X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=f590c2ec41c4233621e425d9b53eae5560d2fd91;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=d05aee1878666314d7f9b094332330d4d3ef97ae;hpb=9fff97021c2c637e426f6971d54dcf3fd4191985;p=jalview.git diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index d05aee1..f590c2e 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -1,776 +1,1065 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 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 - * 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. - * - * 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 - */ -package jalview.gui; - -import jalview.analysis.*; - -import jalview.datamodel.*; - -import jalview.schemes.*; - -import jalview.util.*; - -import java.awt.*; -import java.awt.event.*; -import java.awt.print.*; - -import java.util.*; - -import javax.swing.*; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class TreeCanvas extends JPanel implements MouseListener, Runnable, - Printable -{ - /** DOCUMENT ME!! */ - public static final String PLACEHOLDER = " * "; - NJTree tree; - JScrollPane scrollPane; - AlignViewport av; - Font font; - int fontSize = 12; - boolean fitToWindow = true; - boolean showDistances = false; - boolean showBootstrap = false; - boolean markPlaceholders = false; - int offx = 20; - int offy = 20; - float threshold; - String longestName; - int labelLength = -1; - - //RubberbandRectangle rubberband; - Vector listeners; - Hashtable nameHash = new Hashtable(); - Hashtable nodeHash = new Hashtable(); - - /** - * Creates a new TreeCanvas object. - * - * @param av DOCUMENT ME! - * @param tree DOCUMENT ME! - * @param scroller DOCUMENT ME! - * @param label DOCUMENT ME! - */ - public TreeCanvas(AlignViewport av, NJTree tree, JScrollPane scroller, - String label) - { - this.av = av; - this.tree = tree; - scrollPane = scroller; - addMouseListener(this); - tree.findHeight(tree.getTopNode()); - longestName = label; - - PaintRefresher.Register(this, av.alignment); - } - - /** - * DOCUMENT ME! - * - * @param sequence DOCUMENT ME! - */ - public void TreeSelectionChanged(Sequence sequence) - { - SequenceGroup selected = av.getSelectionGroup(); - - if (selected == null) - { - selected = new SequenceGroup(); - av.setSelectionGroup(selected); - } - - selected.setEndRes(av.alignment.getWidth()); - selected.addOrRemove(sequence, true); - - PaintRefresher.Refresh(this, av.alignment); - repaint(); - } - - /** - * DOCUMENT ME! - * - * @param tree DOCUMENT ME! - */ - public void setTree(NJTree tree) - { - this.tree = tree; - tree.findHeight(tree.getTopNode()); - } - - /** - * 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! - */ - public void drawNode(Graphics g, SequenceNode node, float chunk, - float scale, int width, int offx, int offy) - { - if (node == null) - { - return; - } - - if ((node.left() == null) && (node.right() == null)) - { - // Drawing leaf node - float height = node.height; - float dist = node.dist; - - int xstart = (int) ((height - dist) * scale) + offx; - int xend = (int) (height * scale) + offx; - - int ypos = (int) (node.ycount * chunk) + offy; - - if (node.element() instanceof SequenceI) - { - if (((SequenceI) ((SequenceNode) node).element()).getColor() == Color.white) - { - g.setColor(Color.black); - } - else - { - g.setColor(((SequenceI) ((SequenceNode) node).element()).getColor() - .darker()); - } - } - else - { - g.setColor(Color.black); - } - - // Draw horizontal line - g.drawLine(xstart, ypos, xend, ypos); - - String nodeLabel = ""; - - if (showDistances && (node.dist > 0)) - { - nodeLabel = new Format("%5.2f").form(node.dist); - } - - if (showBootstrap) - { - if (showDistances) - { - nodeLabel = nodeLabel + " : "; - } - - nodeLabel = nodeLabel + String.valueOf(node.getBootstrap()); - } - - if (!nodeLabel.equals("")) - { - g.drawString(nodeLabel, xstart, ypos - 10); - } - - String name = (markPlaceholders && node.isPlaceholder()) - ? (PLACEHOLDER + node.getName()) : node.getName(); - FontMetrics fm = g.getFontMetrics(font); - int charWidth = fm.stringWidth(name) + 3; - int charHeight = fm.getHeight(); - - Rectangle rect = new Rectangle(xend + 20, ypos - charHeight, - charWidth, charHeight); - - nameHash.put((SequenceI) node.element(), rect); - - // Colour selected leaves differently - SequenceGroup selected = av.getSelectionGroup(); - - if ((selected != null) && - selected.sequences.contains((SequenceI) node.element())) - { - g.setColor(Color.gray); - - g.fillRect(xend + 10, ypos - charHeight + 3, charWidth, - charHeight); - g.setColor(Color.white); - } - - g.drawString(name, xend + 10, ypos); - g.setColor(Color.black); - } - else - { - drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx, - offy); - drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx, - offy); - - float height = node.height; - float dist = node.dist; - - int xstart = (int) ((height - dist) * scale) + offx; - int xend = (int) (height * scale) + offx; - int ypos = (int) (node.ycount * chunk) + offy; - - g.setColor(((SequenceNode) node).color.darker()); - - // Draw horizontal line - g.drawLine(xstart, ypos, xend, ypos); - 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; - - 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); - - if (showDistances && (node.dist > 0)) - { - g.drawString(new Format("%5.2f").form(node.dist), xstart, - ypos - 5); - } - } - } - - /** - * DOCUMENT ME! - * - * @param x DOCUMENT ME! - * @param y DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public Object findElement(int x, int y) - { - Enumeration keys = nameHash.keys(); - - while (keys.hasMoreElements()) - { - 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))) - { - return ob; - } - } - - keys = nodeHash.keys(); - - while (keys.hasMoreElements()) - { - 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))) - { - return ob; - } - } - - return null; - } - - /** - * DOCUMENT ME! - * - * @param pickBox DOCUMENT ME! - */ - public void pickNodes(Rectangle pickBox) - { - int width = getWidth(); - int height = getHeight(); - - SequenceNode top = tree.getTopNode(); - - float wscale = (float) ((width * .8) - (offx * 2)) / tree.getMaxHeight(); - - if (top.count == 0) - { - top.count = ((SequenceNode) top.left()).count + - ((SequenceNode) top.right()).count; - } - - float chunk = (float) (height - (offy * 2)) / top.count; - - pickNode(pickBox, top, chunk, wscale, width, offx, offy); - } - - /** - * 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! - */ - public void pickNode(Rectangle pickBox, SequenceNode node, float chunk, - float scale, int width, int offx, int offy) - { - if (node == null) - { - return; - } - - 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; - - int ypos = (int) (node.ycount * chunk) + offy; - - if (pickBox.contains(new Point(xend, ypos))) - { - if (node.element() instanceof SequenceI) - { - SequenceI seq = (SequenceI) node.element(); - SequenceGroup sg = av.getSelectionGroup(); - - if (sg != null) - { - sg.addOrRemove(seq, true); - } - } - } - } - else - { - pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width, - offx, offy); - pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width, - offx, offy); - } - } - - /** - * DOCUMENT ME! - * - * @param node DOCUMENT ME! - * @param c DOCUMENT ME! - */ - public void setColor(SequenceNode node, Color c) - { - if (node == null) - { - return; - } - - if ((node.left() == null) && (node.right() == null)) - { - node.color = c; - - if (node.element() instanceof SequenceI) - { - ((SequenceI) node.element()).setColor(c); - } - } - else - { - node.color = c; - setColor((SequenceNode) node.left(), c); - setColor((SequenceNode) node.right(), c); - } - } - - /** - * DOCUMENT ME! - */ - void startPrinting() - { - Thread thread = new Thread(this); - thread.start(); - } - - // put printing in a thread to avoid painting problems - public void run() - { - PrinterJob printJob = PrinterJob.getPrinterJob(); - PageFormat pf = printJob.pageDialog(printJob.defaultPage()); - - printJob.setPrintable(this, pf); - - if (printJob.printDialog()) - { - try - { - printJob.print(); - } - catch (Exception PrintException) - { - PrintException.printStackTrace(); - } - } - } - - /** - * DOCUMENT ME! - * - * @param pg DOCUMENT ME! - * @param pf DOCUMENT ME! - * @param pi DOCUMENT ME! - * - * @return DOCUMENT ME! - * - * @throws PrinterException DOCUMENT ME! - */ - public int print(Graphics pg, PageFormat pf, int pi) - throws PrinterException - { - pg.setFont(font); - pg.translate((int) pf.getImageableX(), (int) pf.getImageableY()); - - int pwidth = (int) pf.getImageableWidth(); - int pheight = (int) pf.getImageableHeight(); - - int noPages = getHeight() / pheight; - - if (pi > noPages) - { - return Printable.NO_SUCH_PAGE; - } - - if (pwidth > getWidth()) - { - pwidth = getWidth(); - } - - if (fitToWindow) - { - if (pheight > getHeight()) - { - pheight = getHeight(); - } - - noPages = 0; - } - else - { - FontMetrics fm = pg.getFontMetrics(font); - int height = fm.getHeight() * nameHash.size(); - pg.translate(0, -pi * pheight); - pg.setClip(0, pi * pheight, pwidth, (pi * pheight) + pheight); - - // translate number of pages, - // height is screen size as this is the - // non overlapping text size - pheight = height; - } - - draw(pg, pwidth, pheight); - - return Printable.PAGE_EXISTS; - } - - /** - * DOCUMENT ME! - * - * @param g DOCUMENT ME! - */ - public void paintComponent(Graphics g) - { - super.paintComponent(g); - font = new Font("Verdana", Font.PLAIN, fontSize); - g.setFont(font); - - FontMetrics fm = g.getFontMetrics(font); - - if (nameHash.size() == 0) - { - repaint(); - } - - if (fitToWindow || - (!fitToWindow && - (scrollPane.getHeight() > ((fm.getHeight() * nameHash.size()) + - offy)))) - { - draw(g, scrollPane.getWidth(), scrollPane.getHeight()); - setPreferredSize(null); - } - else - { - setPreferredSize(new Dimension(scrollPane.getWidth(), - fm.getHeight() * nameHash.size())); - draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size()); - } - - scrollPane.revalidate(); - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getFontSize() - { - return fontSize; - } - - /** - * DOCUMENT ME! - * - * @param fontSize DOCUMENT ME! - */ - public void setFontSize(int fontSize) - { - this.fontSize = fontSize; - repaint(); - } - - /** - * 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); - g2.setColor(Color.white); - g2.fillRect(0, 0, width, height); - - labelLength = g2.getFontMetrics(font).stringWidth(longestName) + 20; //20 allows for scrollbar - - float wscale = (float) (width - labelLength - (offx * 2)) / tree.getMaxHeight(); - - SequenceNode top = tree.getTopNode(); - - if (top.count == 0) - { - top.count = ((SequenceNode) top.left()).count + - ((SequenceNode) top.right()).count; - } - - float chunk = (float) (height - (offy * 2)) / top.count; - - drawNode(g2, tree.getTopNode(), chunk, wscale, width, offx, offy); - - if (threshold != 0) - { - if (av.getCurrentTree() == tree) - { - g2.setColor(Color.red); - } - else - { - g2.setColor(Color.gray); - } - - int x = (int) ((threshold * (float) (getWidth() - labelLength - - (2 * offx))) + offx); - - g2.drawLine(x, 0, x, getHeight()); - } - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void mouseReleased(MouseEvent e) - { - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void mouseEntered(MouseEvent e) - { - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void mouseExited(MouseEvent e) - { - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void mouseClicked(MouseEvent e) - { - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void mousePressed(MouseEvent e) - { - av.setCurrentTree(tree); - - int x = e.getX(); - int y = e.getY(); - - Object ob = findElement(x, y); - - if (ob instanceof SequenceI) - { - TreeSelectionChanged((Sequence) ob); - repaint(); - - return; - } - else if (ob instanceof SequenceNode) - { - SequenceNode tmpnode = (SequenceNode) ob; - tree.swapNodes(tmpnode); - tree.reCount(tree.getTopNode()); - tree.findHeight(tree.getTopNode()); - } - else - { - // Find threshold - if (tree.getMaxHeight() != 0) - { - threshold = (float) (x - offx) / (float) (getWidth() - - labelLength - (2 * offx)); - - tree.getGroups().removeAllElements(); - tree.groupNodes(tree.getTopNode(), threshold); - setColor(tree.getTopNode(), Color.black); - - av.setSelectionGroup(null); - av.alignment.deleteAllGroups(); - - 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()); - - Vector l = tree.findLeaves((SequenceNode) tree.getGroups() - .elementAt(i), - new Vector()); - - Vector sequences = new Vector(); - - for (int j = 0; j < l.size(); j++) - { - SequenceI s1 = (SequenceI) ((SequenceNode) l.elementAt(j)).element(); - - if (!sequences.contains(s1)) - { - sequences.addElement(s1); - } - } - - ColourSchemeI cs = ColourSchemeProperty.getColour(sequences, - av.alignment.getWidth(), - ColourSchemeProperty.getColourName( - av.getGlobalColourScheme())); - - SequenceGroup sg = new SequenceGroup(sequences, - "TreeGroup", cs, true, true, false, 0, - av.alignment.getWidth()); - - if (sg.cs != null) - { - ((ResidueColourScheme) sg.cs).setThreshold(25, av.getIgnoreGapsConsensus()); - } - - if (av.getGlobalColourScheme() instanceof ConservationColourScheme) - { - ConservationColourScheme ccs = (ConservationColourScheme) av.getGlobalColourScheme(); - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg.sequences, - sg.getStartRes(), sg.getEndRes()); - - c.calculate(); - c.verdict(false, av.ConsPercGaps); - ccs = new ConservationColourScheme(c, ccs.cs); - - sg.cs = ccs; - } - - av.alignment.addGroup(sg); - } - } - } - - PaintRefresher.Refresh(this, av.alignment); - repaint(); - } - - /** - * DOCUMENT ME! - * - * @param state DOCUMENT ME! - */ - public void setShowDistances(boolean state) - { - this.showDistances = state; - repaint(); - } - - /** - * DOCUMENT ME! - * - * @param state DOCUMENT ME! - */ - public void setShowBootstrap(boolean state) - { - this.showBootstrap = state; - repaint(); - } - - /** - * DOCUMENT ME! - * - * @param state DOCUMENT ME! - */ - public void setMarkPlaceholders(boolean state) - { - this.markPlaceholders = state; - repaint(); - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 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. + * + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.gui; + +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.ResidueProperties; +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! + * + * @author $author$ + * @version $Revision$ + */ +public class TreeCanvas extends JPanel implements MouseListener, Runnable, + Printable, MouseMotionListener, SelectionSource +{ + /** DOCUMENT ME!! */ + public static final String PLACEHOLDER = " * "; + + NJTree tree; + + JScrollPane scrollPane; + + TreePanel tp; + + AlignViewport av; + + 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; + + 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! + */ + public TreeCanvas(TreePanel tp, AlignmentPanel ap, JScrollPane scroller) + { + this.tp = tp; + this.av = ap.av; + this.ap = ap; + font = av.getFont(); + scrollPane = scroller; + addMouseListener(this); + addMouseMotionListener(this); + ToolTipManager.sharedInstance().registerComponent(this); + } + + /** + * DOCUMENT ME! + * + * @param sequence + * DOCUMENT ME! + */ + public void treeSelectionChanged(SequenceI sequence) + { + AlignmentPanel[] aps = getAssociatedPanels(); + + for (int a = 0; a < aps.length; a++) + { + SequenceGroup selected = aps[a].av.getSelectionGroup(); + + if (selected == null) + { + selected = new SequenceGroup(); + aps[a].av.setSelectionGroup(selected); + } + + selected.setEndRes(aps[a].av.getAlignment().getWidth() - 1); + selected.addOrRemove(sequence, true); + } + } + + /** + * DOCUMENT ME! + * + * @param tree + * DOCUMENT ME! + */ + public void setTree(NJTree 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()); + boolean has_placeholders = false; + longestName = ""; + + for (int i = 0; i < leaves.size(); i++) + { + SequenceNode lf = (SequenceNode) leaves.elementAt(i); + + if (lf.isPlaceholder()) + { + has_placeholders = true; + } + + if (longestName.length() < ((Sequence) lf.element()).getName() + .length()) + { + longestName = TreeCanvas.PLACEHOLDER + + ((Sequence) lf.element()).getName(); + } + } + + setMarkPlaceholders(has_placeholders); + } + + /** + * 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! + */ + public void drawNode(Graphics g, SequenceNode node, float chunk, + float scale, int width, int offx, int offy) + { + if (node == null) + { + return; + } + + if ((node.left() == null) && (node.right() == null)) + { + // Drawing leaf node + float height = node.height; + float dist = node.dist; + + int xstart = (int) ((height - dist) * scale) + offx; + int xend = (int) (height * scale) + offx; + + int ypos = (int) (node.ycount * chunk) + offy; + + if (node.element() instanceof SequenceI) + { + SequenceI seq = (SequenceI) node.element(); + + if (av.getSequenceColour(seq) == Color.white) + { + g.setColor(Color.black); + } + else + { + g.setColor(av.getSequenceColour(seq).darker()); + } + } + else + { + g.setColor(Color.black); + } + + // Draw horizontal line + g.drawLine(xstart, ypos, xend, ypos); + + String nodeLabel = ""; + + if (showDistances && (node.dist > 0)) + { + nodeLabel = new Format("%-.2f").form(node.dist); + } + + if (showBootstrap && node.bootstrap > -1) + { + if (showDistances) + { + nodeLabel = nodeLabel + " : "; + } + + nodeLabel = nodeLabel + String.valueOf(node.bootstrap); + } + + if (!nodeLabel.equals("")) + { + g.drawString(nodeLabel, xstart + 2, ypos - 2); + } + + String name = (markPlaceholders && node.isPlaceholder()) ? (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); + + nameHash.put(node.element(), rect); + + // Colour selected leaves differently + SequenceGroup selected = av.getSelectionGroup(); + + if ((selected != null) + && selected.getSequences(null).contains(node.element())) + { + g.setColor(Color.gray); + + g.fillRect(xend + 10, ypos - charHeight / 2, charWidth, charHeight); + g.setColor(Color.white); + } + + g.drawString(name, xend + 10, ypos + fm.getDescent()); + g.setColor(Color.black); + } + else + { + drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx, + offy); + drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx, + offy); + + float height = node.height; + float dist = node.dist; + + int xstart = (int) ((height - dist) * scale) + offx; + int xend = (int) (height * scale) + offx; + int ypos = (int) (node.ycount * chunk) + offy; + + g.setColor(node.color.darker()); + + // Draw horizontal line + g.drawLine(xstart, ypos, xend, ypos); + if (node == highlightNode) + { + g.fillRect(xend - 3, ypos - 3, 6, 6); + } + else + { + 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; + + 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); + + String nodeLabel = ""; + + if (showDistances && (node.dist > 0)) + { + nodeLabel = new Format("%-.2f").form(node.dist); + } + + if (showBootstrap && node.bootstrap > -1) + { + if (showDistances) + { + nodeLabel = nodeLabel + " : "; + } + + nodeLabel = nodeLabel + String.valueOf(node.bootstrap); + } + + if (!nodeLabel.equals("")) + { + g.drawString(nodeLabel, xstart + 2, ypos - 2); + } + } + } + + /** + * DOCUMENT ME! + * + * @param x + * DOCUMENT ME! + * @param y + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public Object findElement(int x, int y) + { + Enumeration keys = nameHash.keys(); + + while (keys.hasMoreElements()) + { + 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))) + { + return ob; + } + } + + keys = nodeHash.keys(); + + while (keys.hasMoreElements()) + { + 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))) + { + return ob; + } + } + + return null; + } + + /** + * DOCUMENT ME! + * + * @param pickBox + * DOCUMENT ME! + */ + public void pickNodes(Rectangle pickBox) + { + int width = getWidth(); + int height = getHeight(); + + SequenceNode top = tree.getTopNode(); + + float wscale = (float) ((width * .8) - (offx * 2)) + / tree.getMaxHeight(); + + if (top.count == 0) + { + top.count = ((SequenceNode) top.left()).count + + ((SequenceNode) top.right()).count; + } + + float chunk = (float) (height - (offy)) / top.count; + + pickNode(pickBox, top, chunk, wscale, width, offx, offy); + } + + /** + * 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! + */ + public void pickNode(Rectangle pickBox, SequenceNode node, float chunk, + float scale, int width, int offx, int offy) + { + if (node == null) + { + return; + } + + 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; + + int ypos = (int) (node.ycount * chunk) + offy; + + if (pickBox.contains(new Point(xend, ypos))) + { + if (node.element() instanceof SequenceI) + { + SequenceI seq = (SequenceI) node.element(); + SequenceGroup sg = av.getSelectionGroup(); + + if (sg != null) + { + sg.addOrRemove(seq, true); + } + } + } + } + else + { + pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width, + offx, offy); + pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width, + offx, offy); + } + } + + /** + * DOCUMENT ME! + * + * @param node + * DOCUMENT ME! + * @param c + * DOCUMENT ME! + */ + public void setColor(SequenceNode 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) + { + AlignmentPanel[] aps = getAssociatedPanels(); + if (aps != null) + { + 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); + } + } + + /** + * DOCUMENT ME! + */ + void startPrinting() + { + Thread thread = new Thread(this); + thread.start(); + } + + // put printing in a thread to avoid painting problems + public void run() + { + PrinterJob printJob = PrinterJob.getPrinterJob(); + PageFormat pf = printJob.pageDialog(printJob.defaultPage()); + + printJob.setPrintable(this, pf); + + if (printJob.printDialog()) + { + try + { + printJob.print(); + } catch (Exception PrintException) + { + PrintException.printStackTrace(); + } + } + } + + /** + * DOCUMENT ME! + * + * @param pg + * DOCUMENT ME! + * @param pf + * DOCUMENT ME! + * @param pi + * DOCUMENT ME! + * + * @return DOCUMENT ME! + * + * @throws PrinterException + * DOCUMENT ME! + */ + public int print(Graphics pg, PageFormat pf, int pi) + throws PrinterException + { + pg.setFont(font); + pg.translate((int) pf.getImageableX(), (int) pf.getImageableY()); + + int pwidth = (int) pf.getImageableWidth(); + int pheight = (int) pf.getImageableHeight(); + + int noPages = getHeight() / pheight; + + if (pi > noPages) + { + return Printable.NO_SUCH_PAGE; + } + + if (pwidth > getWidth()) + { + pwidth = getWidth(); + } + + if (fitToWindow) + { + if (pheight > getHeight()) + { + pheight = getHeight(); + } + + noPages = 0; + } + else + { + FontMetrics fm = pg.getFontMetrics(font); + int height = fm.getHeight() * nameHash.size(); + pg.translate(0, -pi * pheight); + pg.setClip(0, pi * pheight, pwidth, (pi * pheight) + pheight); + + // translate number of pages, + // height is screen size as this is the + // non overlapping text size + pheight = height; + } + + draw(pg, pwidth, pheight); + + return Printable.PAGE_EXISTS; + } + + /** + * DOCUMENT ME! + * + * @param g + * DOCUMENT ME! + */ + public void paintComponent(Graphics g) + { + super.paintComponent(g); + g.setFont(font); + + if (tree == null) + { + g.drawString(MessageManager.getString("label.calculating_tree") + + "....", 20, getHeight() / 2); + } + else + { + fm = g.getFontMetrics(font); + + if (nameHash.size() == 0) + { + repaint(); + } + + if (fitToWindow + || (!fitToWindow && (scrollPane.getHeight() > ((fm + .getHeight() * nameHash.size()) + offy)))) + { + draw(g, scrollPane.getWidth(), scrollPane.getHeight()); + setPreferredSize(null); + } + else + { + setPreferredSize(new Dimension(scrollPane.getWidth(), + fm.getHeight() * nameHash.size())); + draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size()); + } + + scrollPane.revalidate(); + } + } + + /** + * DOCUMENT ME! + * + * @param fontSize + * DOCUMENT ME! + */ + public void setFont(Font font) + { + this.font = font; + repaint(); + } + + /** + * 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); + 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 = (width - labelLength - (offx * 2)) / tree.getMaxHeight(); + + SequenceNode top = tree.getTopNode(); + + if (top.count == 0) + { + top.count = ((SequenceNode) top.left()).count + + ((SequenceNode) top.right()).count; + } + + float chunk = (float) (height - (offy)) / top.count; + + drawNode(g2, tree.getTopNode(), chunk, wscale, width, offx, offy); + + if (threshold != 0) + { + if (av.getCurrentTree() == tree) + { + g2.setColor(Color.red); + } + else + { + g2.setColor(Color.gray); + } + + int x = (int) ((threshold * (getWidth() - labelLength - (2 * offx))) + offx); + + g2.drawLine(x, 0, x, getHeight()); + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void mouseReleased(MouseEvent e) + { + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void mouseEntered(MouseEvent e) + { + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void mouseExited(MouseEvent e) + { + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void mouseClicked(MouseEvent evt) + { + if (highlightNode != null) + { + if (SwingUtilities.isRightMouseButton(evt)) + { + Color col = JColorChooser.showDialog(this, + MessageManager.getString("label.select_subtree_colour"), + highlightNode.color); + if (col != null) + { + setColor(highlightNode, col); + } + } + else if (evt.getClickCount() > 1) + { + tree.swapNodes(highlightNode); + tree.reCount(tree.getTopNode()); + tree.findHeight(tree.getTopNode()); + } + else + { + Vector leaves = new Vector(); + tree.findLeaves(highlightNode, leaves); + + 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(); + } + } + + public void mouseMoved(MouseEvent evt) + { + av.setCurrentTree(tree); + + Object ob = findElement(evt.getX(), evt.getY()); + + if (ob instanceof SequenceNode) + { + highlightNode = (SequenceNode) ob; + this.setToolTipText("" + + MessageManager.getString("label.highlightnode")); + repaint(); + + } + else + { + if (highlightNode != null) + { + highlightNode = null; + setToolTipText(null); + repaint(); + } + } + } + + public void mouseDragged(MouseEvent ect) + { + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void mousePressed(MouseEvent e) + { + av.setCurrentTree(tree); + + int x = e.getX(); + int y = e.getY(); + + Object ob = findElement(x, y); + + if (ob instanceof SequenceI) + { + treeSelectionChanged((Sequence) ob); + PaintRefresher.Refresh(tp, ap.av.getSequenceSetId()); + repaint(); + av.sendSelection(); + return; + } + else if (!(ob instanceof SequenceNode)) + { + // Find threshold + if (tree.getMaxHeight() != 0) + { + threshold = (float) (x - offx) + / (float) (getWidth() - labelLength - (2 * offx)); + + tree.getGroups().removeAllElements(); + tree.groupNodes(tree.getTopNode(), 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 (av.getCodingComplement() != null) + { + av.getCodingComplement().setSelectionGroup(null); + av.getCodingComplement().getAlignment().deleteAllGroups(); + av.getCodingComplement().clearSequenceColours(); + } + colourGroups(); + } + + PaintRefresher.Refresh(tp, ap.av.getSequenceSetId()); + repaint(); + } + + } + + 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()); + + Vector l = tree.findLeaves( + (SequenceNode) tree.getGroups().elementAt(i), new Vector()); + + Vector sequences = new Vector(); + + for (int j = 0; j < l.size(); j++) + { + SequenceI s1 = (SequenceI) ((SequenceNode) 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); + + if (av.getGlobalColourScheme() != null) + { + if (av.getGlobalColourScheme() instanceof UserColourScheme) + { + cs = new UserColourScheme( + ((UserColourScheme) av.getGlobalColourScheme()) + .getColours()); + + } + 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.isIgnoreGapsConsensus()); + } + } + 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()) + { + Conservation c = new Conservation("Group", + ResidueProperties.propHash, 3, sg.getSequences(null), + sg.getStartRes(), sg.getEndRes()); + + c.calculate(); + c.verdict(false, aps[a].av.getConsPercGaps()); + sg.cs.setConservation(c); + } + + aps[a].av.getAlignment().addGroup(new SequenceGroup(sg)); + } + + // TODO can we push all of the below into AlignViewportI? + av.getAlignment().addGroup(sg); + final AlignViewportI codingComplement = 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 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 + } + + if (av.getCodingComplement() != null) + { + ((AlignViewport) av.getCodingComplement()).getAlignPanel() + .updateAnnotation(); + /* + * idPanel. repaint () + */ + } + } + + /** + * DOCUMENT ME! + * + * @param state + * DOCUMENT ME! + */ + public void setShowDistances(boolean state) + { + this.showDistances = state; + repaint(); + } + + /** + * DOCUMENT ME! + * + * @param state + * DOCUMENT ME! + */ + public void setShowBootstrap(boolean state) + { + this.showBootstrap = state; + repaint(); + } + + /** + * DOCUMENT ME! + * + * @param state + * DOCUMENT ME! + */ + public void setMarkPlaceholders(boolean state) + { + this.markPlaceholders = state; + repaint(); + } + + AlignmentPanel[] getAssociatedPanels() + { + if (applyToAllViews) + { + return PaintRefresher.getAssociatedPanels(av.getSequenceSetId()); + } + else + { + return new AlignmentPanel[] { ap }; + } + } +}