new getVisibleContigs method mirrors the getVisibleContigs method in AlignmentView

[jalview.git] / src / jalview / datamodel / AlignmentOrder.java

diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java
index 231009a..639dd47 100755 (executable)
--- a/src/jalview/datamodel/AlignmentOrder.java
+++ b/src/jalview/datamodel/AlignmentOrder.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
@@ -171,7 +171,7 @@ public class AlignmentOrder
      * replaces oldref with newref in the alignment order.\r
      * @param oldref\r
      * @param newref\r
-     * @return\r
+     * @return true if oldref was contained in order and replaced with newref\r
      */\r
     public boolean updateSequence(SequenceI oldref, SequenceI newref) {\r
       int found=Order.indexOf(oldref);\r
@@ -181,6 +181,85 @@ public class AlignmentOrder
       return found>-1;\r
     }\r
     /**\r
+     * Exact equivalence of two AlignmentOrders\r
+     * @param o\r
+     * @return true if o orders the same sequenceI objects in the same way\r
+     */\r
+    public boolean equals(AlignmentOrder o) {\r
+      return equals(o, true);\r
+    }\r
+    /**\r
+     * Exact equivalence of two AlignmentOrders\r
+     *  // TODO: Weak SequenceI equivalence - will throw Error at moment\r
+     * @param o\r
+     * @param identity - false - use weak equivalence (refers to same or different parts of same sequence)\r
+     * @return true if o orders equivalent sequenceI objects in the same way\r
+     */\r
+    public boolean equals(AlignmentOrder o, boolean identity) {\r
+      if (o!=this) {\r
+        if (o==null)\r
+          return false;\r
+        if (Order!=null && o.Order!=null && Order.size()==o.Order.size()) {\r
+          if (!identity) {\r
+            throw new Error("Weak sequenceI equivalence not yet implemented.");\r
+          } else {\r
+            for (int i=0,j=o.Order.size(); i<j; i++) {\r
+            if (Order.elementAt(i)!=o.Order.elementAt(i))\r
+              return false;\r
+            }\r
+          }\r
+        } else\r
+          return false;\r
+      }\r
+      return true;\r
+    }\r
+    /**\r
+     * Consistency test for alignmentOrders\r
+     * @param o\r
+     * @return true if o contains or is contained by this and the common SequenceI objects are ordered in the same way\r
+     */\r
+    public boolean isConsistent(AlignmentOrder o) {\r
+      return isConsistent(o, true);\r
+    }\r
+    /**\r
+     * Consistency test for alignmentOrders\r
+     * @param o\r
+     *  // TODO: Weak SequenceI equivalence - will throw Error at moment\r
+     * @param identity - false - use weak equivalence (refers to same or different parts of same sequence)\r
+     * @return true if o contains or is contained by this and the common SequenceI objects are ordered in the same way\r
+     */\r
+    public boolean isConsistent(AlignmentOrder o, boolean identity) {\r
+      if (o!=this) {\r
+        if (o==null)\r
+          return false;\r
+        if (Order!=null && o.Order!=null) {\r
+          Vector c,s;\r
+          if (o.Order.size()>Order.size()) {\r
+            c = o.Order;\r
+            s = Order;\r
+          } else {\r
+            c = Order;\r
+            s = o.Order;\r
+          }\r
+          if (!identity) {\r
+            throw new Error("Weak sequenceI equivalence not yet implemented.");\r
+          } else {\r
+            // test if c contains s and order in s is conserved in c\r
+            int last=-1;\r
+            for (int i=0,j=s.size(); i<j; i++) {\r
+              int pos=c.indexOf(s.elementAt(i)); // JBPNote - optimize by incremental position search\r
+              if (pos>last) {\r
+                last=pos;\r
+              } else\r
+                return false;\r
+            }\r
+          }\r
+        } else\r
+          return false;\r
+      }\r
+      return true;\r
+    }\r
+    /**\r
      * AlignmentOrder\r
      *\r
      * @param orderThis AlignmentI\r