From 85fd6ef49e9d91e829976345987a12b9535970ab Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 13 Jan 2006 16:09:34 +0000 Subject: [PATCH] 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 --- src/org/vamsas/test/objects/Core.java | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) diff --git a/src/org/vamsas/test/objects/Core.java b/src/org/vamsas/test/objects/Core.java index de3bd0a..880c8bd 100644 --- 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(); -- 1.7.10.2