X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=510df943d22a9100d85443f2397e88267b8912f0;hb=400b50efffaa43ae2c3b4d3f653bf8215c5d1edc;hp=92a9649d22b38f205f4b7915d6389578cbe56413;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java index 92a9649..510df94 100755 --- a/src/jalview/appletgui/TreeCanvas.java +++ b/src/jalview/appletgui/TreeCanvas.java @@ -1,32 +1,54 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) - * 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. * * 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.*; +import jalview.analysis.Conservation; +import jalview.analysis.NJTree; +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.Vector; public class TreeCanvas extends Panel implements MouseListener, MouseMotionListener @@ -99,13 +121,13 @@ public class TreeCanvas extends Panel implements MouseListener, tree.findHeight(tree.getTopNode()); // Now have to calculate longest name based on the leaves - Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector()); + Vector leaves = tree.findLeaves(tree.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()) { @@ -502,13 +524,11 @@ 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); } } @@ -579,7 +599,14 @@ public class TreeCanvas extends Panel implements MouseListener, av.setSelectionGroup(null); av.getAlignment().deleteAllGroups(); - av.sequenceColours = null; + av.clearSequenceColours(); + final AlignViewportI codingComplement = av.getCodingComplement(); + if (codingComplement != null) + { + codingComplement.setSelectionGroup(null); + codingComplement.getAlignment().deleteAllGroups(); + codingComplement.clearSequenceColours(); + } colourGroups(); @@ -598,16 +625,15 @@ public class TreeCanvas extends Panel implements MouseListener, 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(tree.getGroups().elementAt(i), col.brighter()); - Vector l = tree.findLeaves( - (SequenceNode) tree.getGroups().elementAt(i), new Vector()); + Vector l = tree.findLeaves(tree.getGroups() + .elementAt(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); @@ -630,43 +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.getViewportColourScheme().getThreshold(), + av.isIgnoreGapsConsensus()); sg.setName("JTreeGroup:" + sg.hashCode()); sg.setIdColour(col); if (av.getGlobalColourScheme() != null - && av.getGlobalColourScheme().conservationApplied()) + && av.getViewportColourScheme().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)