X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Forg%2Fvamsas%2Fobjects%2Futils%2FSeq.java;h=b1955a182a654af765966505c83cbe3122d94d19;hb=5c0c34895c290164caad28e0aeac86b5a52ee655;hp=7564f1d89e72258d79bd982ab26a29ea991d102e;hpb=7cd19d45b73dd3b862cc0c67d18ce976240ac636;p=vamsas.git

diff --git a/src/org/vamsas/objects/utils/Seq.java b/src/org/vamsas/objects/utils/Seq.java
index 7564f1d..b1955a1 100644
--- a/src/org/vamsas/objects/utils/Seq.java
+++ b/src/org/vamsas/objects/utils/Seq.java
@@ -55,12 +55,12 @@ public class Seq {
 		fasta_out.flush();
 	  }
 	/**
-   *validate a SequenceType object as an info:iubmb.org/aminoacid SequenceType
+   *validate a SequenceType Vobject as an info:iubmb.org/aminoacid SequenceType
    *This version resolves references to Sequence objects from AlignmentSequence
    *TODO: Define info: urn for dictionary string (could also be regex of valid characters!)
    * @param s
 	 * @param dict TODO
-   * @return true if a valid amino acid sequence object
+   * @return true if a valid amino acid sequence Vobject
 	 */
 	private static boolean valid_aadictionary_string(String s, String dict) {
     if (s==null)
@@ -73,7 +73,7 @@ public class Seq {
   }
 
   public static Sequence newSequence(String Name, String Sequence, String Dictionary, int start, int end) {
-    //TODO: make hierarchy reflecting the SeqType object.
+    //TODO: make hierarchy reflecting the SeqType Vobject.
     Sequence seq= new Sequence();
      seq.setDictionary(Dictionary);
      seq.setName(Name);
@@ -83,11 +83,10 @@ public class Seq {
        if ((end-start)!=Sequence.length())
          seq.setEnd(start+Sequence.length());
      } else {
-       // reverse topology mapping. TODO: VAMSAS: decide if allowed to do start>end on Sequence object
+       // reverse topology mapping. TODO: VAMSAS: decide if allowed to do start>end on Sequence Vobject
        if ((start-end)!=Sequence.length())
          seq.setEnd(end+Sequence.length());
      }
-     seq.getVorbaId();
      return seq;
   }
   public static AlignmentSequence newAlignmentSequence(String name, String alSequence, Sequence refseq, int start, int end) {