X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=f965ff4686b41d79f7209b7e2b36e76c61736447;hb=fdde9a078d7bdb46ed9fb7fe115ea83c84a19c81;hp=d1c6c614b6813fccbb3b0e74303f8dd93499df96;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java index d1c6c61..f965ff4 100755 --- a/src/jalview/appletgui/TreeCanvas.java +++ b/src/jalview/appletgui/TreeCanvas.java @@ -1,36 +1,61 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * 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. - * + * 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 . + * You should have received a copy of the GNU General Public License + * 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.BinaryNode; +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; @@ -62,11 +87,14 @@ public class TreeCanvas extends Panel implements MouseListener, Hashtable nodeHash = new Hashtable(); - SequenceNode highlightNode; + BinaryNode 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); @@ -85,25 +113,25 @@ 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); } - 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); + BinaryNode lf = leaves.elementAt(i); - if (lf.isPlaceholder()) + if (lf instanceof SequenceNode && ((SequenceNode) lf).isPlaceholder()) { has_placeholders = true; } @@ -119,8 +147,8 @@ public class TreeCanvas extends Panel implements MouseListener, 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, BinaryNode node, float chunk, + double scale, int width, int offx, int offy) { if (node == null) { @@ -131,8 +159,8 @@ public class TreeCanvas extends Panel implements MouseListener, { // 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 xend = (int) (height * scale) + offx; @@ -141,7 +169,7 @@ 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) { @@ -183,9 +211,10 @@ public class TreeCanvas extends Panel implements MouseListener, g.drawString(nodeLabel, xstart + 2, ypos - 2); } - String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node - .getName()) - : node.getName(); + String name = (markPlaceholders && node instanceof SequenceNode + && ((SequenceNode) node).isPlaceholder()) + ? (PLACEHOLDER + node.getName()) + : node.getName(); FontMetrics fm = g.getFontMetrics(font); int charWidth = fm.stringWidth(name) + 3; int charHeight = fm.getHeight(); @@ -193,13 +222,12 @@ 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); @@ -211,19 +239,19 @@ public class TreeCanvas extends Panel implements MouseListener, } else { - drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx, + drawNode(g, (BinaryNode) node.left(), chunk, scale, width, offx, offy); - drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx, + drawNode(g, (BinaryNode) 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 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); @@ -236,10 +264,10 @@ public class TreeCanvas extends Panel implements MouseListener, 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 + : (((BinaryNode) node.left()).ycount * chunk)) + offy; + int yend = (int) (node.right() == null ? 0 + : (((BinaryNode) node.right()).ycount * chunk)) + offy; Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5); nodeHash.put(node, pos); @@ -312,21 +340,21 @@ public class TreeCanvas extends Panel implements MouseListener, int width = getSize().width; int height = getSize().height; - SequenceNode top = tree.getTopNode(); + BinaryNode 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 = ((BinaryNode) top.left()).count + + ((BinaryNode) top.right()).count; } float chunk = (float) (height - offy) / top.count; pickNode(pickBox, top, chunk, wscale, width, offx, offy); } - public void pickNode(Rectangle pickBox, SequenceNode node, float chunk, - float scale, int width, int offx, int offy) + public void pickNode(Rectangle pickBox, BinaryNode node, float chunk, + double scale, int width, int offx, int offy) { if (node == null) { @@ -335,7 +363,7 @@ public class TreeCanvas extends Panel implements MouseListener, if (node.left() == null && node.right() == null) { - float height = node.height; + double height = node.height; // float dist = node.dist; // int xstart = (int) ( (height - dist) * scale) + offx; @@ -358,14 +386,14 @@ public class TreeCanvas extends Panel implements MouseListener, } else { - pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width, - offx, offy); - pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width, + pickNode(pickBox, (BinaryNode) node.left(), chunk, scale, width, offx, + offy); + pickNode(pickBox, (BinaryNode) node.right(), chunk, scale, width, offx, offy); } } - public void setColor(SequenceNode node, Color c) + public void setColor(BinaryNode node, Color c) { if (node == null) { @@ -384,16 +412,18 @@ public class TreeCanvas extends Panel implements MouseListener, else { node.color = c; - setColor((SequenceNode) node.left(), c); - setColor((SequenceNode) node.right(), c); + setColor((BinaryNode) node.left(), c); + setColor((BinaryNode) node.right(), c); } } + @Override public void update(Graphics g) { paint(g); } + @Override public void paint(Graphics g) { if (tree == null) @@ -439,15 +469,14 @@ public class TreeCanvas extends Panel implements MouseListener, // for // scrollbar - float wscale = (float) (width - labelLength - offx * 2) - / tree.getMaxHeight(); + double wscale = (width - labelLength - offx * 2) / tree.getMaxHeight(); - SequenceNode top = tree.getTopNode(); + BinaryNode top = tree.getTopNode(); if (top.count == 0) { - top.count = ((SequenceNode) top.left()).count - + ((SequenceNode) top.right()).count; + top.count = ((BinaryNode) top.left()).count + + ((BinaryNode) top.right()).count; } float chunk = (float) (height - offy) / top.count; @@ -464,26 +493,30 @@ 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) @@ -496,35 +529,36 @@ public class TreeCanvas extends Panel implements MouseListener, } 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); Object ob = findElement(evt.getX(), evt.getY()); - if (ob instanceof SequenceNode) + if (ob instanceof BinaryNode) { - highlightNode = (SequenceNode) ob; + highlightNode = (BinaryNode) ob; repaint(); } else @@ -537,6 +571,7 @@ public class TreeCanvas extends Panel implements MouseListener, } } + @Override public void mousePressed(MouseEvent e) { av.setCurrentTree(tree); @@ -551,6 +586,7 @@ public class TreeCanvas extends Panel implements MouseListener, treeSelectionChanged((Sequence) ob); PaintRefresher.Refresh(this, av.getSequenceSetId()); repaint(); + av.sendSelection(); return; } else if (!(ob instanceof SequenceNode)) @@ -562,15 +598,21 @@ public class TreeCanvas extends Panel implements MouseListener, 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); } } @@ -580,23 +622,21 @@ public class TreeCanvas extends Panel implements MouseListener, } - 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); @@ -605,49 +645,81 @@ 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.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)