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