From 7b3241c464d774516c4295a5023f4aef7939298e Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Wed, 22 Nov 2006 15:59:02 +0000 Subject: [PATCH] Associate trees with views --- src/jalview/gui/PaintRefresher.java | 19 + src/jalview/gui/TreeCanvas.java | 1383 ++++++++++++++++++----------------- src/jalview/gui/TreePanel.java | 51 +- src/jalview/jbgui/GTreePanel.java | 3 + 4 files changed, 776 insertions(+), 680 deletions(-) diff --git a/src/jalview/gui/PaintRefresher.java b/src/jalview/gui/PaintRefresher.java index de1d5d8..6755a88 100755 --- a/src/jalview/gui/PaintRefresher.java +++ b/src/jalview/gui/PaintRefresher.java @@ -200,4 +200,23 @@ public class PaintRefresher } } } + + static AlignmentPanel [] getAssociatedPanels(String id) + { + Vector comps = (Vector)components.get(id); + Vector tmp = new Vector(); + int i, iSize = comps.size(); + for (i = 0; i < iSize; i++) + { + if (comps.elementAt(i) instanceof AlignmentPanel) + { + tmp.addElement(((AlignmentPanel)comps.elementAt(i))); + } + } + AlignmentPanel [] result = new AlignmentPanel[tmp.size()]; + tmp.toArray(result); + + return result; + } + } diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index dc08b9a..9ca36cc 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -44,792 +44,806 @@ import javax.swing.*; public class TreeCanvas extends JPanel implements MouseListener, Runnable, Printable, MouseMotionListener { - /** DOCUMENT ME!! */ - public static final String PLACEHOLDER = " * "; - NJTree tree; - JScrollPane scrollPane; - 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; - - /** - * Creates a new TreeCanvas object. - * - * @param av DOCUMENT ME! - * @param tree DOCUMENT ME! - * @param scroller DOCUMENT ME! - * @param label DOCUMENT ME! - */ - public TreeCanvas(AlignmentPanel ap, JScrollPane scroller) - { - this.av = ap.av; - this.ap = ap; - font = av.getFont(); - scrollPane = scroller; - addMouseListener(this); - addMouseMotionListener(this); - PaintRefresher.Register(this, ap.av.getSequenceSetId()); - ToolTipManager.sharedInstance().registerComponent(this); - } + /** DOCUMENT ME!! */ + public static final String PLACEHOLDER = " * "; + NJTree tree; + JScrollPane scrollPane; + 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(AlignmentPanel ap, JScrollPane scroller) + { + this.av = ap.av; + this.ap = ap; + font = av.getFont(); + scrollPane = scroller; + addMouseListener(this); + addMouseMotionListener(this); + PaintRefresher.Register(this, ap.av.getSequenceSetId()); + ToolTipManager.sharedInstance().registerComponent(this); + } + /** + * DOCUMENT ME! + * + * @param sequence DOCUMENT ME! + */ + public void treeSelectionChanged(SequenceI sequence) + { + AlignmentPanel[] aps = getAssociatedPanels(); - /** - * DOCUMENT ME! - * - * @param sequence DOCUMENT ME! - */ - public void treeSelectionChanged(SequenceI sequence) + for (int a = 0; a < aps.length; a++) { - SequenceGroup selected = av.getSelectionGroup(); + SequenceGroup selected = aps[a].av.getSelectionGroup(); - if (selected == null) - { - selected = new SequenceGroup(); - av.setSelectionGroup(selected); - } + if (selected == null) + { + selected = new SequenceGroup(); + aps[a].av.setSelectionGroup(selected); + } - selected.setEndRes(av.alignment.getWidth()-1); - selected.addOrRemove(sequence, true); + selected.setEndRes(aps[a].av.alignment.getWidth() - 1); + selected.addOrRemove(sequence, true); } + } - /** - * DOCUMENT ME! - * - * @param tree DOCUMENT ME! - */ - public void setTree(NJTree tree) + /** + * 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++) { - 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 = ""; + SequenceNode lf = (SequenceNode) leaves.elementAt(i); - for (int i = 0; i < leaves.size(); i++) - { - SequenceNode lf = (SequenceNode) leaves.elementAt(i); + if (lf.isPlaceholder()) + { + has_placeholders = true; + } - if (lf.isPlaceholder()) - { - has_placeholders = true; - } + if (longestName.length() < ( (Sequence) lf.element()).getName() + .length()) + { + longestName = TreeCanvas.PLACEHOLDER + + ( (Sequence) lf.element()).getName(); + } + } - if (longestName.length() < ( (Sequence) lf.element()).getName() - .length()) - { - longestName = TreeCanvas.PLACEHOLDER + - ( (Sequence) lf.element()).getName(); - } - } + setMarkPlaceholders(has_placeholders); + } - 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; } - /** - * 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.left() == null) && (node.right() == null)) { - if (node == null) - { - return; - } + // 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.left() == null) && (node.right() == null)) + if (node.element() instanceof SequenceI) + { + SequenceI seq = (SequenceI) ( (SequenceNode) node).element(); + + if (av.getSequenceColour(seq) == Color.white) { - // 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)((SequenceNode) 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) - { - if (showDistances) - { - nodeLabel = nodeLabel + " : "; - } - - nodeLabel = nodeLabel + String.valueOf(node.getBootstrap()); - } - - 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((SequenceI) node.element(), rect); - - // Colour selected leaves differently - SequenceGroup selected = av.getSelectionGroup(); - - if ((selected != null) && - selected.getSequences(false).contains((SequenceI) 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); + 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); - 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); - - if (showDistances && (node.dist > 0)) - { - g.drawString(new Format("%-.2f").form(node.dist).trim(), xstart+2, - ypos - 2); - } + g.setColor(av.getSequenceColour(seq).darker()); } - } + } + else + { + g.setColor(Color.black); + } - /** - * DOCUMENT ME! - * - * @param x DOCUMENT ME! - * @param y DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public Object findElement(int x, int y) - { - Enumeration keys = nameHash.keys(); + // Draw horizontal line + g.drawLine(xstart, ypos, xend, ypos); - 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; - } - } + String nodeLabel = ""; - keys = nodeHash.keys(); + if (showDistances && (node.dist > 0)) + { + nodeLabel = new Format("%-.2f").form(node.dist); + } - while (keys.hasMoreElements()) + if (showBootstrap) + { + if (showDistances) { - 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; - } + nodeLabel = nodeLabel + " : "; } - return null; - } + nodeLabel = nodeLabel + String.valueOf(node.getBootstrap()); + } + + 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(); - /** - * DOCUMENT ME! - * - * @param pickBox DOCUMENT ME! - */ - public void pickNodes(Rectangle pickBox) + Rectangle rect = new Rectangle(xend + 10, ypos - charHeight / 2, + charWidth, charHeight); + + nameHash.put( (SequenceI) node.element(), rect); + + // Colour selected leaves differently + SequenceGroup selected = av.getSelectionGroup(); + + if ( (selected != null) && + selected.getSequences(false).contains( (SequenceI) 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 { - int width = getWidth(); - int height = getHeight(); + drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx, + offy); + drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx, + offy); - SequenceNode top = tree.getTopNode(); + float height = node.height; + float dist = node.dist; - float wscale = (float) ((width * .8) - (offx * 2)) / tree.getMaxHeight(); + int xstart = (int) ( (height - dist) * scale) + offx; + int xend = (int) (height * scale) + offx; + int ypos = (int) (node.ycount * chunk) + offy; - if (top.count == 0) - { - top.count = ((SequenceNode) top.left()).count + - ((SequenceNode) top.right()).count; - } + g.setColor( ( (SequenceNode) 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); - float chunk = (float) (height - (offy)) / top.count; + int ystart = (int) ( ( (SequenceNode) node.left()).ycount * chunk) + + offy; + int yend = (int) ( ( (SequenceNode) node.right()).ycount * chunk) + + offy; - pickNode(pickBox, top, chunk, wscale, width, offx, 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("%-.2f").form(node.dist).trim(), xstart + 2, + ypos - 2); + } } + } - /** - * 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) + /** + * 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()) { - if (node == null) - { - return; - } + Object ob = keys.nextElement(); + Rectangle rect = (Rectangle) nameHash.get(ob); - 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); - } + if ( (x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) && + (y <= (rect.y + rect.height))) + { + return ob; + } } - /** - * DOCUMENT ME! - * - * @param node DOCUMENT ME! - * @param c DOCUMENT ME! - */ - public void setColor(SequenceNode node, Color c) - { - if (node == null) - { - return; - } + keys = nodeHash.keys(); - if ((node.left() == null) && (node.right() == null)) - { - node.color = c; + while (keys.hasMoreElements()) + { + Object ob = keys.nextElement(); + Rectangle rect = (Rectangle) nodeHash.get(ob); - if (node.element() instanceof SequenceI) - { - av.setSequenceColour((SequenceI) node.element(), c); - } - } - else - { - node.color = c; - setColor((SequenceNode) node.left(), c); - setColor((SequenceNode) node.right(), c); - } + if ( (x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) && + (y <= (rect.y + rect.height))) + { + return ob; + } } - /** - * DOCUMENT ME! - */ - void startPrinting() + 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) { - Thread thread = new Thread(this); - thread.start(); + top.count = ( (SequenceNode) top.left()).count + + ( (SequenceNode) top.right()).count; } - // put printing in a thread to avoid painting problems - public void run() - { - PrinterJob printJob = PrinterJob.getPrinterJob(); - PageFormat pf = printJob.pageDialog(printJob.defaultPage()); + float chunk = (float) (height - (offy)) / top.count; - printJob.setPrintable(this, pf); + pickNode(pickBox, top, chunk, wscale, width, offx, offy); + } - if (printJob.printDialog()) - { - try - { - printJob.print(); - } - catch (Exception PrintException) - { - PrintException.printStackTrace(); - } - } + /** + * 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; } - /** - * 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 + if ( (node.left() == null) && (node.right() == null)) { - pg.setFont(font); - pg.translate((int) pf.getImageableX(), (int) pf.getImageableY()); + float height = node.height; + float dist = node.dist; - int pwidth = (int) pf.getImageableWidth(); - int pheight = (int) pf.getImageableHeight(); + int xstart = (int) ( (height - dist) * scale) + offx; + int xend = (int) (height * scale) + offx; - int noPages = getHeight() / pheight; + int ypos = (int) (node.ycount * chunk) + offy; - if (pi > noPages) + if (pickBox.contains(new Point(xend, ypos))) + { + if (node.element() instanceof SequenceI) { - return Printable.NO_SUCH_PAGE; - } + SequenceI seq = (SequenceI) node.element(); + SequenceGroup sg = av.getSelectionGroup(); - if (pwidth > getWidth()) - { - pwidth = getWidth(); + 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); + } + } - if (fitToWindow) - { - if (pheight > getHeight()) - { - pheight = getHeight(); - } + /** + * DOCUMENT ME! + * + * @param node DOCUMENT ME! + * @param c DOCUMENT ME! + */ + public void setColor(SequenceNode node, Color c) + { + if (node == null) + { + return; + } - noPages = 0; - } - else + if ( (node.left() == null) && (node.right() == null)) + { + node.color = c; + + if (node.element() instanceof SequenceI) + { + AlignmentPanel[] aps = getAssociatedPanels(); + for (int a = 0; a < aps.length; a++) { - 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; + aps[a].av.setSequenceColour( (SequenceI) node.element(), c); } + } + } + else + { + node.color = c; + setColor( (SequenceNode) node.left(), c); + setColor( (SequenceNode) node.right(), c); + } + } - draw(pg, pwidth, pheight); + /** + * DOCUMENT ME! + */ + void startPrinting() + { + Thread thread = new Thread(this); + thread.start(); + } - return Printable.PAGE_EXISTS; - } + // put printing in a thread to avoid painting problems + public void run() + { + PrinterJob printJob = PrinterJob.getPrinterJob(); + PageFormat pf = printJob.pageDialog(printJob.defaultPage()); - /** - * DOCUMENT ME! - * - * @param g DOCUMENT ME! - */ - public void paintComponent(Graphics g) + printJob.setPrintable(this, pf); + + if (printJob.printDialog()) { - super.paintComponent(g); - g.setFont(font); + try + { + printJob.print(); + } + catch (Exception PrintException) + { + PrintException.printStackTrace(); + } + } + } - if(tree==null) - { - g.drawString("Calculating tree....", 20, getHeight()/2); - } - else - { - fm = g.getFontMetrics(font); + /** + * 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 (nameHash.size() == 0) - { - repaint(); - } + if (pwidth > getWidth()) + { + pwidth = getWidth(); + } - 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()); - } + if (fitToWindow) + { + if (pheight > getHeight()) + { + pheight = getHeight(); + } - scrollPane.revalidate(); - } + 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 fontSize DOCUMENT ME! - */ - public void setFont(Font font) + /** + * DOCUMENT ME! + * + * @param g DOCUMENT ME! + */ + public void paintComponent(Graphics g) + { + super.paintComponent(g); + g.setFont(font); + + if (tree == null) { - this.font = font; - repaint(); + g.drawString("Calculating tree....", 20, getHeight() / 2); } - - /** - * DOCUMENT ME! - * - * @param g1 DOCUMENT ME! - * @param width DOCUMENT ME! - * @param height DOCUMENT ME! - */ - public void draw(Graphics g1, int width, int height) + else { - Graphics2D g2 = (Graphics2D) g1; - g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, - RenderingHints.VALUE_ANTIALIAS_ON); - g2.setColor(Color.white); - g2.fillRect(0, 0, width, height); + fm = g.getFontMetrics(font); + + if (nameHash.size() == 0) + { + repaint(); + } - g2.setFont(font); + 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()); + } - offy = font.getSize()+10; + scrollPane.revalidate(); + } + } - fm = g2.getFontMetrics(font); + /** + * DOCUMENT ME! + * + * @param fontSize DOCUMENT ME! + */ + public void setFont(Font font) + { + this.font = font; + repaint(); + } - labelLength = fm.stringWidth(longestName) + 20; //20 allows for scrollbar + /** + * 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); - float wscale = (float) (width - labelLength - (offx * 2)) / tree.getMaxHeight(); + g2.setFont(font); - SequenceNode top = tree.getTopNode(); + offy = font.getSize() + 10; - if (top.count == 0) - { - top.count = ((SequenceNode) top.left()).count + - ((SequenceNode) top.right()).count; - } + fm = g2.getFontMetrics(font); - float chunk = (float) (height - (offy)) / top.count; + labelLength = fm.stringWidth(longestName) + 20; //20 allows for scrollbar - drawNode(g2, tree.getTopNode(), chunk, wscale, width, offx, offy); + float wscale = (float) (width - labelLength - (offx * 2)) / + tree.getMaxHeight(); - 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()); - } - } + SequenceNode top = tree.getTopNode(); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void mouseReleased(MouseEvent e) + if (top.count == 0) { + top.count = ( (SequenceNode) top.left()).count + + ( (SequenceNode) top.right()).count; } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void mouseEntered(MouseEvent e) - { - } + float chunk = (float) (height - (offy)) / top.count; - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void mouseExited(MouseEvent e) - { - } + drawNode(g2, tree.getTopNode(), chunk, wscale, width, offx, offy); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void mouseClicked(MouseEvent evt) + if (threshold != 0) { - if(highlightNode!=null) + if (av.getCurrentTree() == tree) { - if (SwingUtilities.isRightMouseButton(evt)) - { - Color col = JColorChooser.showDialog(this, "Select Sub-Tree Colour", - highlightNode.color); - - 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); + g2.setColor(Color.red); + } + else + { + g2.setColor(Color.gray); + } - for (int i = 0; i < leaves.size(); i++) - { - SequenceI seq = - (SequenceI) ( (SequenceNode) leaves.elementAt(i)).element(); - treeSelectionChanged(seq); - } - } + int x = (int) ( (threshold * (float) (getWidth() - labelLength - + (2 * offx))) + offx); - PaintRefresher.Refresh(this, av.getSequenceSetId()); - repaint(); - } + 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) + { + } - public void mouseMoved(MouseEvent evt) - { - av.setCurrentTree(tree); - - Object ob = findElement(evt.getX(), evt.getY()); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseExited(MouseEvent e) + { + } - if (ob instanceof SequenceNode) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseClicked(MouseEvent evt) + { + if (highlightNode != null) + { + if (SwingUtilities.isRightMouseButton(evt)) { - highlightNode = (SequenceNode) ob; - this.setToolTipText( - "Left click to select leaves" - + "
Double-click to invert leaves" - + "
Right click to change colour"); - repaint(); + Color col = JColorChooser.showDialog(this, "Select Sub-Tree Colour", + highlightNode.color); + setColor(highlightNode, col); + } + else + if (evt.getClickCount() > 1) + { + tree.swapNodes(highlightNode); + tree.reCount(tree.getTopNode()); + tree.findHeight(tree.getTopNode()); } else { - if (highlightNode != null) + Vector leaves = new Vector(); + tree.findLeaves(highlightNode, leaves); + + for (int i = 0; i < leaves.size(); i++) { - highlightNode = null; - setToolTipText(null); - repaint(); + SequenceI seq = + (SequenceI) ( (SequenceNode) leaves.elementAt(i)).element(); + treeSelectionChanged(seq); } } + + PaintRefresher.Refresh(this, av.getSequenceSetId()); + repaint(); + } } - public void mouseDragged(MouseEvent ect) - {} + public void mouseMoved(MouseEvent evt) + { + av.setCurrentTree(tree); + + Object ob = findElement(evt.getX(), evt.getY()); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void mousePressed(MouseEvent e) + if (ob instanceof SequenceNode) { - av.setCurrentTree(tree); + highlightNode = (SequenceNode) ob; + this.setToolTipText( + "Left click to select leaves" + + "
Double-click to invert leaves" + + "
Right click to change colour"); + repaint(); - int x = e.getX(); - int y = e.getY(); + } + else + { + if (highlightNode != null) + { + highlightNode = null; + setToolTipText(null); + repaint(); + } + } + } - Object ob = findElement(x, y); + public void mouseDragged(MouseEvent ect) + {} - if (ob instanceof SequenceI) - { - treeSelectionChanged( (Sequence) ob); - PaintRefresher.Refresh(this, ap.av.getSequenceSetId()); - repaint(); - return; - } - else if( !(ob instanceof SequenceNode) ) - { - // Find threshold - if (tree.getMaxHeight() != 0) - { - threshold = (float) (x - offx) / (float) (getWidth() - - labelLength - (2 * offx)); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mousePressed(MouseEvent e) + { + av.setCurrentTree(tree); - tree.getGroups().removeAllElements(); - tree.groupNodes(tree.getTopNode(), threshold); - setColor(tree.getTopNode(), Color.black); + int x = e.getX(); + int y = e.getY(); - av.setSelectionGroup(null); - av.alignment.deleteAllGroups(); - av.sequenceColours=null; + Object ob = findElement(x, y); - colourGroups(); - } + if (ob instanceof SequenceI) + { + treeSelectionChanged( (Sequence) ob); + PaintRefresher.Refresh(this, ap.av.getSequenceSetId()); + repaint(); + return; + } + else if (! (ob instanceof SequenceNode)) + { + // Find threshold + if (tree.getMaxHeight() != 0) + { + threshold = (float) (x - offx) / (float) (getWidth() - + labelLength - (2 * offx)); - PaintRefresher.Refresh(this, ap.av.getSequenceSetId()); - repaint(); - } + tree.getGroups().removeAllElements(); + tree.groupNodes(tree.getTopNode(), threshold); + setColor(tree.getTopNode(), Color.black); + AlignmentPanel[] aps = getAssociatedPanels(); + for (int a = 0; a < aps.length; a++) + { + aps[a].av.setSelectionGroup(null); + aps[a].av.alignment.deleteAllGroups(); + aps[a].av.sequenceColours = null; + } + colourGroups(); + } + + PaintRefresher.Refresh(this, ap.av.getSequenceSetId()); + repaint(); } - void colourGroups() + } + + void colourGroups() + { + for (int i = 0; i < tree.getGroups().size(); i++) { - 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( (SequenceNode) tree.getGroups().elementAt(i), + col.brighter()); - Vector l = tree.findLeaves( (SequenceNode) tree.getGroups() - .elementAt(i), - new Vector()); + Vector l = tree.findLeaves( (SequenceNode) tree.getGroups() + .elementAt(i), + new Vector()); - Vector sequences = new Vector(); + Vector sequences = new Vector(); - for (int j = 0; j < l.size(); j++) - { - SequenceI s1 = (SequenceI) ( (SequenceNode) l.elementAt(j)).element(); + for (int j = 0; j < l.size(); j++) + { + SequenceI s1 = (SequenceI) ( (SequenceNode) l.elementAt(j)).element(); - if (!sequences.contains(s1)) - { - sequences.addElement(s1); - } + if (!sequences.contains(s1)) + { + sequences.addElement(s1); } + } - ColourSchemeI cs = null; + ColourSchemeI cs = null; - if (av.getGlobalColourScheme() != null) + if (av.getGlobalColourScheme() != null) + { + if (av.getGlobalColourScheme() instanceof UserColourScheme) { - 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.setThreshold(av.getGlobalColourScheme().getThreshold(), - av.getIgnoreGapsConsensus()); } + else + cs = ColourSchemeProperty.getColour(sequences, + av.alignment.getWidth(), + ColourSchemeProperty. + getColourName( + av.getGlobalColourScheme())); + + cs.setThreshold(av.getGlobalColourScheme().getThreshold(), + av.getIgnoreGapsConsensus()); + } - SequenceGroup sg = new SequenceGroup(sequences, - "TreeGroup", cs, true, true, false, - 0, - av.alignment.getWidth() - 1); + SequenceGroup sg = new SequenceGroup(sequences, + "TreeGroup", cs, true, true, false, + 0, + av.alignment.getWidth() - 1); - if (av.getGlobalColourScheme() != null - && av.getGlobalColourScheme().conservationApplied()) + 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, @@ -837,45 +851,56 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, sg.getStartRes(), sg.getEndRes()); c.calculate(); - c.verdict(false, av.ConsPercGaps); + c.verdict(false, aps[a].av.ConsPercGaps); sg.cs.setConservation(c); } - av.alignment.addGroup(sg); + aps[a].av.alignment.addGroup(sg); } - } - /** - * 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 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) + /** + * DOCUMENT ME! + * + * @param state DOCUMENT ME! + */ + public void setMarkPlaceholders(boolean state) + { + this.markPlaceholders = state; + repaint(); + } + + AlignmentPanel[] getAssociatedPanels() + { + if (applyToAllViews) { - this.markPlaceholders = state; - repaint(); + return PaintRefresher.getAssociatedPanels(av.getSequenceSetId()); } + else + return new AlignmentPanel[]{ap}; + } } diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index c22a8e7..3bb9108 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -36,6 +36,7 @@ import java.io.*; import java.util.*; +import javax.swing.*; import javax.imageio.*; import java.beans.PropertyChangeEvent; @@ -91,7 +92,7 @@ public class TreePanel extends GTreePanel super(); initTreePanel(ap, type, pwtype, newtree, null); } - + public TreePanel(AlignmentPanel av, String type, String pwtype, @@ -116,6 +117,8 @@ public class TreePanel extends GTreePanel this.type = type; this.pwtype = pwtype; + buildAssociatedViewMenu(); + treeCanvas = new TreeCanvas(ap, scrollPane); scrollPane.setViewportView(treeCanvas); @@ -145,6 +148,52 @@ public class TreePanel extends GTreePanel } + void buildAssociatedViewMenu() + { + AlignmentPanel [] aps = PaintRefresher.getAssociatedPanels(av.getSequenceSetId()); + if(aps.length<2) + { + associateLeavesMenu.setVisible(false); + return; + } + associateLeavesMenu.addSeparator(); + + JRadioButtonMenuItem item; + ButtonGroup buttonGroup = new ButtonGroup(); + int i, iSize = aps.length; + for(i=0; i