Associate trees with views

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

diff --git a/src/jalview/gui/PaintRefresher.java b/src/jalview/gui/PaintRefresher.java
index e05f44d..6755a88 100755 (executable)
--- a/src/jalview/gui/PaintRefresher.java
+++ b/src/jalview/gui/PaintRefresher.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\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
@@ -33,7 +33,7 @@ import java.util.*;
  */\r
 public class PaintRefresher\r
 {\r
-    static Hashtable components = new Hashtable();\r
+    static Hashtable components;\r
 \r
     /**\r
      * DOCUMENT ME!\r
@@ -41,57 +41,182 @@ public class PaintRefresher
      * @param comp DOCUMENT ME!\r
      * @param al DOCUMENT ME!\r
      */\r
-    public static void Register(Component comp, AlignmentI al)\r
+    public static void Register(Component comp, String seqSetId)\r
     {\r
-        if (components.containsKey(al))\r
+      if (components == null)\r
+        components = new Hashtable();\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
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param al DOCUMENT ME!\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
+        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.remove(comp);\r
+        if(comps.size()==0)\r
+        {\r
+          components.remove(id);\r
+        }\r
+      }\r
     }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param c DOCUMENT ME!\r
-     * @param al DOCUMENT ME!\r
-     */\r
-    public static void Refresh(Component c, AlignmentI al)\r
+    public static void Refresh(Component source, String id)\r
     {\r
-        Component temp;\r
-        Vector coms = (Vector) components.get(al);\r
-        Enumeration e = coms.elements();\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
-        while (e.hasMoreElements())\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
-            temp = (Component) e.nextElement();\r
+          continue;\r
+        }\r
 \r
-            if (!temp.isValid())\r
-            {\r
-                coms.removeElement(temp);\r
-            }\r
-            else if (temp == c)\r
-            {\r
-                continue;\r
-            }\r
-            else\r
-                temp.repaint();\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
+    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(((AlignmentPanel)comps.elementAt(i)));\r
+        }\r
+      }\r
+      AlignmentPanel [] result = new AlignmentPanel[tmp.size()];\r
+      tmp.toArray(result);\r
+\r
+      return result;\r
+    }\r
+\r
 }\r