X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=2e5f93884eef308441c1fb29ffa7c3dced893b2d;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=dd062d30fe01fe7462d6b5879434f6238d29b422;hpb=8ea2930d1b4a23415ec924674d043999d3d6f2ce;p=jalview.git diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java index dd062d3..2e5f938 100755 --- a/src/jalview/appletgui/TreeCanvas.java +++ b/src/jalview/appletgui/TreeCanvas.java @@ -1,63 +1,99 @@ /* - * 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 + * 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. - * - * 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 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; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import jalview.analysis.*; -import jalview.datamodel.*; -import jalview.schemes.*; -import jalview.util.*; - -public class TreeCanvas - extends Panel implements MouseListener, MouseMotionListener +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.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemeProperty; +import jalview.schemes.UserColourScheme; +import jalview.util.Format; +import jalview.util.MappingUtils; +import jalview.viewmodel.AlignmentViewport; + +import java.awt.Color; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.FontMetrics; +import java.awt.Graphics; +import java.awt.Panel; +import java.awt.Point; +import java.awt.Rectangle; +import java.awt.ScrollPane; +import java.awt.event.MouseEvent; +import java.awt.event.MouseListener; +import java.awt.event.MouseMotionListener; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.List; +import java.util.Vector; + +public class TreeCanvas extends Panel + implements MouseListener, MouseMotionListener { - NJTree tree; + TreeModel 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); @@ -76,42 +112,42 @@ public class TreeCanvas av.setSelectionGroup(selected); } - selected.setEndRes(av.alignment.getWidth() - 1); + selected.setEndRes(av.getAlignment().getWidth() - 1); selected.addOrRemove(sequence, true); } - public void setTree(NJTree tree) + public void setTree(TreeModel tree2) { - this.tree = tree; - tree.findHeight(tree.getTopNode()); + this.tree = tree2; + tree2.findHeight(tree2.getTopNode()); // Now have to calculate longest name based on the leaves - Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector()); + Vector leaves = tree2.findLeaves(tree2.getTopNode()); boolean has_placeholders = false; longestName = ""; for (int i = 0; i < leaves.size(); i++) { - SequenceNode lf = (SequenceNode) leaves.elementAt(i); + SequenceNode lf = leaves.elementAt(i); if (lf.isPlaceholder()) { 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, + double scale, int width, int offx, int offy) { if (node == null) { @@ -122,17 +158,17 @@ public class TreeCanvas { // Drawing leaf node - float height = node.height; - float dist = node.dist; + double height = node.height; + double 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) node.element(); if (av.getSequenceColour(seq) == Color.white) { @@ -159,32 +195,37 @@ 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(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(node.element())) { g.setColor(Color.gray); @@ -196,17 +237,19 @@ 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; + double height = node.height; + double 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(node.color.darker()); // Draw horizontal line g.drawLine(xstart, ypos, xend, ypos); @@ -219,14 +262,16 @@ 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) (node.left() == null ? 0 + : (((SequenceNode) node.left()).ycount * chunk)) + offy; + int yend = (int) (node.right() == null ? 0 + : (((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 +282,15 @@ 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 +310,8 @@ 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 +323,8 @@ 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 +340,11 @@ public class TreeCanvas SequenceNode top = tree.getTopNode(); - float wscale = (float) (width * .8 - offx * 2) / tree.getMaxHeight() - ; + double 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 +352,7 @@ public class TreeCanvas } public void pickNode(Rectangle pickBox, SequenceNode node, float chunk, - float scale, int width, int offx, int offy) + double scale, int width, int offx, int offy) { if (node == null) { @@ -314,10 +361,10 @@ public class TreeCanvas if (node.left() == null && node.right() == null) { - float height = node.height; - //float dist = node.dist; + double 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; @@ -337,10 +384,10 @@ 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); } } @@ -357,22 +404,24 @@ 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); } } + @Override public void update(Graphics g) { paint(g); } + @Override public void paint(Graphics g) { if (tree == null) @@ -402,9 +451,8 @@ 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 +462,19 @@ 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(); + 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; + top.count = ((SequenceNode) top.left()).count + + ((SequenceNode) top.right()).count; } float chunk = (float) (height - offy) / top.count; @@ -440,23 +491,30 @@ public class TreeCanvas 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) @@ -469,25 +527,27 @@ public class TreeCanvas } else { - Vector leaves = new Vector(); - tree.findLeaves(highlightNode, leaves); + Vector leaves = tree.findLeaves(highlightNode); for (int i = 0; i < leaves.size(); i++) { - SequenceI seq = - (SequenceI) ( (SequenceNode) leaves.elementAt(i)).element(); + SequenceI seq = (SequenceI) leaves.elementAt(i).element(); treeSelectionChanged(seq); } } PaintRefresher.Refresh(this, av.getSequenceSetId()); repaint(); + av.sendSelection(); } } + @Override public void mouseDragged(MouseEvent ect) - {} + { + } + @Override public void mouseMoved(MouseEvent evt) { av.setCurrentTree(tree); @@ -509,6 +569,7 @@ public class TreeCanvas } } + @Override public void mousePressed(MouseEvent e) { av.setCurrentTree(tree); @@ -520,29 +581,36 @@ 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); + List groups = tree.groupNodes(threshold); setColor(tree.getTopNode(), Color.black); av.setSelectionGroup(null); - av.alignment.deleteAllGroups(); - av.sequenceColours = null; + av.getAlignment().deleteAllGroups(); + av.clearSequenceColours(); + final AlignViewportI codingComplement = av.getCodingComplement(); + if (codingComplement != null) + { + codingComplement.setSelectionGroup(null); + codingComplement.getAlignment().deleteAllGroups(); + codingComplement.clearSequenceColours(); + } - colourGroups(); + colourGroups(groups); } } @@ -552,23 +620,21 @@ public class TreeCanvas } - void colourGroups() + void colourGroups(List groups) { - for (int i = 0; i < tree.getGroups().size(); i++) + 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( (SequenceNode) tree.getGroups().elementAt(i), col.brighter()); + Color col = new Color((int) (Math.random() * 255), + (int) (Math.random() * 255), (int) (Math.random() * 255)); + setColor(groups.get(i), col.brighter()); - Vector l = tree.findLeaves( (SequenceNode) tree.getGroups().elementAt( - i), new Vector()); + Vector l = tree.findLeaves(groups.get(i)); - Vector sequences = 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) l.elementAt(j).element(); if (!sequences.contains(s1)) { sequences.addElement(s1); @@ -577,55 +643,81 @@ public class TreeCanvas 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()); + ((UserColourScheme) av.getGlobalColourScheme()) + .getColours()); } else { - cs = ColourSchemeProperty.getColour(sequences, - av.alignment.getWidth(), - ColourSchemeProperty. - getColourName( - av.getGlobalColourScheme())); + cs = ColourSchemeProperty.getColourScheme(av, sg, + ColourSchemeProperty + .getColourName(av.getGlobalColourScheme())); } - - cs.setThreshold(av.getGlobalColourScheme().getThreshold(), - av.getIgnoreGapsConsensus()); + // cs is null if shading is an annotationColourGradient + // if (cs != null) + // { + // cs.setThreshold(av.getViewportColourScheme().getThreshold(), + // av.isIgnoreGapsConsensus()); + // } } - - 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.setColourScheme(cs); + sg.getGroupColourScheme().setThreshold( + av.getResidueShading().getThreshold(), + av.isIgnoreGapsConsensus()); sg.setName("JTreeGroup:" + sg.hashCode()); - + sg.setIdColour(col); if (av.getGlobalColourScheme() != null - && av.getGlobalColourScheme().conservationApplied()) + && av.getResidueShading().conservationApplied()) { - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, - sg.getSequences(null), - sg.getStartRes(), - sg.getEndRes()); + Conservation c = new Conservation("Group", sg.getSequences(null), + sg.getStartRes(), sg.getEndRes()); c.calculate(); - c.verdict(false, av.ConsPercGaps); - cs.setConservation(c); - - sg.cs = cs; + c.verdict(false, av.getConsPercGaps()); + sg.setColourScheme(cs); + sg.getGroupColourScheme().setConservation(c); } - av.alignment.addGroup(sg); + av.getAlignment().addGroup(sg); - } + // TODO this is duplicated with gui TreeCanvas - refactor + av.getAlignment().addGroup(sg); + final AlignViewportI codingComplement = av.getCodingComplement(); + if (codingComplement != null) + { + SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, av, + codingComplement); + if (mappedGroup.getSequences().size() > 0) + { + codingComplement.getAlignment().addGroup(mappedGroup); + for (SequenceI seq : mappedGroup.getSequences()) + { + // TODO why does gui require col.brighter() here?? + codingComplement.setSequenceColour(seq, col); + } + } + } + } + ap.updateAnnotation(); + if (av.getCodingComplement() != null) + { + ((AlignmentViewport) av.getCodingComplement()).firePropertyChange( + "alignment", null, ap.av.getAlignment().getSequences()); + } } public void setShowDistances(boolean state)