jpayne@68: package aligner;
jpayne@68: 
jpayne@68: public interface Aligner {
jpayne@68: 
jpayne@68: 	/** return new int[] {rows, maxCol, maxState, maxScore, maxStart};
jpayne@68: 	 * Will not fill areas that cannot match minScore */
jpayne@68: 	int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minScore);
jpayne@68: 	
jpayne@68: 	/** return new int[] {rows, maxCol, maxState, maxScore, maxStart};
jpayne@68: 	 * Does not require a min score (ie, same as old method) */
jpayne@68: 	int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc);
jpayne@68: 	
jpayne@68: 	/** return new int[] {rows, maxCol, maxState, maxScore, maxStart};
jpayne@68: 	 * Min score is optional */
jpayne@68: 	int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minScore);
jpayne@68: 
jpayne@68: 	/** Generates the match string */
jpayne@68: 	byte[] traceback(byte[] query, byte[] ref, int refStartLoc, int refEndLoc, int row, int col, int state);
jpayne@68: 
jpayne@68: 	/** Generates identity;
jpayne@68: 	 * fills 'extra' with {match, sub, del, ins, N, clip} if present */
jpayne@68: 	float tracebackIdentity(byte[] query, byte[] ref, int refStartLoc, int refEndLoc, int row, int col, int state, int[] extra);
jpayne@68: 	
jpayne@68: 	/** @return {score, bestRefStart, bestRefStop} */
jpayne@68: 	int[] score(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int maxRow, int maxCol,
jpayne@68: 			int maxState/*, final int maxScore, final int maxStart*/);
jpayne@68: 
jpayne@68: 	/** Will not fill areas that cannot match minScore.
jpayne@68: 	 * @return {score, bestRefStart, bestRefStop}  */
jpayne@68: 	int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minScore);
jpayne@68: 	
jpayne@68: 	/** Lowest possible alignment score for a read with this length and this identity */
jpayne@68: 	int minScoreByIdentity(int len, float identity);
jpayne@68: 
jpayne@68: //	int maxRows();
jpayne@68: //	int maxColumns();
jpayne@68: 	int rows();
jpayne@68: 	int columns();
jpayne@68: 	
jpayne@68: }