/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
*/
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);
* 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
+ */
+ public void setIndex(int index);
+
+ /**
+ * @return The index of the sequence in the alignment
+ */
+ public int getIndex();
}