public class Ambiguizer
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
private static Motif.ScoreData |
ambiguizerUnscoredMotif |
static java.lang.String |
COLLAPSE_DEGEN_GEN_NEIGHBORS_RECON_METHOD |
static java.lang.String |
COLLAPSE_DEGEN_RECON_METHOD |
static java.lang.String |
GEN_NEIGHBORS_RECON_METHOD |
static double |
MAX_AMB
The maximum ambiguity we will allow a motif to have.
|
static java.lang.String |
MUTATION_METHOD |
Constructor and Description |
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Ambiguizer() |
Modifier and Type | Method and Description |
---|---|
static Motif[] |
ambiguizeMotifs(Motif[] motifs,
Scorer scorer,
UberProperties properties)
This is the master method for Motif arrays.
|
static MotifList |
findMaxList(Motif[] motifs,
Scorer scorer,
int INIT_BEAM_WIDTH,
int BEAM_WIDTH)
Creates that subset of the given list of motifs that forms the highest scoring MotifList.
|
static Motif[] |
GR(Motif[] motifs,
Scorer scorer,
UberProperties properties)
Calls GR on all the Motifs.
|
static Motif |
GR(Motif m,
Scorer scorer,
int INIT_BEAM_WIDTH,
int BEAM_WIDTH,
int MIN_MOTIF_LEN,
int MIN_NON_N_COUNT)
Given a Motif, generates all the 1HD neighbors using expandNeighbors(), then reconstructs a new motif from those neighbors using
reconstructFromList().
|
static Motif[] |
linearlyOptimize(Motif[] motifs,
Scorer scorer,
UberProperties properties)
The mutational ambiguizer method.
|
static Motif |
mutate(Motif motif,
int i,
Scorer scorer,
int minMotifLen)
Tests all the possible expansions of motif at position i and returns the best result.
|
static Motif |
mutate(Motif motif,
Scorer scorer,
int minMotifLen)
Mutates each base in the Motif.
|
static Motif |
reconstructFromList(Motif[] motifs,
Scorer scorer,
int INIT_BEAM_WIDTH,
int BEAM_WIDTH,
int MIN_MOTIF_LEN,
int MIN_NON_N_COUNT)
Given a list of motifs, this will combine that list into an optimal ambiguous motif.
|
public static final java.lang.String COLLAPSE_DEGEN_GEN_NEIGHBORS_RECON_METHOD
public static final java.lang.String COLLAPSE_DEGEN_RECON_METHOD
public static final java.lang.String GEN_NEIGHBORS_RECON_METHOD
public static final double MAX_AMB
public static final java.lang.String MUTATION_METHOD
private static final Motif.ScoreData ambiguizerUnscoredMotif
public static Motif[] ambiguizeMotifs(Motif[] motifs, Scorer scorer, UberProperties properties)
public static MotifList findMaxList(Motif[] motifs, Scorer scorer, int INIT_BEAM_WIDTH, int BEAM_WIDTH)
public static Motif GR(Motif m, Scorer scorer, int INIT_BEAM_WIDTH, int BEAM_WIDTH, int MIN_MOTIF_LEN, int MIN_NON_N_COUNT)
public static Motif[] GR(Motif[] motifs, Scorer scorer, UberProperties properties)
public static Motif[] linearlyOptimize(Motif[] motifs, Scorer scorer, UberProperties properties)
public static Motif mutate(Motif motif, int i, Scorer scorer, int minMotifLen)
public static Motif mutate(Motif motif, Scorer scorer, int minMotifLen)
mutate(Motif, int, Scorer, int)
.
Leading and trailing Ns will be stripped off, and the returned motif is guaranteed to be at least minMotifLen long.