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 7c155b7..6755a88 100755 (executable)
--- a/src/jalview/gui/PaintRefresher.java
+++ b/src/jalview/gui/PaintRefresher.java
@@ -50,7 +50,9 @@ public class PaintRefresher
         {\r
             Vector comps = (Vector) components.get(seqSetId);\r
             if(!comps.contains(comp))\r
+            {\r
               comps.addElement(comp);\r
+            }\r
         }\r
         else\r
         {\r
@@ -80,12 +82,13 @@ public class PaintRefresher
 \r
     public static void Refresh(Component source, String id)\r
     {\r
-      Refresh( source, id,  null, null);\r
+      Refresh( source, id, false, false);\r
     }\r
 \r
-    public static void Refresh(Component source, String id,\r
-                                    SequenceI removeSeq,\r
-                                    SequenceI addSeq)\r
+    public static void Refresh(Component source,\r
+                               String id,\r
+                               boolean alignmentChanged,\r
+                               boolean validateSequences)\r
     {\r
       if (components == null)\r
         return;\r
@@ -104,27 +107,116 @@ public class PaintRefresher
         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(comp instanceof AlignmentPanel)\r
+        else if(validateSequences\r
+                && comp instanceof AlignmentPanel\r
+                && source instanceof AlignmentPanel )\r
         {\r
-          AlignmentPanel ap = (AlignmentPanel)comp;\r
-          if(addSeq!=null)\r
-            ap.av.alignment.addSequence(addSeq);\r
-          if(removeSeq!=null)\r
-            ap.av.alignment.deleteSequence(removeSeq);\r
-\r
-         // if(source instanceof AlignmentPanel)\r
-          //  ap.av.alignment.setGroups(\r
-         //       ((AlignmentPanel)source).av.alignment.getGroups() );\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