renamed base class for all vamsas document objects (now org.vamsas.client.Vobject)

[vamsas.git] / src / org / vamsas / objects / utils / Seq.java

diff --git a/src/org/vamsas/objects/utils/Seq.java b/src/org/vamsas/objects/utils/Seq.java
index ca83223..b1955a1 100644 (file)
--- 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);
@@ -83,7 +83,7 @@ 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());
      }