X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPaintRefresher.java;h=1b90d827d3e90b7e08120c109844446a7702ec56;hp=0fe4b85e7a19ac63c83373aeeed3b93840c58877;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14 diff --git a/src/jalview/gui/PaintRefresher.java b/src/jalview/gui/PaintRefresher.java index 0fe4b85..1b90d82 100755 --- a/src/jalview/gui/PaintRefresher.java +++ b/src/jalview/gui/PaintRefresher.java @@ -1,97 +1,259 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 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 - * 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. - * - * 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 - */ -package jalview.gui; - -import jalview.datamodel.*; - -import java.awt.*; - -import java.util.*; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class PaintRefresher -{ - static Hashtable components = new Hashtable(); - - /** - * DOCUMENT ME! - * - * @param comp DOCUMENT ME! - * @param al DOCUMENT ME! - */ - public static void Register(Component comp, AlignmentI al) - { - if (components.containsKey(al)) - { - Vector comps = (Vector) components.get(al); - comps.addElement(comp); - } - else - { - Vector vcoms = new Vector(); - vcoms.addElement(comp); - components.put(al, vcoms); - } - } - - /** - * DOCUMENT ME! - * - * @param al DOCUMENT ME! - */ - public static void Refresh(AlignmentI al) - { - Refresh(null, al); - } - - /** - * DOCUMENT ME! - * - * @param c DOCUMENT ME! - * @param al DOCUMENT ME! - */ - public static void Refresh(Component c, AlignmentI al) - { - Component temp; - Vector coms = (Vector) components.get(al); - Enumeration e = coms.elements(); - - while (e.hasMoreElements()) - { - temp = (Component) e.nextElement(); - - if (!temp.isValid()) - { - coms.removeElement(temp); - } - else if (temp == c) - { - continue; - } - - temp.repaint(); - } - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 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. + * + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.gui; + +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SequenceI; + +import java.awt.Component; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.Map.Entry; + +/** + * Route datamodel/view update events for a sequence set to any display + * components involved TODO: JV3 refactor to abstract gui/view package + * + * @author $author$ + * @version $Revision$ + */ +public class PaintRefresher +{ + static Map> components = new HashMap>(); + + /** + * Add the given component to those registered under the given sequence set + * id. Does nothing if already added. + * + * @param comp + * @param al + */ + public static void Register(Component comp, String seqSetId) + { + if (components.containsKey(seqSetId)) + { + List comps = components.get(seqSetId); + if (!comps.contains(comp)) + { + comps.add(comp); + } + } + else + { + List vcoms = new ArrayList(); + vcoms.add(comp); + components.put(seqSetId, vcoms); + } + } + + /** + * Remove this component from all registrations. Also removes a registered + * sequence set id if there are no remaining components registered against it. + * + * @param comp + */ + public static void RemoveComponent(Component comp) + { + List emptied = new ArrayList(); + for (Entry> registered : components.entrySet()) + { + String id = registered.getKey(); + List comps = components.get(id); + comps.remove(comp); + if (comps.isEmpty()) + { + emptied.add(id); + } + } + + /* + * Remove now empty ids after the above (to avoid + * ConcurrentModificationException). + */ + for (String id : emptied) + { + components.remove(id); + } + } + + public static void Refresh(Component source, String id) + { + Refresh(source, id, false, false); + } + + public static void Refresh(Component source, String id, + boolean alignmentChanged, boolean validateSequences) + { + List comps = components.get(id); + + if (comps == null) + { + return; + } + + for (Component comp : comps) + { + if (comp == source) + { + continue; + } + + if (validateSequences && comp instanceof AlignmentPanel + && source instanceof AlignmentPanel) + { + validateSequences(((AlignmentPanel) source).av.getAlignment(), + ((AlignmentPanel) comp).av.getAlignment()); + } + + if (comp instanceof AlignmentPanel && alignmentChanged) + { + ((AlignmentPanel) comp).alignmentChanged(); + } + + comp.repaint(); + } + } + + static void validateSequences(AlignmentI source, AlignmentI comp) + { + SequenceI[] a1; + if (source.getHiddenSequences().getSize() > 0) + { + a1 = source.getHiddenSequences().getFullAlignment() + .getSequencesArray(); + } + else + { + a1 = source.getSequencesArray(); + } + + SequenceI[] a2; + if (comp.getHiddenSequences().getSize() > 0) + { + a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray(); + } + else + { + a2 = comp.getSequencesArray(); + } + + int i, iSize = a1.length, j, jSize = a2.length; + + if (iSize == jSize) + { + return; + } + + boolean exists = false; + for (i = 0; i < iSize; i++) + { + exists = false; + + for (j = 0; j < jSize; j++) + { + if (a2[j] == a1[i]) + { + exists = true; + break; + } + } + + if (!exists) + { + if (i < comp.getHeight()) + { + // TODO: the following does not trigger any recalculation of + // height/etc, or maintain the dataset + if (comp.getDataset() != source.getDataset()) + { + // raise an implementation warning here - not sure if this situation + // will ever occur + System.err + .println("IMPLEMENTATION PROBLEM: DATASET out of sync due to an insert whilst calling PaintRefresher.validateSequences(AlignmentI, ALignmentI)"); + } + List alsq; + synchronized (alsq = comp.getSequences()) + { + alsq.add(i, a1[i]); + } + } + else + { + comp.addSequence(a1[i]); + } + + if (comp.getHiddenSequences().getSize() > 0) + { + a2 = comp.getHiddenSequences().getFullAlignment() + .getSequencesArray(); + } + else + { + a2 = comp.getSequencesArray(); + } + + jSize = a2.length; + } + } + + iSize = a1.length; + jSize = a2.length; + + for (j = 0; j < jSize; j++) + { + exists = false; + for (i = 0; i < iSize; i++) + { + if (a2[j] == a1[i]) + { + exists = true; + break; + } + } + + if (!exists) + { + comp.deleteSequence(a2[j]); + } + } + } + + static AlignmentPanel[] getAssociatedPanels(String id) + { + List comps = components.get(id); + if (comps == null) + { + return new AlignmentPanel[0]; + } + List tmp = new ArrayList(); + for (Component comp : comps) + { + if (comp instanceof AlignmentPanel) + { + tmp.add((AlignmentPanel) comp); + } + } + return tmp.toArray(new AlignmentPanel[tmp.size()]); + } + +}