Formatting

[jalview.git] / src / jalview / appletgui / PaintRefresher.java

diff --git a/src/jalview/appletgui/PaintRefresher.java b/src/jalview/appletgui/PaintRefresher.java
index 12a0040..f7bec98 100755 (executable)
--- a/src/jalview/appletgui/PaintRefresher.java
+++ b/src/jalview/appletgui/PaintRefresher.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 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
@@ -16,57 +16,213 @@
  * 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
-\r
-\r
-\r
 package jalview.appletgui;\r
 \r
-import java.awt.*;\r
 import java.util.*;\r
+\r
+import java.awt.*;\r
+\r
 import jalview.datamodel.*;\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
+  static Hashtable components;\r
 \r
-  public static void Register(Component comp, AlignmentI al)\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.containsKey(al))\r
+    if (components == null)\r
+    {\r
+      components = new Hashtable();\r
+    }\r
+\r
+    if (components.containsKey(seqSetId))\r
     {\r
-      Vector comps = (Vector)components.get(al);\r
-      comps.addElement(comp);\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(al, vcoms);\r
+      components.put(seqSetId, vcoms);\r
     }\r
   }\r
 \r
-  public static void Refresh(AlignmentI al)\r
+  public static void RemoveComponent(Component comp)\r
   {\r
-    Refresh(null, al);\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 c, AlignmentI al)\r
+  public static void Refresh(Component source,\r
+                             String id,\r
+                             boolean alignmentChanged,\r
+                             boolean validateSequences)\r
   {\r
-    Component temp;\r
-    Vector coms = (Vector)components.get(al);\r
-    Enumeration e = coms.elements();\r
-    while( e.hasMoreElements() )\r
+    if (components == null)\r
     {\r
-      temp = (Component)e.nextElement();\r
+      return;\r
+    }\r
 \r
-      if(!temp.isValid())\r
-        coms.removeElement( temp );\r
-      else if( temp == c )\r
-        continue;\r
-      else\r
-        temp.repaint();\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
-}\r
+  static void validateSequences(AlignmentI source, AlignmentI comp)\r
+  {\r
+    SequenceI[] a1;\r
+    if (source.getHiddenSequences().getSize() > 0)\r
+    {\r
+      a1 = source.getHiddenSequences().getFullAlignment().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 < jSize)\r
+        {\r
+          comp.getSequences().insertElementAt(a1[i], i);\r
+        }\r
+        else\r
+        {\r
+          comp.addSequence(a1[i]);\r
+        }\r
+\r
+        jSize++;\r
+\r
+        if (comp.getHiddenSequences().getSize() > 0)\r
+        {\r
+          a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();\r
+        }\r
+        else\r
+        {\r
+          a2 = comp.getSequencesArray();\r
+        }\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