-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 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.appletgui;\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;\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param comp DOCUMENT ME!\r
- * @param al DOCUMENT ME!\r
- */\r
- public static void Register(Component comp, String seqSetId)\r
- {\r
- if (components == null)\r
- components = new Hashtable();\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
- return;\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,\r
- String id,\r
- boolean alignmentChanged,\r
- boolean validateSequences)\r
- {\r
- if (components == null)\r
- return;\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\r
- && comp instanceof AlignmentPanel\r
- && source instanceof AlignmentPanel )\r
- {\r
- validateSequences( ((AlignmentPanel)source).av.alignment,\r
- ((AlignmentPanel)comp).av.alignment);\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
- a1 = source.getHiddenSequences().getFullAlignment().getSequencesArray();\r
- else\r
- a1 = source.getSequencesArray();\r
-\r
- SequenceI[] a2;\r
- if (comp.getHiddenSequences().getSize() > 0)\r
- a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();\r
- else\r
- a2 = comp.getSequencesArray();\r
-\r
- int i, iSize=a1.length, j, jSize=a2.length;\r
-\r
- if(iSize == jSize)\r
- return;\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
- if (a2[j]==a1[i] )\r
- {\r
- exists = true;\r
- break;\r
- }\r
-\r
- if(!exists)\r
- {\r
- if (i < jSize)\r
- comp.getSequences().insertElementAt(a1[i], i);\r
- else\r
- comp.addSequence(a1[i]);\r
-\r
- jSize++;\r
-\r
- if (comp.getHiddenSequences().getSize() > 0)\r
- a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();\r
- else\r
- a2 = comp.getSequencesArray();\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
+/*
+ * 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.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;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff