-/*
- * 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 <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.appletgui;
-
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
-
-import java.awt.Component;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
-/**
- * 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.removeElement(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 (!comp.isValid())
- {
- comps.removeElement(comp);
- }
- else 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
- 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]);
- }
- }
- }
-
- public 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(comps.elementAt(i));
- }
- }
- AlignmentPanel[] result = new AlignmentPanel[tmp.size()];
- for (int ix = 0; ix < result.length; ix++)
- {
- result[ix] = (AlignmentPanel) tmp.elementAt(ix);
- }
-
- return result;
- }
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)\r
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview 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 3\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ * The Jalview Authors are detailed in the 'AUTHORS' file.\r
+ */\r
+package jalview.appletgui;\r
+\r
+import jalview.datamodel.AlignmentI;\r
+import jalview.datamodel.SequenceI;\r
+\r
+import java.awt.Component;\r
+import java.util.Enumeration;\r
+import java.util.Hashtable;\r
+import java.util.List;\r
+import java.util.Vector;\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class PaintRefresher\r
+{\r
+ static Hashtable components;\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param comp\r
+ * DOCUMENT ME!\r
+ * @param al\r
+ * DOCUMENT ME!\r
+ */\r
+ public static void Register(Component comp, String seqSetId)\r
+ {\r
+ if (components == null)\r
+ {\r
+ components = new Hashtable();\r
+ }\r
+\r
+ if (components.containsKey(seqSetId))\r
+ {\r
+ Vector comps = (Vector) components.get(seqSetId);\r
+ if (!comps.contains(comp))\r
+ {\r
+ comps.addElement(comp);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ Vector vcoms = new Vector();\r
+ vcoms.addElement(comp);\r
+ components.put(seqSetId, vcoms);\r
+ }\r
+ }\r
+\r
+ public static void RemoveComponent(Component comp)\r
+ {\r
+ if (components == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ Enumeration en = components.keys();\r
+ while (en.hasMoreElements())\r
+ {\r
+ String id = en.nextElement().toString();\r
+ Vector comps = (Vector) components.get(id);\r
+ comps.removeElement(comp);\r
+ if (comps.size() == 0)\r
+ {\r
+ components.remove(id);\r
+ }\r
+ }\r
+ }\r
+\r
+ public static void Refresh(Component source, String id)\r
+ {\r
+ Refresh(source, id, false, false);\r
+ }\r
+\r
+ public static void Refresh(Component source, String id,\r
+ boolean alignmentChanged, boolean validateSequences)\r
+ {\r
+ if (components == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ Component comp;\r
+ Vector comps = (Vector) components.get(id);\r
+\r
+ if (comps == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ Enumeration e = comps.elements();\r
+ while (e.hasMoreElements())\r
+ {\r
+ comp = (Component) e.nextElement();\r
+\r
+ if (comp == source)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (!comp.isValid())\r
+ {\r
+ comps.removeElement(comp);\r
+ }\r
+ else if (validateSequences && comp instanceof AlignmentPanel\r
+ && source instanceof AlignmentPanel)\r
+ {\r
+ validateSequences(((AlignmentPanel) source).av.getAlignment(),\r
+ ((AlignmentPanel) comp).av.getAlignment());\r
+ }\r
+\r
+ if (comp instanceof AlignmentPanel && alignmentChanged)\r
+ {\r
+ ((AlignmentPanel) comp).alignmentChanged();\r
+ }\r
+\r
+ comp.repaint();\r
+ }\r
+ }\r
+\r
+ static void validateSequences(AlignmentI source, AlignmentI comp)\r
+ {\r
+ SequenceI[] a1;\r
+ if (source.getHiddenSequences().getSize() > 0)\r
+ {\r
+ a1 = source.getHiddenSequences().getFullAlignment()\r
+ .getSequencesArray();\r
+ }\r
+ else\r
+ {\r
+ a1 = source.getSequencesArray();\r
+ }\r
+\r
+ SequenceI[] a2;\r
+ if (comp.getHiddenSequences().getSize() > 0)\r
+ {\r
+ a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();\r
+ }\r
+ else\r
+ {\r
+ a2 = comp.getSequencesArray();\r
+ }\r
+\r
+ int i, iSize = a1.length, j, jSize = a2.length;\r
+\r
+ if (iSize == jSize)\r
+ {\r
+ return;\r
+ }\r
+\r
+ boolean exists = false;\r
+ for (i = 0; i < iSize; i++)\r
+ {\r
+ exists = false;\r
+\r
+ for (j = 0; j < jSize; j++)\r
+ {\r
+ if (a2[j] == a1[i])\r
+ {\r
+ exists = true;\r
+ break;\r
+ }\r
+ }\r
+\r
+ if (!exists)\r
+ {\r
+ if (i < comp.getHeight())\r
+ {\r
+ // TODO: the following does not trigger any recalculation of\r
+ // height/etc, or maintain the dataset\r
+ List<SequenceI> alsq;\r
+ synchronized (alsq = comp.getSequences())\r
+ {\r
+ alsq.add(i, a1[i]);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ comp.addSequence(a1[i]);\r
+ }\r
+\r
+ if (comp.getHiddenSequences().getSize() > 0)\r
+ {\r
+ a2 = comp.getHiddenSequences().getFullAlignment()\r
+ .getSequencesArray();\r
+ }\r
+ else\r
+ {\r
+ a2 = comp.getSequencesArray();\r
+ }\r
+\r
+ jSize = a2.length;\r
+ }\r
+ }\r
+\r
+ iSize = a1.length;\r
+ jSize = a2.length;\r
+\r
+ for (j = 0; j < jSize; j++)\r
+ {\r
+ exists = false;\r
+ for (i = 0; i < iSize; i++)\r
+ {\r
+ if (a2[j] == a1[i])\r
+ {\r
+ exists = true;\r
+ break;\r
+ }\r
+ }\r
+\r
+ if (!exists)\r
+ {\r
+ comp.deleteSequence(a2[j]);\r
+ }\r
+ }\r
+ }\r
+\r
+ public static AlignmentPanel[] getAssociatedPanels(String id)\r
+ {\r
+ Vector comps = (Vector) components.get(id);\r
+ Vector tmp = new Vector();\r
+ int i, iSize = comps.size();\r
+ for (i = 0; i < iSize; i++)\r
+ {\r
+ if (comps.elementAt(i) instanceof AlignmentPanel)\r
+ {\r
+ tmp.addElement(comps.elementAt(i));\r
+ }\r
+ }\r
+ AlignmentPanel[] result = new AlignmentPanel[tmp.size()];\r
+ for (int ix = 0; ix < result.length; ix++)\r
+ {\r
+ result[ix] = (AlignmentPanel) tmp.elementAt(ix);\r
+ }\r
+\r
+ return result;\r
+ }\r
+\r
+}\r
git://source.jalview.org / jalviewjs.git / blobdiff