X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=5d5b7ba3300e2441084288b3f0137450d321fa11;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=dd062d30fe01fe7462d6b5879434f6238d29b422;hpb=8ea2930d1b4a23415ec924674d043999d3d6f2ce;p=jalview.git diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java index dd062d3..5d5b7ba 100755 --- a/src/jalview/appletgui/TreeCanvas.java +++ b/src/jalview/appletgui/TreeCanvas.java @@ -1,22 +1,20 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * 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 . */ - package jalview.appletgui; import java.util.*; @@ -29,35 +27,48 @@ import jalview.datamodel.*; import jalview.schemes.*; import jalview.util.*; -public class TreeCanvas - extends Panel implements MouseListener, MouseMotionListener +public class TreeCanvas extends Panel implements MouseListener, + MouseMotionListener { NJTree tree; + ScrollPane scrollPane; + AlignViewport av; + public static final String PLACEHOLDER = " * "; + Font font; + 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; - public TreeCanvas(AlignViewport av, ScrollPane scroller) + AlignmentPanel ap; + public TreeCanvas(AlignmentPanel ap, ScrollPane scroller) { - this.av = av; + this.ap = ap; + this.av = ap.av; font = av.getFont(); scrollPane = scroller; addMouseListener(this); @@ -99,19 +110,19 @@ public class TreeCanvas has_placeholders = true; } - if (longestName.length() < ( (Sequence) lf.element()).getName() - .length()) + if (longestName.length() < ((Sequence) lf.element()).getName() + .length()) { - longestName = TreeCanvas.PLACEHOLDER + - ( (Sequence) lf.element()).getName(); + longestName = TreeCanvas.PLACEHOLDER + + ((Sequence) lf.element()).getName(); } } setMarkPlaceholders(has_placeholders); } - public void drawNode(Graphics g, SequenceNode node, float chunk, float scale, - int width, int offx, int offy) + public void drawNode(Graphics g, SequenceNode node, float chunk, + float scale, int width, int offx, int offy) { if (node == null) { @@ -125,14 +136,14 @@ public class TreeCanvas float height = node.height; float dist = node.dist; - int xstart = (int) ( (height - dist) * scale) + offx; + 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(); + SequenceI seq = (SequenceI) ((SequenceNode) node).element(); if (av.getSequenceColour(seq) == Color.white) { @@ -159,32 +170,37 @@ public class TreeCanvas } if (showBootstrap) { - if (showDistances) + int btstrap = node.getBootstrap(); + if (btstrap > -1) { - nodeLabel = nodeLabel + " : "; + if (showDistances) + { + nodeLabel = nodeLabel + " : "; + } + nodeLabel = nodeLabel + String.valueOf(node.getBootstrap()); } - 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(); + 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 + 10, ypos - charHeight, - charWidth, charHeight); + charWidth, charHeight); - nameHash.put( (SequenceI) node.element(), rect); + nameHash.put((SequenceI) node.element(), rect); // Colour selected leaves differently SequenceGroup selected = av.getSelectionGroup(); - if (selected != null && - selected.getSequences(null).contains( (SequenceI) node.element())) + if (selected != null + && selected.getSequences(null).contains( + (SequenceI) node.element())) { g.setColor(Color.gray); @@ -196,17 +212,19 @@ public class TreeCanvas } else { - drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx, offy); - drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx, offy); + drawNode(g, (SequenceNode) node.left(), chunk, 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 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()); + g.setColor(((SequenceNode) node).color.darker()); // Draw horizontal line g.drawLine(xstart, ypos, xend, ypos); @@ -219,14 +237,16 @@ public class TreeCanvas g.fillRect(xend - 2, ypos - 2, 4, 4); } - int ystart = (int) ( ( (SequenceNode) node.left()).ycount * chunk) + offy; - int yend = (int) ( ( (SequenceNode) node.right()).ycount * chunk) + offy; + int ystart = (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); + g.drawLine((int) (height * scale) + offx, ystart, + (int) (height * scale) + offx, yend); String nodeLabel = ""; @@ -237,12 +257,15 @@ public class TreeCanvas if (showBootstrap) { - if (showDistances) + int btstrap = node.getBootstrap(); + if (btstrap > -1) { - nodeLabel = nodeLabel + " : "; + if (showDistances) + { + nodeLabel = nodeLabel + " : "; + } + nodeLabel = nodeLabel + String.valueOf(node.getBootstrap()); } - - nodeLabel = nodeLabel + String.valueOf(node.bootstrap); } if (!nodeLabel.equals("")) @@ -262,8 +285,8 @@ public class TreeCanvas Object ob = keys.nextElement(); Rectangle rect = (Rectangle) nameHash.get(ob); - if (x >= rect.x && x <= (rect.x + rect.width) && - y >= rect.y && y <= (rect.y + rect.height)) + if (x >= rect.x && x <= (rect.x + rect.width) && y >= rect.y + && y <= (rect.y + rect.height)) { return ob; } @@ -275,8 +298,8 @@ public class TreeCanvas Object ob = keys.nextElement(); Rectangle rect = (Rectangle) nodeHash.get(ob); - if (x >= rect.x && x <= (rect.x + rect.width) && - y >= rect.y && y <= (rect.y + rect.height)) + if (x >= rect.x && x <= (rect.x + rect.width) && y >= rect.y + && y <= (rect.y + rect.height)) { return ob; } @@ -292,12 +315,11 @@ public class TreeCanvas SequenceNode top = tree.getTopNode(); - float wscale = (float) (width * .8 - offx * 2) / tree.getMaxHeight() - ; + float wscale = (float) (width * .8 - offx * 2) / tree.getMaxHeight(); if (top.count == 0) { - top.count = ( (SequenceNode) top.left()).count + - ( (SequenceNode) top.right()).count; + top.count = ((SequenceNode) top.left()).count + + ((SequenceNode) top.right()).count; } float chunk = (float) (height - offy) / top.count; @@ -305,7 +327,7 @@ public class TreeCanvas } public void pickNode(Rectangle pickBox, SequenceNode node, float chunk, - float scale, int width, int offx, int offy) + float scale, int width, int offx, int offy) { if (node == null) { @@ -315,9 +337,9 @@ public class TreeCanvas if (node.left() == null && node.right() == null) { float height = node.height; - //float dist = node.dist; + // float dist = node.dist; - //int xstart = (int) ( (height - dist) * scale) + offx; + // int xstart = (int) ( (height - dist) * scale) + offx; int xend = (int) (height * scale) + offx; int ypos = (int) (node.ycount * chunk) + offy; @@ -337,10 +359,10 @@ public class TreeCanvas } else { - pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width, offx, - offy); - pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width, offx, - offy); + pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width, + offx, offy); + pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width, + offx, offy); } } @@ -357,14 +379,14 @@ public class TreeCanvas if (node.element() instanceof SequenceI) { - av.setSequenceColour( (SequenceI) node.element(), c); + av.setSequenceColour((SequenceI) node.element(), c); } } else { node.color = c; - setColor( (SequenceNode) node.left(), c); - setColor( (SequenceNode) node.right(), c); + setColor((SequenceNode) node.left(), c); + setColor((SequenceNode) node.right(), c); } } @@ -402,9 +424,8 @@ public class TreeCanvas setSize(new Dimension(width, height)); g.setFont(font); - draw(g, width, height); - + validate(); } public void draw(Graphics g, int width, int height) @@ -414,16 +435,20 @@ public class TreeCanvas g.setColor(Color.white); g.fillRect(0, 0, width, height); - labelLength = g.getFontMetrics(font).stringWidth(longestName) + 20; //20 allows for scrollbar + labelLength = g.getFontMetrics(font).stringWidth(longestName) + 20; // 20 + // allows + // for + // scrollbar - float wscale = (float) (width - labelLength - offx * 2) / tree.getMaxHeight(); + 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; + top.count = ((SequenceNode) top.left()).count + + ((SequenceNode) top.right()).count; } float chunk = (float) (height - offy) / top.count; @@ -440,8 +465,8 @@ public class TreeCanvas g.setColor(Color.gray); } - int x = (int) (threshold * - (float) (getSize().width - labelLength - 2 * offx) + offx); + int x = (int) (threshold + * (float) (getSize().width - labelLength - 2 * offx) + offx); g.drawLine(x, 0, x, getSize().height); } @@ -449,13 +474,16 @@ public class TreeCanvas } public void mouseReleased(MouseEvent e) - {} + { + } public void mouseEntered(MouseEvent e) - {} + { + } public void mouseExited(MouseEvent e) - {} + { + } public void mouseClicked(MouseEvent evt) { @@ -474,19 +502,21 @@ public class TreeCanvas for (int i = 0; i < leaves.size(); i++) { - SequenceI seq = - (SequenceI) ( (SequenceNode) leaves.elementAt(i)).element(); + SequenceI seq = (SequenceI) ((SequenceNode) leaves.elementAt(i)) + .element(); treeSelectionChanged(seq); } } PaintRefresher.Refresh(this, av.getSequenceSetId()); repaint(); + av.sendSelection(); } } public void mouseDragged(MouseEvent ect) - {} + { + } public void mouseMoved(MouseEvent evt) { @@ -520,19 +550,20 @@ public class TreeCanvas if (ob instanceof SequenceI) { - treeSelectionChanged( (Sequence) ob); + treeSelectionChanged((Sequence) ob); PaintRefresher.Refresh(this, av.getSequenceSetId()); repaint(); + av.sendSelection(); return; } - else if (! (ob instanceof SequenceNode)) + else if (!(ob instanceof SequenceNode)) { // Find threshold if (tree.getMaxHeight() != 0) { - threshold = (float) (x - offx) / - (float) (getSize().width - labelLength - 2 * offx); + threshold = (float) (x - offx) + / (float) (getSize().width - labelLength - 2 * offx); tree.getGroups().removeAllElements(); tree.groupNodes(tree.getTopNode(), threshold); @@ -557,18 +588,18 @@ public class TreeCanvas 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(); for (int j = 0; j < l.size(); j++) { - SequenceI s1 = (SequenceI) ( (SequenceNode) l.elementAt(j)).element(); + SequenceI s1 = (SequenceI) ((SequenceNode) l.elementAt(j)) + .element(); if (!sequences.contains(s1)) { sequences.addElement(s1); @@ -582,37 +613,35 @@ public class TreeCanvas if (av.getGlobalColourScheme() instanceof UserColourScheme) { cs = new UserColourScheme( - ( (UserColourScheme) av.getGlobalColourScheme()).getColours()); + ((UserColourScheme) av.getGlobalColourScheme()) + .getColours()); } else { - cs = ColourSchemeProperty.getColour(sequences, - av.alignment.getWidth(), - ColourSchemeProperty. - getColourName( - av.getGlobalColourScheme())); + cs = ColourSchemeProperty.getColour(sequences, av.alignment + .getWidth(), ColourSchemeProperty.getColourName(av + .getGlobalColourScheme())); + } + // cs is null if shading is an annotationColourGradient + if (cs!=null) + { + cs.setThreshold(av.getGlobalColourScheme().getThreshold(), + av.getIgnoreGapsConsensus()); } - - cs.setThreshold(av.getGlobalColourScheme().getThreshold(), - av.getIgnoreGapsConsensus()); } - SequenceGroup sg = new SequenceGroup(sequences, "", - cs, true, true, - false, 0, - av.alignment.getWidth() - 1); + SequenceGroup sg = new SequenceGroup(sequences, "", cs, true, true, + false, 0, av.alignment.getWidth() - 1); sg.setName("JTreeGroup:" + sg.hashCode()); - + sg.setIdColour(col); if (av.getGlobalColourScheme() != null - && av.getGlobalColourScheme().conservationApplied()) + && av.getGlobalColourScheme().conservationApplied()) { Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, - sg.getSequences(null), - sg.getStartRes(), - sg.getEndRes()); + ResidueProperties.propHash, 3, sg.getSequences(null), + sg.getStartRes(), sg.getEndRes()); c.calculate(); c.verdict(false, av.ConsPercGaps); @@ -625,7 +654,8 @@ public class TreeCanvas av.alignment.addGroup(sg); } - + ap.updateAnnotation(); + } public void setShowDistances(boolean state)