-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-import jalview.analysis.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import jalview.schemes.*;\r
-\r
-import jalview.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import java.awt.print.*;\r
-\r
-import java.util.*;\r
-\r
-import javax.swing.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class TreeCanvas extends JPanel implements MouseListener, Runnable,\r
- Printable, MouseMotionListener\r
-{\r
- /** DOCUMENT ME!! */\r
- public static final String PLACEHOLDER = " * ";\r
- NJTree tree;\r
- JScrollPane scrollPane;\r
- AlignViewport av;\r
- AlignmentPanel ap;\r
- Font font;\r
- FontMetrics fm;\r
- boolean fitToWindow = true;\r
- boolean showDistances = false;\r
- boolean showBootstrap = false;\r
- boolean markPlaceholders = false;\r
- int offx = 20;\r
- int offy;\r
- float threshold;\r
- String longestName;\r
- int labelLength = -1;\r
-\r
- Hashtable nameHash = new Hashtable();\r
- Hashtable nodeHash = new Hashtable();\r
- SequenceNode highlightNode;\r
-\r
- /**\r
- * Creates a new TreeCanvas object.\r
- *\r
- * @param av DOCUMENT ME!\r
- * @param tree DOCUMENT ME!\r
- * @param scroller DOCUMENT ME!\r
- * @param label DOCUMENT ME!\r
- */\r
- public TreeCanvas(AlignmentPanel ap, JScrollPane scroller)\r
- {\r
- this.av = ap.av;\r
- this.ap = ap;\r
- font = av.getFont();\r
- scrollPane = scroller;\r
- addMouseListener(this);\r
- addMouseMotionListener(this);\r
- PaintRefresher.Register(this, ap.av.getSequenceSetId());\r
- ToolTipManager.sharedInstance().registerComponent(this);\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param sequence DOCUMENT ME!\r
- */\r
- public void treeSelectionChanged(SequenceI sequence)\r
- {\r
- SequenceGroup selected = av.getSelectionGroup();\r
-\r
- if (selected == null)\r
- {\r
- selected = new SequenceGroup();\r
- av.setSelectionGroup(selected);\r
- }\r
-\r
- selected.setEndRes(av.alignment.getWidth()-1);\r
- selected.addOrRemove(sequence, true);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param tree DOCUMENT ME!\r
- */\r
- public void setTree(NJTree tree)\r
- {\r
- this.tree = tree;\r
- tree.findHeight(tree.getTopNode());\r
-\r
- // Now have to calculate longest name based on the leaves\r
- Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());\r
- boolean has_placeholders = false;\r
- longestName = "";\r
-\r
- for (int i = 0; i < leaves.size(); i++)\r
- {\r
- SequenceNode lf = (SequenceNode) leaves.elementAt(i);\r
-\r
- if (lf.isPlaceholder())\r
- {\r
- has_placeholders = true;\r
- }\r
-\r
- if (longestName.length() < ( (Sequence) lf.element()).getName()\r
- .length())\r
- {\r
- longestName = TreeCanvas.PLACEHOLDER +\r
- ( (Sequence) lf.element()).getName();\r
- }\r
- }\r
-\r
- setMarkPlaceholders(has_placeholders);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param g DOCUMENT ME!\r
- * @param node DOCUMENT ME!\r
- * @param chunk DOCUMENT ME!\r
- * @param scale DOCUMENT ME!\r
- * @param width DOCUMENT ME!\r
- * @param offx DOCUMENT ME!\r
- * @param offy DOCUMENT ME!\r
- */\r
- public void drawNode(Graphics g, SequenceNode node, float chunk,\r
- float scale, int width, int offx, int offy)\r
- {\r
- if (node == null)\r
- {\r
- return;\r
- }\r
-\r
- if ((node.left() == null) && (node.right() == null))\r
- {\r
- // Drawing leaf node\r
- float height = node.height;\r
- float dist = node.dist;\r
-\r
- int xstart = (int) ((height - dist) * scale) + offx;\r
- int xend = (int) (height * scale) + offx;\r
-\r
- int ypos = (int) (node.ycount * chunk) + offy;\r
-\r
- if (node.element() instanceof SequenceI)\r
- {\r
- if (((SequenceI) ((SequenceNode) node).element()).getColor() == Color.white)\r
- {\r
- g.setColor(Color.black);\r
- }\r
- else\r
- {\r
- g.setColor(((SequenceI) ((SequenceNode) node).element()).getColor()\r
- .darker());\r
- }\r
- }\r
- else\r
- {\r
- g.setColor(Color.black);\r
- }\r
-\r
- // Draw horizontal line\r
- g.drawLine(xstart, ypos, xend, ypos);\r
-\r
- String nodeLabel = "";\r
-\r
- if (showDistances && (node.dist > 0))\r
- {\r
- nodeLabel = new Format("%-.2f").form(node.dist);\r
- }\r
-\r
- if (showBootstrap)\r
- {\r
- if (showDistances)\r
- {\r
- nodeLabel = nodeLabel + " : ";\r
- }\r
-\r
- nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());\r
- }\r
-\r
- if (!nodeLabel.equals(""))\r
- {\r
- g.drawString(nodeLabel, xstart+2, ypos - 2);\r
- }\r
-\r
- String name = (markPlaceholders && node.isPlaceholder())\r
- ? (PLACEHOLDER + node.getName()) : node.getName();\r
-\r
- int charWidth = fm.stringWidth(name) + 3;\r
- int charHeight = font.getSize();\r
-\r
- Rectangle rect = new Rectangle(xend+10, ypos-charHeight/2,\r
- charWidth, charHeight);\r
-\r
- nameHash.put((SequenceI) node.element(), rect);\r
-\r
- // Colour selected leaves differently\r
- SequenceGroup selected = av.getSelectionGroup();\r
-\r
- if ((selected != null) &&\r
- selected.getSequences(false).contains((SequenceI) node.element()))\r
- {\r
- g.setColor(Color.gray);\r
-\r
- g.fillRect(xend + 10, ypos-charHeight/2, charWidth,\r
- charHeight);\r
- g.setColor(Color.white);\r
- }\r
-\r
- g.drawString(name, xend + 10, ypos+fm.getDescent());\r
- g.setColor(Color.black);\r
- }\r
- else\r
- {\r
- drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx,\r
- offy);\r
- drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx,\r
- offy);\r
-\r
- float height = node.height;\r
- float dist = node.dist;\r
-\r
- int xstart = (int) ((height - dist) * scale) + offx;\r
- int xend = (int) (height * scale) + offx;\r
- int ypos = (int) (node.ycount * chunk) + offy;\r
-\r
- g.setColor(((SequenceNode) node).color.darker());\r
-\r
- // Draw horizontal line\r
- g.drawLine(xstart, ypos, xend, ypos);\r
- if (node == highlightNode)\r
- g.fillRect(xend - 3, ypos - 3, 6, 6);\r
- else\r
- g.fillRect(xend - 2, ypos - 2, 4, 4);\r
-\r
- int ystart = (int) (((SequenceNode) node.left()).ycount * chunk) +\r
- offy;\r
- int yend = (int) (((SequenceNode) node.right()).ycount * chunk) +\r
- offy;\r
-\r
- Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);\r
- nodeHash.put(node, pos);\r
-\r
- g.drawLine((int) (height * scale) + offx, ystart,\r
- (int) (height * scale) + offx, yend);\r
-\r
- if (showDistances && (node.dist > 0))\r
- {\r
- g.drawString(new Format("%-.2f").form(node.dist).trim(), xstart+2,\r
- ypos - 2);\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param x DOCUMENT ME!\r
- * @param y DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Object findElement(int x, int y)\r
- {\r
- Enumeration keys = nameHash.keys();\r
-\r
- while (keys.hasMoreElements())\r
- {\r
- Object ob = keys.nextElement();\r
- Rectangle rect = (Rectangle) nameHash.get(ob);\r
-\r
- if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) &&\r
- (y <= (rect.y + rect.height)))\r
- {\r
- return ob;\r
- }\r
- }\r
-\r
- keys = nodeHash.keys();\r
-\r
- while (keys.hasMoreElements())\r
- {\r
- Object ob = keys.nextElement();\r
- Rectangle rect = (Rectangle) nodeHash.get(ob);\r
-\r
- if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) &&\r
- (y <= (rect.y + rect.height)))\r
- {\r
- return ob;\r
- }\r
- }\r
-\r
- return null;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param pickBox DOCUMENT ME!\r
- */\r
- public void pickNodes(Rectangle pickBox)\r
- {\r
- int width = getWidth();\r
- int height = getHeight();\r
-\r
- SequenceNode top = tree.getTopNode();\r
-\r
- float wscale = (float) ((width * .8) - (offx * 2)) / tree.getMaxHeight();\r
-\r
- if (top.count == 0)\r
- {\r
- top.count = ((SequenceNode) top.left()).count +\r
- ((SequenceNode) top.right()).count;\r
- }\r
-\r
- float chunk = (float) (height - (offy)) / top.count;\r
-\r
- pickNode(pickBox, top, chunk, wscale, width, offx, offy);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param pickBox DOCUMENT ME!\r
- * @param node DOCUMENT ME!\r
- * @param chunk DOCUMENT ME!\r
- * @param scale DOCUMENT ME!\r
- * @param width DOCUMENT ME!\r
- * @param offx DOCUMENT ME!\r
- * @param offy DOCUMENT ME!\r
- */\r
- public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,\r
- float scale, int width, int offx, int offy)\r
- {\r
- if (node == null)\r
- {\r
- return;\r
- }\r
-\r
- if ((node.left() == null) && (node.right() == null))\r
- {\r
- float height = node.height;\r
- float dist = node.dist;\r
-\r
- int xstart = (int) ((height - dist) * scale) + offx;\r
- int xend = (int) (height * scale) + offx;\r
-\r
- int ypos = (int) (node.ycount * chunk) + offy;\r
-\r
- if (pickBox.contains(new Point(xend, ypos)))\r
- {\r
- if (node.element() instanceof SequenceI)\r
- {\r
- SequenceI seq = (SequenceI) node.element();\r
- SequenceGroup sg = av.getSelectionGroup();\r
-\r
- if (sg != null)\r
- {\r
- sg.addOrRemove(seq, true);\r
- }\r
- }\r
- }\r
- }\r
- else\r
- {\r
- pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width,\r
- offx, offy);\r
- pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width,\r
- offx, offy);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param node DOCUMENT ME!\r
- * @param c DOCUMENT ME!\r
- */\r
- public void setColor(SequenceNode node, Color c)\r
- {\r
- if (node == null)\r
- {\r
- return;\r
- }\r
-\r
- if ((node.left() == null) && (node.right() == null))\r
- {\r
- node.color = c;\r
-\r
- if (node.element() instanceof SequenceI)\r
- {\r
- ((SequenceI) node.element()).setColor(c);\r
- }\r
- }\r
- else\r
- {\r
- node.color = c;\r
- setColor((SequenceNode) node.left(), c);\r
- setColor((SequenceNode) node.right(), c);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- void startPrinting()\r
- {\r
- Thread thread = new Thread(this);\r
- thread.start();\r
- }\r
-\r
- // put printing in a thread to avoid painting problems\r
- public void run()\r
- {\r
- PrinterJob printJob = PrinterJob.getPrinterJob();\r
- PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
-\r
- printJob.setPrintable(this, pf);\r
-\r
- if (printJob.printDialog())\r
- {\r
- try\r
- {\r
- printJob.print();\r
- }\r
- catch (Exception PrintException)\r
- {\r
- PrintException.printStackTrace();\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param pg DOCUMENT ME!\r
- * @param pf DOCUMENT ME!\r
- * @param pi DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- *\r
- * @throws PrinterException DOCUMENT ME!\r
- */\r
- public int print(Graphics pg, PageFormat pf, int pi)\r
- throws PrinterException\r
- {\r
- pg.setFont(font);\r
- pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());\r
-\r
- int pwidth = (int) pf.getImageableWidth();\r
- int pheight = (int) pf.getImageableHeight();\r
-\r
- int noPages = getHeight() / pheight;\r
-\r
- if (pi > noPages)\r
- {\r
- return Printable.NO_SUCH_PAGE;\r
- }\r
-\r
- if (pwidth > getWidth())\r
- {\r
- pwidth = getWidth();\r
- }\r
-\r
- if (fitToWindow)\r
- {\r
- if (pheight > getHeight())\r
- {\r
- pheight = getHeight();\r
- }\r
-\r
- noPages = 0;\r
- }\r
- else\r
- {\r
- FontMetrics fm = pg.getFontMetrics(font);\r
- int height = fm.getHeight() * nameHash.size();\r
- pg.translate(0, -pi * pheight);\r
- pg.setClip(0, pi * pheight, pwidth, (pi * pheight) + pheight);\r
-\r
- // translate number of pages,\r
- // height is screen size as this is the\r
- // non overlapping text size\r
- pheight = height;\r
- }\r
-\r
- draw(pg, pwidth, pheight);\r
-\r
- return Printable.PAGE_EXISTS;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param g DOCUMENT ME!\r
- */\r
- public void paintComponent(Graphics g)\r
- {\r
- super.paintComponent(g);\r
- g.setFont(font);\r
-\r
- if(tree==null)\r
- {\r
- g.drawString("Calculating tree....", 20, getHeight()/2);\r
- }\r
- else\r
- {\r
- fm = g.getFontMetrics(font);\r
-\r
- if (nameHash.size() == 0)\r
- {\r
- repaint();\r
- }\r
-\r
- if (fitToWindow ||\r
- (!fitToWindow &&\r
- (scrollPane.getHeight() > ( (fm.getHeight() * nameHash.size()) +\r
- offy))))\r
- {\r
- draw(g, scrollPane.getWidth(), scrollPane.getHeight());\r
- setPreferredSize(null);\r
- }\r
- else\r
- {\r
- setPreferredSize(new Dimension(scrollPane.getWidth(),\r
- fm.getHeight() * nameHash.size()));\r
- draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size());\r
- }\r
-\r
- scrollPane.revalidate();\r
- }\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param fontSize DOCUMENT ME!\r
- */\r
- public void setFont(Font font)\r
- {\r
- this.font = font;\r
- repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param g1 DOCUMENT ME!\r
- * @param width DOCUMENT ME!\r
- * @param height DOCUMENT ME!\r
- */\r
- public void draw(Graphics g1, int width, int height)\r
- {\r
- Graphics2D g2 = (Graphics2D) g1;\r
- g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
- RenderingHints.VALUE_ANTIALIAS_ON);\r
- g2.setColor(Color.white);\r
- g2.fillRect(0, 0, width, height);\r
-\r
- g2.setFont(font);\r
-\r
- offy = font.getSize()+10;\r
-\r
- fm = g2.getFontMetrics(font);\r
-\r
- labelLength = fm.stringWidth(longestName) + 20; //20 allows for scrollbar\r
-\r
- float wscale = (float) (width - labelLength - (offx * 2)) / tree.getMaxHeight();\r
-\r
- SequenceNode top = tree.getTopNode();\r
-\r
- if (top.count == 0)\r
- {\r
- top.count = ((SequenceNode) top.left()).count +\r
- ((SequenceNode) top.right()).count;\r
- }\r
-\r
- float chunk = (float) (height - (offy)) / top.count;\r
-\r
- drawNode(g2, tree.getTopNode(), chunk, wscale, width, offx, offy);\r
-\r
- if (threshold != 0)\r
- {\r
- if (av.getCurrentTree() == tree)\r
- {\r
- g2.setColor(Color.red);\r
- }\r
- else\r
- {\r
- g2.setColor(Color.gray);\r
- }\r
-\r
- int x = (int) ((threshold * (float) (getWidth() - labelLength -\r
- (2 * offx))) + offx);\r
-\r
- g2.drawLine(x, 0, x, getHeight());\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void mouseReleased(MouseEvent e)\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void mouseEntered(MouseEvent e)\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void mouseExited(MouseEvent e)\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void mouseClicked(MouseEvent evt)\r
- {\r
- if(highlightNode!=null)\r
- {\r
- if (SwingUtilities.isRightMouseButton(evt))\r
- {\r
- Color col = JColorChooser.showDialog(this, "Select Background Colour",\r
- highlightNode.color);\r
-\r
- setColor(highlightNode, col);\r
- }\r
- else\r
- if(evt.getClickCount()>1)\r
- {\r
- tree.swapNodes(highlightNode);\r
- tree.reCount(tree.getTopNode());\r
- tree.findHeight(tree.getTopNode());\r
- }\r
- else\r
- {\r
- Vector leaves = new Vector();\r
- tree.findLeaves(highlightNode, leaves);\r
-\r
- for (int i = 0; i < leaves.size(); i++)\r
- {\r
- SequenceI seq =\r
- (SequenceI) ( (SequenceNode) leaves.elementAt(i)).element();\r
- treeSelectionChanged(seq);\r
- }\r
- }\r
-\r
- PaintRefresher.Refresh(this, av.getSequenceSetId());\r
- repaint();\r
- }\r
- }\r
-\r
-\r
-\r
- public void mouseMoved(MouseEvent evt)\r
- {\r
- av.setCurrentTree(tree);\r
-\r
- Object ob = findElement(evt.getX(), evt.getY());\r
-\r
- if (ob instanceof SequenceNode)\r
- {\r
- highlightNode = (SequenceNode) ob;\r
- this.setToolTipText(\r
- "<html>Left click to select leaves"\r
- + "<br>Double-click to invert leaves"\r
- + "<br>Right click to change colour");\r
- repaint();\r
-\r
- }\r
- else\r
- {\r
- if (highlightNode != null)\r
- {\r
- highlightNode = null;\r
- setToolTipText("");\r
- repaint();\r
- }\r
- }\r
- }\r
-\r
- public void mouseDragged(MouseEvent ect)\r
- {}\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void mousePressed(MouseEvent e)\r
- {\r
- av.setCurrentTree(tree);\r
-\r
- int x = e.getX();\r
- int y = e.getY();\r
-\r
- Object ob = findElement(x, y);\r
-\r
- if (ob instanceof SequenceI)\r
- {\r
- treeSelectionChanged( (Sequence) ob);\r
- PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
- repaint();\r
- return;\r
- }\r
- else if( !(ob instanceof SequenceNode) )\r
- {\r
- // Find threshold\r
- if (tree.getMaxHeight() != 0)\r
- {\r
- threshold = (float) (x - offx) / (float) (getWidth() -\r
- labelLength - (2 * offx));\r
-\r
- tree.getGroups().removeAllElements();\r
- tree.groupNodes(tree.getTopNode(), threshold);\r
- setColor(tree.getTopNode(), Color.black);\r
-\r
- av.setSelectionGroup(null);\r
- av.alignment.deleteAllGroups();\r
-\r
- colourGroups();\r
- }\r
-\r
- PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
- repaint();\r
- }\r
-\r
-\r
- }\r
-\r
- void colourGroups()\r
- {\r
- for (int i = 0; i < tree.getGroups().size(); i++)\r
- {\r
- Color col = new Color( (int) (Math.random() * 255),\r
- (int) (Math.random() * 255),\r
- (int) (Math.random() * 255));\r
- setColor( (SequenceNode) tree.getGroups().elementAt(i),\r
- col.brighter());\r
-\r
- Vector l = tree.findLeaves( (SequenceNode) tree.getGroups()\r
- .elementAt(i),\r
- new Vector());\r
-\r
- Vector sequences = new Vector();\r
-\r
- for (int j = 0; j < l.size(); j++)\r
- {\r
- SequenceI s1 = (SequenceI) ( (SequenceNode) l.elementAt(j)).element();\r
-\r
- if (!sequences.contains(s1))\r
- {\r
- sequences.addElement(s1);\r
- }\r
- }\r
-\r
- ColourSchemeI cs = null;\r
-\r
- if (av.getGlobalColourScheme() != null)\r
- {\r
- if (av.getGlobalColourScheme() instanceof UserColourScheme)\r
- {\r
- cs = new UserColourScheme(\r
- ( (UserColourScheme) av.getGlobalColourScheme()).getColours());\r
-\r
- }\r
- else\r
- cs = ColourSchemeProperty.getColour(sequences,\r
- av.alignment.getWidth(),\r
- ColourSchemeProperty.\r
- getColourName(\r
- av.getGlobalColourScheme()));\r
-\r
- cs.setThreshold(av.getGlobalColourScheme().getThreshold(),\r
- av.getIgnoreGapsConsensus());\r
- }\r
-\r
- SequenceGroup sg = new SequenceGroup(sequences,\r
- "TreeGroup", cs, true, true, false,\r
- 0,\r
- av.alignment.getWidth() - 1);\r
-\r
- if (av.getGlobalColourScheme() != null\r
- && av.getGlobalColourScheme().conservationApplied())\r
- {\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3,\r
- sg.getSequences(false),\r
- sg.getStartRes(), sg.getEndRes());\r
-\r
- c.calculate();\r
- c.verdict(false, av.ConsPercGaps);\r
- sg.cs.setConservation(c);\r
- }\r
-\r
- av.alignment.addGroup(sg);\r
- }\r
-\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param state DOCUMENT ME!\r
- */\r
- public void setShowDistances(boolean state)\r
- {\r
- this.showDistances = state;\r
- repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param state DOCUMENT ME!\r
- */\r
- public void setShowBootstrap(boolean state)\r
- {\r
- this.showBootstrap = state;\r
- repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param state DOCUMENT ME!\r
- */\r
- public void setMarkPlaceholders(boolean state)\r
- {\r
- this.markPlaceholders = state;\r
- repaint();\r
- }\r
-}\r
+/*
+ * 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.
+ *
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+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!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class TreeCanvas extends JPanel implements MouseListener, Runnable,
+ Printable, MouseMotionListener, SelectionSource
+{
+ /** DOCUMENT ME!! */
+ public static final String PLACEHOLDER = " * ";
+
+ TreeModel tree;
+
+ JScrollPane scrollPane;
+
+ TreePanel tp;
+
+ 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;
+
+ private float threshold;
+
+ String longestName;
+
+ int labelLength = -1;
+
+ Map<Object, Rectangle> nameHash = new Hashtable<>();
+
+ Map<SequenceNode, Rectangle> 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.setAssociatedPanel(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(TreeModel tree)
+ {
+ this.tree = tree;
+ tree.findHeight(tree.getTopNode());
+
+ // Now have to calculate longest name based on the leaves
+ Vector<SequenceNode> leaves = tree.findLeaves(tree.getTopNode());
+ boolean has_placeholders = false;
+ longestName = "";
+
+ for (int i = 0; i < leaves.size(); i++)
+ {
+ SequenceNode lf = 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 wscale
+ * DOCUMENT ME!
+ * @param width
+ * DOCUMENT ME!
+ * @param offx
+ * DOCUMENT ME!
+ * @param offy
+ * DOCUMENT ME!
+ */
+ public void drawNode(Graphics g, SequenceNode node, float chunk,
+ double wscale, int width, int offx, int offy)
+ {
+ if (node == null)
+ {
+ return;
+ }
+
+ if ((node.left() == null) && (node.right() == null))
+ {
+ // Drawing leaf node
+ 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;
+
+ 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("%g").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, wscale, width, offx,
+ offy);
+ drawNode(g, (SequenceNode) node.right(), chunk, wscale, width, offx,
+ offy);
+
+ 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;
+
+ 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 = (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 * wscale) + offx, ystart,
+ (int) (height * wscale) + offx, yend);
+
+ String nodeLabel = "";
+
+ if (showDistances && (node.dist > 0))
+ {
+ nodeLabel = new Format("%g").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)
+ {
+ for (Entry<Object, Rectangle> entry : nameHash.entrySet())
+ {
+ Rectangle rect = entry.getValue();
+
+ if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y)
+ && (y <= (rect.y + rect.height)))
+ {
+ return entry.getKey();
+ }
+ }
+
+ for (Entry<SequenceNode, Rectangle> entry : nodeHash.entrySet())
+ {
+ Rectangle rect = entry.getValue();
+
+ if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y)
+ && (y <= (rect.y + rect.height)))
+ {
+ return entry.getKey();
+ }
+ }
+
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pickBox
+ * DOCUMENT ME!
+ */
+ public void pickNodes(Rectangle pickBox)
+ {
+ int width = getWidth();
+ int height = getHeight();
+
+ SequenceNode top = tree.getTopNode();
+
+ double wscale = ((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 wscale
+ * DOCUMENT ME!
+ * @param width
+ * DOCUMENT ME!
+ * @param offx
+ * DOCUMENT ME!
+ * @param offy
+ * DOCUMENT ME!
+ */
+ public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,
+ double wscale, int width, int offx, int offy)
+ {
+ if (node == null)
+ {
+ return;
+ }
+
+ if ((node.left() == null) && (node.right() == null))
+ {
+ 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;
+
+ 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, wscale, width,
+ offx, offy);
+ pickNode(pickBox, (SequenceNode) node.right(), chunk, wscale, width,
+ offx, offy);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node
+ * DOCUMENT ME!
+ * @param c
+ * DOCUMENT ME!
+ */
+ public void setColor(SequenceNode node, Color c)
+ {
+ if (node == null)
+ {
+ return;
+ }
+
+ node.color = c;
+ if (node.element() instanceof SequenceI)
+ {
+ final SequenceI seq = (SequenceI) node.element();
+ AlignmentPanel[] aps = getAssociatedPanels();
+ if (aps != null)
+ {
+ for (int a = 0; a < aps.length; a++)
+ {
+ aps[a].av.setSequenceColour(seq, 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
+ @Override
+ public void run()
+ {
+ PrinterJob printJob = PrinterJob.getPrinterJob();
+ PageFormat defaultPage = printJob.defaultPage();
+ PageFormat pf = printJob.pageDialog(defaultPage);
+
+ if (defaultPage == pf)
+ {
+ /*
+ * user cancelled
+ */
+ return;
+ }
+
+ 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!
+ */
+ @Override
+ 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!
+ */
+ @Override
+ 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);
+
+ int nameCount = nameHash.size();
+ if (nameCount == 0)
+ {
+ repaint();
+ }
+
+ if (fitToWindow || (!fitToWindow && (scrollPane
+ .getHeight() > ((fm.getHeight() * nameCount) + offy))))
+ {
+ draw(g, scrollPane.getWidth(), scrollPane.getHeight());
+ setPreferredSize(null);
+ }
+ else
+ {
+ setPreferredSize(new Dimension(scrollPane.getWidth(),
+ fm.getHeight() * nameCount));
+ draw(g, scrollPane.getWidth(), fm.getHeight() * nameCount);
+ }
+
+ scrollPane.revalidate();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param fontSize
+ * DOCUMENT ME!
+ */
+ @Override
+ 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
+
+ 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;
+ }
+
+ 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());
+ }
+ }
+
+ /**
+ * 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
+ }
+ }
+
+ /**
+ * Empty method to satisfy the MouseListener interface
+ *
+ * @param e
+ */
+ @Override
+ public void mouseEntered(MouseEvent e)
+ {
+ }
+
+ /**
+ * Empty method to satisfy the MouseListener interface
+ *
+ * @param e
+ */
+ @Override
+ public void mouseExited(MouseEvent e)
+ {
+ }
+
+ /**
+ * 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)
+ {
+ return;
+ }
+
+ if (evt.getClickCount() > 1)
+ {
+ tree.swapNodes(highlightNode);
+ tree.reCount(tree.getTopNode());
+ tree.findHeight(tree.getTopNode());
+ }
+ else
+ {
+ Vector<SequenceNode> leaves = tree.findLeaves(highlightNode);
+
+ for (int i = 0; i < leaves.size(); i++)
+ {
+ SequenceI seq = (SequenceI) leaves.elementAt(i).element();
+ treeSelectionChanged(seq);
+ }
+ av.sendSelection();
+ }
+
+ 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);
+
+ Object ob = findElement(evt.getX(), evt.getY());
+
+ if (ob instanceof SequenceNode)
+ {
+ highlightNode = (SequenceNode) ob;
+ this.setToolTipText(
+ "<html>" + MessageManager.getString("label.highlightnode"));
+ repaint();
+
+ }
+ else
+ {
+ if (highlightNode != null)
+ {
+ highlightNode = null;
+ setToolTipText(null);
+ repaint();
+ }
+ }
+ }
+
+ @Override
+ public void mouseDragged(MouseEvent ect)
+ {
+ }
+
+ /**
+ * 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();
+
+ Object ob = findElement(x, y);
+
+ if (ob instanceof SequenceI)
+ {
+ treeSelectionChanged((Sequence) ob);
+ PaintRefresher.Refresh(tp,
+ getAssociatedPanel().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));
+
+ List<SequenceNode> 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;
+ }
+ }
+
+ PaintRefresher.Refresh(tp,
+ getAssociatedPanel().av.getSequenceSetId());
+ repaint();
+ }
+
+ }
+
+ void colourGroups(List<SequenceNode> groups)
+ {
+ 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(groups.get(i), col.brighter());
+
+ Vector<SequenceNode> l = tree.findLeaves(groups.get(i));
+
+ Vector<SequenceI> sequences = new Vector<>();
+
+ for (int j = 0; j < l.size(); j++)
+ {
+ SequenceI s1 = (SequenceI) l.elementAt(j).element();
+
+ if (!sequences.contains(s1))
+ {
+ sequences.addElement(s1);
+ }
+ }
+
+ ColourSchemeI cs = null;
+ SequenceGroup _sg = new SequenceGroup(sequences, null, cs, true, true,
+ false, 0, av.getAlignment().getWidth() - 1);
+
+ _sg.setName("JTreeGroup:" + _sg.hashCode());
+ _sg.setIdColour(col);
+
+ for (int a = 0; a < aps.length; a++)
+ {
+ SequenceGroup sg = new SequenceGroup(_sg);
+ AlignViewport viewport = aps[a].av;
+
+ // Propagate group colours in each view
+ if (viewport.getGlobalColourScheme() != null)
+ {
+ cs = viewport.getGlobalColourScheme().getInstance(viewport, sg);
+ sg.setColourScheme(cs);
+ sg.getGroupColourScheme().setThreshold(
+ viewport.getResidueShading().getThreshold(),
+ viewport.isIgnoreGapsConsensus());
+
+ if (viewport.getResidueShading().conservationApplied())
+ {
+ Conservation c = new Conservation("Group",
+ sg.getSequences(null), sg.getStartRes(),
+ sg.getEndRes());
+ c.calculate();
+ c.verdict(false, viewport.getConsPercGaps());
+ sg.cs.setConservation(c);
+ }
+ }
+ // indicate that associated structure views will need an update
+ viewport.setUpdateStructures(true);
+ // propagate structure view update and sequence group to complement view
+ viewport.addSequenceGroup(sg);
+ }
+ }
+
+ // notify the panel(s) to redo any group specific stuff
+ // also updates structure views if necessary
+ for (int a = 0; a < aps.length; a++)
+ {
+ aps[a].updateAnnotation();
+ final AlignViewportI codingComplement = aps[a].av
+ .getCodingComplement();
+ if (codingComplement != null)
+ {
+ ((AlignViewport) codingComplement).getAlignPanel()
+ .updateAnnotation();
+ }
+ }
+ }
+
+ /**
+ * 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[] { 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;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff