-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import java.awt.*;\r
-\r
-import java.util.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class PaintRefresher\r
-{\r
- static Hashtable components = new Hashtable();\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param comp DOCUMENT ME!\r
- * @param al DOCUMENT ME!\r
- */\r
- public static void Register(Component comp, AlignmentI al)\r
- {\r
- if (components.containsKey(al))\r
- {\r
- Vector comps = (Vector) components.get(al);\r
- comps.addElement(comp);\r
- }\r
- else\r
- {\r
- Vector vcoms = new Vector();\r
- vcoms.addElement(comp);\r
- components.put(al, vcoms);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param al DOCUMENT ME!\r
- */\r
- public static void Refresh(AlignmentI al)\r
- {\r
- Refresh(null, al);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param c DOCUMENT ME!\r
- * @param al DOCUMENT ME!\r
- */\r
- public static void Refresh(Component c, AlignmentI al)\r
- {\r
- Component temp;\r
- Vector coms = (Vector) components.get(al);\r
- Enumeration e = coms.elements();\r
-\r
- while (e.hasMoreElements())\r
- {\r
- temp = (Component) e.nextElement();\r
-\r
- if (!temp.isValid())\r
- {\r
- coms.removeElement(temp);\r
- }\r
- else if (temp == c)\r
- {\r
- continue;\r
- }\r
-\r
- temp.repaint();\r
- }\r
- }\r
-}\r
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * 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<String, List<Component>> components = new HashMap<String, List<Component>>();
+
+ /**
+ * 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<Component> comps = components.get(seqSetId);
+ if (!comps.contains(comp))
+ {
+ comps.add(comp);
+ }
+ }
+ else
+ {
+ List<Component> vcoms = new ArrayList<Component>();
+ 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<String> emptied = new ArrayList<String>();
+ for (Entry<String, List<Component>> registered : components.entrySet())
+ {
+ String id = registered.getKey();
+ List<Component> 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<Component> 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<SequenceI> 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<Component> comps = components.get(id);
+ if (comps == null)
+ {
+ return new AlignmentPanel[0];
+ }
+ List<AlignmentPanel> tmp = new ArrayList<AlignmentPanel>();
+ for (Component comp : comps)
+ {
+ if (comp instanceof AlignmentPanel)
+ {
+ tmp.add((AlignmentPanel) comp);
+ }
+ }
+ return tmp.toArray(new AlignmentPanel[tmp.size()]);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff