more plus added VAMAS: tag for a policy decision

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@121 be28352e-c001-0410-b1a7-c7978e42abec

diff --git a/src/org/vamsas/test/objects/Core.java b/src/org/vamsas/test/objects/Core.java
index de3bd0a..880c8bd 100644 (file)
--- a/src/org/vamsas/test/objects/Core.java
+++ b/src/org/vamsas/test/objects/Core.java
@@ -36,7 +36,7 @@ public class Core {
        if ((end-start)!=Sequence.length())
          seq.setEnd(start+Sequence.length());
      } else {
-       // reverse topology mapping. TODO: decide if allowed to do start>end on Sequence object
+       // reverse topology mapping. TODO: VAMSAS: decide if allowed to do start>end on Sequence object
        if ((start-end)!=Sequence.length())
          seq.setEnd(end+Sequence.length());
      }
@@ -45,14 +45,7 @@ public class Core {
   public static VAMSAS getDemoVamsas() {
      VAMSAS v=new VAMSAS();
      DataSet ds = new DataSet();
-     ds.addSequence(Sequence("Dummy1","ASDFLEQ",
-     seq.setDictionary("info:iubmb.org/aminoacids");
-     seq.setName(
-     ds.addSequence(seq);
-    seq = new Sequence();
-     seq.setDictionary("info:iubmb.org/aminoacids");
-     seq.setName("Dummy1");
-     seq.setSequence("ASDFLEQ");
+     ds.addSequence(Sequence("Dummy1","ASDFLEQ","info:iubmb.org/aminoacids", 5, 11));
      complete(ds);
      v.addDataSet(ds);
      Alignment al = new Alignment();