public String getDescription();
/**
- * Return the alignment column for a sequence position
- * * Return the alignment position for a sequence position
+ * Return the alignment column for a sequence position * Return the alignment
+ * position for a sequence position
*
* @param pos
* lying from start to end
*
- * @return aligned column for residue (0 if residue is upstream from alignment, -1 if residue is downstream from alignment)
- * note. Sequence object returns sequence.getEnd() for positions upstream currently. TODO: change sequence for assert(findIndex(seq.getEnd()+1)==-1) and fix incremental bugs
+ * @return aligned column for residue (0 if residue is upstream from
+ * alignment, -1 if residue is downstream from alignment) note.
+ * Sequence object returns sequence.getEnd() for positions upstream
+ * currently. TODO: change sequence for
+ * assert(findIndex(seq.getEnd()+1)==-1) and fix incremental bugs
*
*/
public int findIndex(int pos);
* null or mapping from entry's numbering to local start/end
*/
public void transferAnnotation(SequenceI entry, Mapping mp);
-
+
/**
- * @param index The sequence index in the MSA
+ * @param index
+ * The sequence index in the MSA
*/
public void setIndex(int index);
-
+
/**
* @return The index of the sequence in the alignment
*/