X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPaintRefresher.java;h=36849b0a77524056fa20809bce4269c6f5d16b8e;hb=afe4b88500a5d61bc8d312909cfdde2b7cdd53df;hp=e05f44d02b1dc16a85fed04268b121fb8d125ecf;hpb=dced869b5a728ef726f85893b0b0a6a7be75ec48;p=jalview.git
diff --git a/src/jalview/gui/PaintRefresher.java b/src/jalview/gui/PaintRefresher.java
index e05f44d..36849b0 100755
--- a/src/jalview/gui/PaintRefresher.java
+++ b/src/jalview/gui/PaintRefresher.java
@@ -1,97 +1,265 @@
-/*
- * 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;
- }
- else
- temp.repaint();
- }
- }
-}
+/*
+ * 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 jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Component;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * 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)
+ {
+ if (components == null)
+ {
+ return;
+ }
+
+ Iterator it = components.keySet().iterator();
+ while (it.hasNext())
+ {
+ List comps = components.get(it.next());
+ comps.remove(comp);
+ if (comps.isEmpty())
+ {
+ it.remove();
+ }
+ }
+ }
+
+ 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 (comp instanceof AlignmentPanel)
+ {
+ if (validateSequences && source instanceof AlignmentPanel)
+ {
+ validateSequences(((AlignmentPanel) source).av.getAlignment(),
+ ((AlignmentPanel) comp).av.getAlignment());
+ }
+ if (alignmentChanged)
+ {
+ ((AlignmentPanel) comp).alignmentChanged();
+ }
+ }
+ else if (comp instanceof IdCanvas)
+ {
+ // BH 2019.04.22 fixes JS problem of repaint() consolidation
+ // that occurs in JavaScript but not Java [JAL-3226]
+ ((IdCanvas) comp).fastPaint = false;
+ }
+ else if (comp instanceof SeqCanvas)
+ {
+ // BH 2019.04.22 fixes JS problem of repaint() consolidation
+ // that occurs in JavaScript but not Java [JAL-3226]
+ ((SeqCanvas) comp).fastPaint = false;
+ }
+ 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
+ jalview.bin.Console.errPrintln(
+ "IMPLEMENTATION PROBLEM: DATASET out of sync due to an insert whilst calling PaintRefresher.validateSequences(AlignmentI, ALignmentI)");
+ }
+ List alsq = comp.getSequences();
+ synchronized (alsq)
+ {
+ 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()]);
+ }
+
+}