X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=745520b5f91fe4d057f4cf9ec7e03765bb0afced;hb=9493ac8f3b6a02d3cf9747ed6c0d6cf407d284e8;hp=4e15fd39c02c6be64e11e0a97daff708e0f31e3a;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java index 4e15fd3..745520b 100755 --- a/src/jalview/appletgui/TreeCanvas.java +++ b/src/jalview/appletgui/TreeCanvas.java @@ -1,20 +1,22 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 The Jalview Authors * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.appletgui; @@ -65,9 +67,12 @@ public class TreeCanvas extends Panel implements MouseListener, 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); @@ -86,7 +91,7 @@ public class TreeCanvas extends Panel implements MouseListener, av.setSelectionGroup(selected); } - selected.setEndRes(av.alignment.getWidth() - 1); + selected.setEndRes(av.getAlignment().getWidth() - 1); selected.addOrRemove(sequence, true); } @@ -142,7 +147,7 @@ public class TreeCanvas extends Panel implements MouseListener, if (node.element() instanceof SequenceI) { - SequenceI seq = (SequenceI) ((SequenceNode) node).element(); + SequenceI seq = (SequenceI) node.element(); if (av.getSequenceColour(seq) == Color.white) { @@ -185,8 +190,7 @@ public class TreeCanvas extends Panel implements MouseListener, } String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node - .getName()) - : node.getName(); + .getName()) : node.getName(); FontMetrics fm = g.getFontMetrics(font); int charWidth = fm.stringWidth(name) + 3; int charHeight = fm.getHeight(); @@ -194,13 +198,12 @@ public class TreeCanvas extends Panel implements MouseListener, Rectangle rect = new Rectangle(xend + 10, ypos - charHeight, charWidth, charHeight); - nameHash.put((SequenceI) node.element(), rect); + nameHash.put(node.element(), rect); // Colour selected leaves differently SequenceGroup selected = av.getSelectionGroup(); if (selected != null - && selected.getSequences(null).contains( - (SequenceI) node.element())) + && selected.getSequences(null).contains(node.element())) { g.setColor(Color.gray); @@ -224,7 +227,7 @@ public class TreeCanvas extends Panel implements MouseListener, int xend = (int) (height * scale) + offx; int ypos = (int) (node.ycount * chunk) + offy; - g.setColor(((SequenceNode) node).color.darker()); + g.setColor(node.color.darker()); // Draw horizontal line g.drawLine(xstart, ypos, xend, ypos); @@ -390,11 +393,13 @@ public class TreeCanvas extends Panel implements MouseListener, } } + @Override public void update(Graphics g) { paint(g); } + @Override public void paint(Graphics g) { if (tree == null) @@ -424,9 +429,8 @@ public class TreeCanvas extends Panel implements MouseListener, setSize(new Dimension(width, height)); g.setFont(font); - draw(g, width, height); - + validate(); } public void draw(Graphics g, int width, int height) @@ -437,12 +441,11 @@ public class TreeCanvas extends Panel implements MouseListener, g.fillRect(0, 0, width, height); labelLength = g.getFontMetrics(font).stringWidth(longestName) + 20; // 20 - // allows - // for - // scrollbar + // allows + // for + // scrollbar - float wscale = (float) (width - labelLength - offx * 2) - / tree.getMaxHeight(); + float wscale = (width - labelLength - offx * 2) / tree.getMaxHeight(); SequenceNode top = tree.getTopNode(); @@ -466,26 +469,29 @@ public class TreeCanvas extends Panel implements MouseListener, g.setColor(Color.gray); } - int x = (int) (threshold - * (float) (getSize().width - labelLength - 2 * offx) + offx); + int x = (int) (threshold * (getSize().width - labelLength - 2 * offx) + offx); g.drawLine(x, 0, x, getSize().height); } } + @Override public void mouseReleased(MouseEvent e) { } + @Override public void mouseEntered(MouseEvent e) { } + @Override public void mouseExited(MouseEvent e) { } + @Override public void mouseClicked(MouseEvent evt) { if (highlightNode != null) @@ -511,13 +517,16 @@ public class TreeCanvas extends Panel implements MouseListener, PaintRefresher.Refresh(this, av.getSequenceSetId()); repaint(); + av.sendSelection(); } } + @Override public void mouseDragged(MouseEvent ect) { } + @Override public void mouseMoved(MouseEvent evt) { av.setCurrentTree(tree); @@ -539,6 +548,7 @@ public class TreeCanvas extends Panel implements MouseListener, } } + @Override public void mousePressed(MouseEvent e) { av.setCurrentTree(tree); @@ -553,6 +563,7 @@ public class TreeCanvas extends Panel implements MouseListener, treeSelectionChanged((Sequence) ob); PaintRefresher.Refresh(this, av.getSequenceSetId()); repaint(); + av.sendSelection(); return; } else if (!(ob instanceof SequenceNode)) @@ -569,8 +580,8 @@ public class TreeCanvas extends Panel implements MouseListener, setColor(tree.getTopNode(), Color.black); av.setSelectionGroup(null); - av.alignment.deleteAllGroups(); - av.sequenceColours = null; + av.getAlignment().deleteAllGroups(); + av.clearSequenceColours(); colourGroups(); @@ -587,12 +598,12 @@ public class TreeCanvas extends Panel implements MouseListener, 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)); + 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++) @@ -607,27 +618,34 @@ public class TreeCanvas extends Panel implements MouseListener, ColourSchemeI cs = null; + SequenceGroup sg = new SequenceGroup(sequences, "", cs, true, true, + false, 0, av.getAlignment().getWidth() - 1); + if (av.getGlobalColourScheme() != null) { if (av.getGlobalColourScheme() instanceof UserColourScheme) { - cs = new UserColourScheme(((UserColourScheme) av - .getGlobalColourScheme()).getColours()); + cs = new UserColourScheme( + ((UserColourScheme) av.getGlobalColourScheme()) + .getColours()); } else { - cs = ColourSchemeProperty.getColour(sequences, av.alignment - .getWidth(), ColourSchemeProperty.getColourName(av - .getGlobalColourScheme())); + cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty + .getColourName(av.getGlobalColourScheme())); + } + // cs is null if shading is an annotationColourGradient + if (cs != null) + { + cs.setThreshold(av.getGlobalColourScheme().getThreshold(), + av.getIgnoreGapsConsensus()); } - - cs.setThreshold(av.getGlobalColourScheme().getThreshold(), av - .getIgnoreGapsConsensus()); } - - SequenceGroup sg = new SequenceGroup(sequences, "", cs, true, true, - false, 0, av.alignment.getWidth() - 1); + // TODO: cs used to be initialized with a sequence collection and + // recalcConservation called automatically + // instead we set it manually - recalc called after updateAnnotation + sg.cs = cs; sg.setName("JTreeGroup:" + sg.hashCode()); sg.setIdColour(col); @@ -635,20 +653,21 @@ public class TreeCanvas extends Panel implements MouseListener, && 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); + c.verdict(false, av.getConsPercGaps()); cs.setConservation(c); sg.cs = cs; } - av.alignment.addGroup(sg); + av.getAlignment().addGroup(sg); } + ap.updateAnnotation(); }