public class SearchUtils
extends java.lang.Object
Constructor and Description |
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SearchUtils() |
Modifier and Type | Method and Description |
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static Motif[] |
getAlignedInstances(Motif motif,
MotifFinder mf)
Returns all the instances of motif in mf as "little r", but such that the motifs will align properly.
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static java.lang.String[] |
getFlankingSequences(int prefixLength,
Motif motif,
int suffixLength,
MotifFinder finder)
Returns an array of all the instances of motif in finder, flanked by prefixLength bases upstream of the motif and suffixLength bases
downstream of the motif.
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static java.lang.String |
getGene(int hit,
MotifFinder mf)
Returns the sequence of the gene where the hit is; assumes hit is in a valid sequence range.
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static Motif[] |
getInstances(Motif m,
MotifFinder mf)
Returns all the instances of of m in mf as motifs with "little r".
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static MotifInstance[] |
getMotifInstances(Motif m,
MotifFinder mf)
Same as getInstances, but returns the array of , which includes gene, position and sequence information.
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static Motif[] |
getOccurringInstantiations(Motif m,
MotifFinder mf)
Returns all of the non-degenerate, "little r" instantiations of m that actually occur in mf.
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static Motif[] |
getRandomNeighbors(int numReturned,
Motif m,
MotifFinder mf)
Pulls a specified number of random neighbors from this motif, where a neighbor is a random motif of the same length and ambiguity of m
that is found in one of the genes that m is found in.
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static Motif[] |
getWellBehavedInstantiations(Motif m,
MotifFinder mf)
Returns all the non-degenerate instantiations of m that actually occur in mf, and forces them to be in the same orientiation; the
motifs returned will have the same flag as the given motif, will be sorted in alphabetical order, and will contain no duplicates.
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static Motif[] |
sampleRandomMotifs(int numReturned,
boolean allowRepetitiveMotifs,
Motif m,
MotifFinder mf)
Samples random Motifs from the motif finder that are the same length as m and have the same ambiguities in the same places.
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public static Motif[] getAlignedInstances(Motif motif, MotifFinder mf)
public static java.lang.String[] getFlankingSequences(int prefixLength, Motif motif, int suffixLength, MotifFinder finder)
public static java.lang.String getGene(int hit, MotifFinder mf)
public static Motif[] getInstances(Motif m, MotifFinder mf)
public static MotifInstance[] getMotifInstances(Motif m, MotifFinder mf)
public static Motif[] getOccurringInstantiations(Motif m, MotifFinder mf)
public static Motif[] getRandomNeighbors(int numReturned, Motif m, MotifFinder mf)
public static Motif[] getWellBehavedInstantiations(Motif m, MotifFinder mf)
public static Motif[] sampleRandomMotifs(int numReturned, boolean allowRepetitiveMotifs, Motif m, MotifFinder mf)