X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPaintRefresher.java;h=b6d5a4177f94ec6e0916f984d69151e0e39a1b27;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=1b253859e3a4e60ca35979da416c7dedbd0ee1fd;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git
diff --git a/src/jalview/gui/PaintRefresher.java b/src/jalview/gui/PaintRefresher.java
index 1b25385..b6d5a41 100755
--- a/src/jalview/gui/PaintRefresher.java
+++ b/src/jalview/gui/PaintRefresher.java
@@ -1,243 +1,271 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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 java.util.*;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class PaintRefresher
-{
- static Hashtable components;
-
- /**
- * DOCUMENT ME!
- *
- * @param comp DOCUMENT ME!
- * @param al DOCUMENT ME!
- */
- public static void Register(Component comp, String seqSetId)
- {
- if (components == null)
- {
- components = new Hashtable();
- }
-
- if (components.containsKey(seqSetId))
- {
- Vector comps = (Vector) components.get(seqSetId);
- if (!comps.contains(comp))
- {
- comps.addElement(comp);
- }
- }
- else
- {
- Vector vcoms = new Vector();
- vcoms.addElement(comp);
- components.put(seqSetId, vcoms);
- }
- }
-
- public static void RemoveComponent(Component comp)
- {
- if (components == null)
- {
- return;
- }
-
- Enumeration en = components.keys();
- while (en.hasMoreElements())
- {
- String id = en.nextElement().toString();
- Vector comps = (Vector) components.get(id);
- comps.remove(comp);
- if (comps.size() == 0)
- {
- 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)
- {
- if (components == null)
- {
- return;
- }
-
- Component comp;
- Vector comps = (Vector) components.get(id);
-
- if (comps == null)
- {
- return;
- }
-
- Enumeration e = comps.elements();
- while (e.hasMoreElements())
- {
- comp = (Component) e.nextElement();
-
- if (comp == source)
- {
- continue;
- }
-
- if (validateSequences
- && comp instanceof AlignmentPanel
- && source instanceof AlignmentPanel)
- {
- validateSequences( ( (AlignmentPanel) source).av.alignment,
- ( (AlignmentPanel) comp).av.alignment);
- }
-
- 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 < jSize)
- {
- comp.getSequences().insertElementAt(a1[i], i);
- }
- else
- {
- comp.addSequence(a1[i]);
- }
-
- jSize++;
-
- if (comp.getHiddenSequences().getSize() > 0)
- {
- a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
- }
- else
- {
- a2 = comp.getSequencesArray();
- }
- }
- }
-
- 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)
- {
- Vector comps = (Vector) components.get(id);
- Vector tmp = new Vector();
- int i, iSize = comps.size();
- for (i = 0; i < iSize; i++)
- {
- if (comps.elementAt(i) instanceof AlignmentPanel)
- {
- tmp.addElement( ( (AlignmentPanel) comps.elementAt(i)));
- }
- }
- AlignmentPanel[] result = new AlignmentPanel[tmp.size()];
- tmp.toArray(result);
-
- return result;
- }
-
-}
+/*
+ * 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.
+ *
+ * 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 java.util.*;
+import java.util.List;
+
+import java.awt.*;
+
+import jalview.datamodel.*;
+
+/**
+ * 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 Hashtable components;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param comp
+ * DOCUMENT ME!
+ * @param al
+ * DOCUMENT ME!
+ */
+ public static void Register(Component comp, String seqSetId)
+ {
+ if (components == null)
+ {
+ components = new Hashtable();
+ }
+
+ if (components.containsKey(seqSetId))
+ {
+ Vector comps = (Vector) components.get(seqSetId);
+ if (!comps.contains(comp))
+ {
+ comps.addElement(comp);
+ }
+ }
+ else
+ {
+ Vector vcoms = new Vector();
+ vcoms.addElement(comp);
+ components.put(seqSetId, vcoms);
+ }
+ }
+
+ public static void RemoveComponent(Component comp)
+ {
+ if (components == null)
+ {
+ return;
+ }
+
+ Enumeration en = components.keys();
+ while (en.hasMoreElements())
+ {
+ String id = en.nextElement().toString();
+ Vector comps = (Vector) components.get(id);
+ comps.remove(comp);
+ if (comps.size() == 0)
+ {
+ 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)
+ {
+ if (components == null)
+ {
+ return;
+ }
+
+ Component comp;
+ Vector comps = (Vector) components.get(id);
+
+ if (comps == null)
+ {
+ return;
+ }
+
+ Enumeration e = comps.elements();
+ while (e.hasMoreElements())
+ {
+ comp = (Component) e.nextElement();
+
+ 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)
+ {
+ if (components == null)
+ {
+ return new AlignmentPanel[0];
+ }
+ ;
+ Vector comps = (Vector) components.get(id);
+ if (comps == null)
+ {
+ return new AlignmentPanel[0];
+ }
+ ;
+ Vector tmp = new Vector();
+ int i, iSize = comps.size();
+ for (i = 0; i < iSize; i++)
+ {
+ if (comps.elementAt(i) instanceof AlignmentPanel)
+ {
+ tmp.addElement(comps.elementAt(i));
+ }
+ }
+ AlignmentPanel[] result = new AlignmentPanel[tmp.size()];
+ tmp.toArray(result);
+
+ return result;
+ }
+
+}