X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=272a2b3f172cfc536289690cd4de34fcdba2fd74;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=745520b5f91fe4d057f4cf9ec7e03765bb0afced;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java index 745520b..272a2b3 100755 --- a/src/jalview/appletgui/TreeCanvas.java +++ b/src/jalview/appletgui/TreeCanvas.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,20 +20,41 @@ */ 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.*; +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; @@ -95,19 +116,19 @@ public class TreeCanvas extends Panel implements MouseListener, 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()) { @@ -126,7 +147,7 @@ public class TreeCanvas extends Panel implements MouseListener, } public void drawNode(Graphics g, SequenceNode node, float chunk, - float scale, int width, int offx, int offy) + double scale, int width, int offx, int offy) { if (node == null) { @@ -137,8 +158,8 @@ 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; @@ -220,8 +241,8 @@ public class TreeCanvas extends Panel implements MouseListener, 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 xend = (int) (height * scale) + offx; @@ -240,10 +261,11 @@ 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) + 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); @@ -318,7 +340,7 @@ public class TreeCanvas extends Panel implements MouseListener, 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 @@ -330,7 +352,7 @@ public class TreeCanvas extends Panel implements MouseListener, } 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) { @@ -339,7 +361,7 @@ 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; @@ -445,7 +467,7 @@ public class TreeCanvas extends Panel implements MouseListener, // for // scrollbar - float wscale = (width - labelLength - offx * 2) / tree.getMaxHeight(); + double wscale = (width - labelLength - offx * 2) / tree.getMaxHeight(); SequenceNode top = tree.getTopNode(); @@ -504,13 +526,11 @@ 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); } } @@ -575,15 +595,21 @@ 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.getAlignment().deleteAllGroups(); av.clearSequenceColours(); + final AlignViewportI codingComplement = av.getCodingComplement(); + if (codingComplement != null) + { + codingComplement.setSelectionGroup(null); + codingComplement.getAlignment().deleteAllGroups(); + codingComplement.clearSequenceColours(); + } - colourGroups(); + colourGroups(groups); } } @@ -593,23 +619,21 @@ 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()); + 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); @@ -632,43 +656,67 @@ public class TreeCanvas extends Panel implements MouseListener, } else { - cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty - .getColourName(av.getGlobalColourScheme())); + cs = ColourSchemeProperty.getColourScheme(sg, + ColourSchemeProperty.getColourName(av + .getGlobalColourScheme())); } // cs is null if shading is an annotationColourGradient - if (cs != null) - { - cs.setThreshold(av.getGlobalColourScheme().getThreshold(), - av.getIgnoreGapsConsensus()); - } + // if (cs != null) + // { + // cs.setThreshold(av.getViewportColourScheme().getThreshold(), + // av.isIgnoreGapsConsensus()); + // } } // 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.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), + Conservation c = new Conservation("Group", sg.getSequences(null), sg.getStartRes(), sg.getEndRes()); c.calculate(); c.verdict(false, av.getConsPercGaps()); - cs.setConservation(c); - - sg.cs = cs; + sg.setColourScheme(cs); + sg.getGroupColourScheme().setConservation(c); } 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)