.getName(); int charWidth = fm.stringWidth(name) + 3; int charHeight = font.getSize(); @@ -257,14 +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); @@ -289,7 +318,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, int xend = (int) (height * scale) + 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); @@ -341,9 +370,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * DOCUMENT ME! * * @param x - * DOCUMENT ME! + * DOCUMENT ME! * @param y - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -384,7 +413,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * DOCUMENT ME! * * @param pickBox - * DOCUMENT ME! + * DOCUMENT ME! */ public void pickNodes(Rectangle pickBox) { @@ -411,19 +440,19 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * DOCUMENT ME! * * @param pickBox - * DOCUMENT ME! + * DOCUMENT ME! * @param node - * DOCUMENT ME! + * DOCUMENT ME! * @param chunk - * DOCUMENT ME! + * DOCUMENT ME! * @param scale - * DOCUMENT ME! + * DOCUMENT ME! * @param width - * DOCUMENT ME! + * DOCUMENT ME! * @param offx - * DOCUMENT ME! + * DOCUMENT ME! * @param offy - * DOCUMENT ME! + * DOCUMENT ME! */ public void pickNode(Rectangle pickBox, SequenceNode node, float chunk, float scale, int width, int offx, int offy) @@ -470,9 +499,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * DOCUMENT ME! * * @param node - * DOCUMENT ME! + * DOCUMENT ME! * @param c - * DOCUMENT ME! + * DOCUMENT ME! */ public void setColor(SequenceNode node, Color c) { @@ -488,9 +517,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, 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); + } } } } @@ -512,6 +545,7 @@ 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(); @@ -535,17 +569,18 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * DOCUMENT ME! * * @param pg - * DOCUMENT ME! + * DOCUMENT ME! * @param pf - * DOCUMENT ME! + * DOCUMENT ME! * @param pi - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! * * @throws PrinterException - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException { @@ -598,8 +633,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * DOCUMENT ME! * * @param g - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void paintComponent(Graphics g) { super.paintComponent(g); @@ -607,7 +643,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (tree == null) { - g.drawString("Calculating tree....", 20, getHeight() / 2); + g.drawString(MessageManager.getString("label.calculating_tree") + + "....", 20, getHeight() / 2); } else { @@ -627,9 +664,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } else { - setPreferredSize(new Dimension(scrollPane.getWidth(), fm - .getHeight() - * nameHash.size())); + setPreferredSize(new Dimension(scrollPane.getWidth(), + fm.getHeight() * nameHash.size())); draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size()); } @@ -641,8 +677,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * DOCUMENT ME! * * @param fontSize - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void setFont(Font font) { this.font = font; @@ -653,11 +690,11 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * DOCUMENT ME! * * @param g1 - * DOCUMENT ME! + * DOCUMENT ME! * @param width - * DOCUMENT ME! + * DOCUMENT ME! * @param height - * DOCUMENT ME! + * DOCUMENT ME! */ public void draw(Graphics g1, int width, int height) { @@ -666,17 +703,19 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, 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 - float wscale = (float) (width - labelLength - (offx * 2)) - / tree.getMaxHeight(); + float wscale = (width - labelLength - (offx * 2)) / tree.getMaxHeight(); SequenceNode top = tree.getTopNode(); @@ -701,86 +740,106 @@ 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()); + /** + * 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, ap.av.getSequenceSetId()); repaint(); } } + @Override public void mouseMoved(MouseEvent evt) { av.setCurrentTree(tree); @@ -790,9 +849,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (ob instanceof SequenceNode) { highlightNode = (SequenceNode) ob; - this.setToolTipText("Left click to select leaves" - + "
Double-click to invert leaves" - + "
Right click to change colour"); + this.setToolTipText("" + + MessageManager.getString("label.highlightnode")); repaint(); } @@ -807,20 +865,48 @@ 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(); @@ -848,11 +934,20 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, 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(); } @@ -865,21 +960,21 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, void colourGroups() { + AlignmentPanel[] aps = getAssociatedPanels(); for (int i = 0; i < tree.getGroups().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(tree.getGroups().elementAt(i), col.brighter()); - Vector l = tree.findLeaves((SequenceNode) tree.getGroups().elementAt( - i), new Vector()); + Vector l = tree.findLeaves(tree.getGroups() + .elementAt(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)) { @@ -888,57 +983,88 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } 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()); + cs = new UserColourScheme( + ((UserColourScheme) av.getGlobalColourScheme()) + .getColours()); } else { - cs = ColourSchemeProperty.getColour(sequences, av.alignment - .getWidth(), ColourSchemeProperty.getColourName(av - .getGlobalColourScheme())); + 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.isIgnoreGapsConsensus()); } - - cs.setThreshold(av.getGlobalColourScheme().getThreshold(), av - .getIgnoreGapsConsensus()); } - - SequenceGroup sg = new SequenceGroup(sequences, null, cs, true, true, - false, 0, av.alignment.getWidth() - 1); - + sg.cs = cs; + // 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()) { - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg.getSequences(null), sg - .getStartRes(), sg.getEndRes()); - + Conservation c = new Conservation("Group", 3, + 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! + * DOCUMENT ME! */ public void setShowDistances(boolean state) { @@ -950,7 +1076,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setShowBootstrap(boolean state) { @@ -962,7 +1088,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * DOCUMENT ME! * * @param state - * DOCUMENT ME! + * DOCUMENT ME! */ public void setMarkPlaceholders(boolean state) { @@ -978,8 +1104,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } else { - return new AlignmentPanel[] - { ap }; + return new AlignmentPanel[] { ap }; } } }