Mercurial > repos > rliterman > csp2

annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/aligner/Aligner.java @ 68:5028fdace37b

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
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jpayne@68 1 package aligner;
jpayne@68 2
jpayne@68 3 public interface Aligner {
jpayne@68 4
jpayne@68 5 /** return new int[] {rows, maxCol, maxState, maxScore, maxStart};
jpayne@68 6 * Will not fill areas that cannot match minScore */
jpayne@68 7 int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minScore);
jpayne@68 8
jpayne@68 9 /** return new int[] {rows, maxCol, maxState, maxScore, maxStart};
jpayne@68 10 * Does not require a min score (ie, same as old method) */
jpayne@68 11 int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc);
jpayne@68 12
jpayne@68 13 /** return new int[] {rows, maxCol, maxState, maxScore, maxStart};
jpayne@68 14 * Min score is optional */
jpayne@68 15 int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minScore);
jpayne@68 16
jpayne@68 17 /** Generates the match string */
jpayne@68 18 byte[] traceback(byte[] query, byte[] ref, int refStartLoc, int refEndLoc, int row, int col, int state);
jpayne@68 19
jpayne@68 20 /** Generates identity;
jpayne@68 21 * fills 'extra' with {match, sub, del, ins, N, clip} if present */
jpayne@68 22 float tracebackIdentity(byte[] query, byte[] ref, int refStartLoc, int refEndLoc, int row, int col, int state, int[] extra);
jpayne@68 23
jpayne@68 24 /** @return {score, bestRefStart, bestRefStop} */
jpayne@68 25 int[] score(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int maxRow, int maxCol,
jpayne@68 26 int maxState/*, final int maxScore, final int maxStart*/);
jpayne@68 27
jpayne@68 28 /** Will not fill areas that cannot match minScore.
jpayne@68 29 * @return {score, bestRefStart, bestRefStop} */
jpayne@68 30 int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minScore);
jpayne@68 31
jpayne@68 32 /** Lowest possible alignment score for a read with this length and this identity */
jpayne@68 33 int minScoreByIdentity(int len, float identity);
jpayne@68 34
jpayne@68 35 // int maxRows();
jpayne@68 36 // int maxColumns();
jpayne@68 37 int rows();
jpayne@68 38 int columns();
jpayne@68 39
jpayne@68 40 }