*/
package jalview.datamodel;
-import java.util.*;
+import java.util.Vector;
/**
* DOCUMENT ME!
public String getDescription();
/**
- * DOCUMENT ME!
+ * Return the alignment column for a sequence position * Return the alignment
+ * position for a sequence position
*
* @param pos
- * DOCUMENT ME!
+ * 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 DOCUMENT ME!
*/
public int findIndex(int pos);
*/
public void transferAnnotation(SequenceI entry, Mapping mp);
+ /**
+ * @param index
+ * The sequence index in the MSA
+ */
+ public void setIndex(int index);
+
+ /**
+ * @return The index of the sequence in the alignment
+ */
+ public int getIndex();
+
}