| /dports/biology/bbmap/bbmap/current/aligner/ |
| H A D | Aligner.java | 7 int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minScore); in fillLimited()
11 int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc); in fillUnlimited()
15 int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minScore); in fillUnlimited()
18 …byte[] traceback(byte[] query, byte[] ref, int refStartLoc, int refEndLoc, int row, int col, int s… in traceback()
22 …float tracebackIdentity(byte[] query, byte[] ref, int refStartLoc, int refEndLoc, int row, int col… in tracebackIdentity()
25 int[] score(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int maxRow, int maxCol, in score()
30 int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minScore); in fillAndScoreLimited()
|
| H A D | SingleStateAlignerPacBioAdapter.java | 69 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited()
76 …private final int[] fillLimitedX(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillLimitedX()
83 …private final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, final i… in fillUnlimited()
|
| H A D | SingleStateAlignerFlat.java | 94 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited()
99 public final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc){ in fillUnlimited()
106 …public final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillUnlimited()
|
| H A D | SingleStateAlignerFlat2Amino.java | 78 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited()
83 public final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc){ in fillUnlimited()
90 …public final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillUnlimited()
190 …public final byte[] traceback(byte[] query, byte[] ref, int refStartLoc, int refEndLoc, int row, i… in traceback()
263 …public float tracebackIdentity(byte[] query, byte[] ref, int refStartLoc, int refEndLoc, int row, … in tracebackIdentity()
333 …public float tracebackIdentityAmino(byte[] query, byte[] ref, int refStartLoc, int refEndLoc, int … in tracebackIdentityAmino()
403 …public final int[] score(final byte[] read, final byte[] ref, final int refStartLoc, final int ref… in score()
484 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in… in fillAndScoreLimited()
|
| H A D | MultiStateAligner9PacBioAdapter2.java | 141 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited()
148 …private final int[] fillLimitedX(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillLimitedX()
566 …public final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillUnlimited()
572 public final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc){ in fillUnlimited()
|
| H A D | SingleStateAlignerFlat2.java | 79 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited()
84 public final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc){ in fillUnlimited()
91 …public final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillUnlimited()
193 …public final byte[] traceback(byte[] query, byte[] ref, int refStartLoc, int refEndLoc, int row, i… in traceback()
265 …public float tracebackIdentity(byte[] query, byte[] ref, int refStartLoc, int refEndLoc, int row, … in tracebackIdentity()
335 …public final int[] score(final byte[] read, final byte[] ref, final int refStartLoc, final int ref… in score()
416 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in… in fillAndScoreLimited()
|
| H A D | SingleStateAlignerFlat3.java | 79 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited()
84 public final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc){ in fillUnlimited()
91 …public final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillUnlimited()
192 …public final byte[] traceback(byte[] query, byte[] ref, int refStartLoc, int refEndLoc, int row, i… in traceback()
263 …public float tracebackIdentity(byte[] query, byte[] ref, int refStartLoc, int refEndLoc, int row, … in tracebackIdentity()
333 …public final int[] score(final byte[] read, final byte[] ref, final int refStartLoc, final int ref… in score()
414 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in… in fillAndScoreLimited()
|
| H A D | MultiStateAligner9PacBioAdapter_WithBarriers.java | 114 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited()
126 …private final int[] fillLimitedX(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillLimitedX()
562 …public final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int[] ga… in fillUnlimited()
574 private final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc){ in fillUnlimited()
|
| H A D | SingleStateAlignerFlat2_1D.java | 68 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited()
73 public final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc){ in fillUnlimited()
80 …public final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillUnlimited()
178 …public final byte[] traceback(byte[] query, byte[] ref, int refStartLoc, int refEndLoc, int row, i… in traceback()
249 …public float tracebackIdentity(byte[] query, byte[] ref, int refStartLoc, int refEndLoc, int row, … in tracebackIdentity()
319 …public final int[] score(final byte[] read, final byte[] ref, final int refStartLoc, final int ref… in score()
396 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in… in fillAndScoreLimited()
|
| H A D | MultiStateAligner9PacBioAdapter.java | 82 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited()
89 …private final int[] fillLimitedX(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillLimitedX()
499 …private final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, final i… in fillUnlimited()
|
| H A D | SingleStateAlignerFlatFloat.java | 79 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited()
84 public final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc){ in fillUnlimited()
91 …public final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillUnlimited()
228 …public final byte[] traceback(byte[] query, byte[] ref, int refStartLoc, int refEndLoc, int row, i… in traceback()
302 …public float tracebackIdentity(byte[] query, byte[] ref, int refStartLoc, int refEndLoc, int row, … in tracebackIdentity()
374 …public final int[] score(final byte[] read, final byte[] ref, final int refStartLoc, final int ref… in score()
457 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in… in fillAndScoreLimited()
|
| H A D | MultiStateAligner9PacBioAdapter3.java | 78 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited()
85 …private final int[] fillLimitedX(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillLimitedX()
492 private final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc){ in fillUnlimited()
839 …public final int[] score(final byte[] read, final byte[] ref, final int refStartLoc, final int ref… in score()
951 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in… in fillAndScoreLimited()
|
| /dports/biology/bbmap/bbmap/current/align2/ |
| H A D | MultiStateAligner11tsJNI.java | 18 …private native void fillUnlimitedJNI(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int[… in fillUnlimitedJNI()
20 …private native void fillLimitedXJNI(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int m… in fillLimitedXJNI()
75 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited()
91 …private final int[] fillLimitedX(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillLimitedX()
126 …public final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int[] ga… in fillUnlimited()
137 private final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc){ in fillUnlimited()
156 …public final int[] fillQ(byte[] read, byte[] ref, byte[] baseScores, int refStartLoc, int refEndLo… in fillQ()
|
| H A D | MultiStateAligner9ts.java | 93 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited()
105 …private final int[] fillLimitedX(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillLimitedX()
570 …public final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int[] ga… in fillUnlimited()
582 private final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc){ in fillUnlimited()
|
| H A D | MultiStateAligner9Flat.java | 92 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited()
109 …private final int[] fillLimitedX(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillLimitedX()
590 …public final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int[] ga… in fillUnlimited()
602 private final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc){ in fillUnlimited()
|
| H A D | MultiStateAligner9PacBio.java | 92 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited()
109 …private final int[] fillLimitedX(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillLimitedX()
590 …public final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int[] ga… in fillUnlimited()
602 private final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc){ in fillUnlimited()
|
| H A D | MultiStateAligner9XFlat.java | 91 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited()
108 …private final int[] fillLimitedX(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillLimitedX()
584 …public final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int[] ga… in fillUnlimited()
596 private final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc){ in fillUnlimited()
|
| H A D | MultiStateAligner11ts.java | 95 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited()
112 …private final int[] fillLimitedX(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillLimitedX()
593 …public final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int[] ga… in fillUnlimited()
622 private final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc){ in fillUnlimited()
924 …public final int[] fillQ(byte[] read, byte[] ref, byte[] baseScores, int refStartLoc, int refEndLo… in fillQ()
|
| H A D | NeedlemanWunsch.java | 49 public void fill(byte[] read, byte[] ref, int refStartLoc, int refEndLoc){ in fill()
76 public byte[] traceback(byte[] read, byte[] ref, int refStartLoc, int refEndLoc){ in traceback()
|
| H A D | MultiStateAligner10ts.java | 106 …public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSco… in fillLimited()
123 …private final int[] fillLimitedX(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minS… in fillLimitedX()
598 …private final int[] fillBanded1(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minSc… in fillBanded1()
|
| H A D | MSA.java | 53 …public abstract int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int min… in fillLimited()
58 …public abstract int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int[]… in fillUnlimited()
62 …public abstract int[] fillQ(byte[] read, byte[] ref, byte[] baseScores, int refStartLoc, int refEn… in fillQ()
67 …public abstract byte[] traceback(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int row,… in traceback()
71 …public abstract byte[] traceback2(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int row… in traceback2()
74 …public abstract int[] score(final byte[] read, final byte[] ref, final int refStartLoc, final int … in score()
78 …public abstract int[] score2(final byte[] read, final byte[] ref, final int refStartLoc, final int… in score2()
84 …public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, in… in fillAndScoreLimited()
128 …public final int[] fillAndScoreQ(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, byte[] b… in fillAndScoreQ()
|
| /dports/biology/bbmap/bbmap/jni/ |
| H A D | MultiStateAligner11tsJNI.c | 105 jint refStartLoc, in fillUnlimited()
366 jint refStartLoc, in fillLimitedX()
712 jint refStartLoc, in Java_align2_MultiStateAligner11tsJNI_fillUnlimitedJNI()
758 jint refStartLoc, in Java_align2_MultiStateAligner11tsJNI_fillLimitedXJNI()
|