public class Beam
extends java.lang.Object
Modifier and Type | Field and Description |
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private static Motif.ScoreData |
beamUnscoredMotif |
Constructor and Description |
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Beam() |
Modifier and Type | Method and Description |
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private static int |
bipartiteLength(Motif m)
Returns the number of non-N characters in m.
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static Motif[] |
runBeam(Motif[] motifs,
Scorer scorer,
Alphabet alf,
Alphabet primaryAlf,
UberProperties properties)
Expands motifs using a beam width algorithm.
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static Motif[] |
runBeam(Scorer scorer,
Alphabet alf,
Alphabet primaryAlf,
UberProperties properties)
Generates all possible motifs of length beam.motif.length.min, then runs
runBeam(Motif[], Scorer, Alphabet, Alphabet, UberProperties) on them. |
static Motif[] |
runBipartiteBeam(Scorer scorer,
Alphabet alf,
Alphabet primaryAlf,
UberProperties properties)
Generates all possible motifs of length beam.motif.length.min, then runs a beam algorithm to expand them and return only the top
scorers.
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private static final Motif.ScoreData beamUnscoredMotif
private static int bipartiteLength(Motif m)
public static Motif[] runBeam(Motif[] motifs, Scorer scorer, Alphabet alf, Alphabet primaryAlf, UberProperties properties)
public static Motif[] runBeam(Scorer scorer, Alphabet alf, Alphabet primaryAlf, UberProperties properties)
runBeam(Motif[], Scorer, Alphabet, Alphabet, UberProperties)
on them.public static Motif[] runBipartiteBeam(Scorer scorer, Alphabet alf, Alphabet primaryAlf, UberProperties properties)