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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();
}
/**
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
*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)
*/
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) {
}
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);
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 {
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());
}
if ((start-end)!=Sequence.length())
seq.setEnd(end+Sequence.length());
}