public class ComparatorMotifFinder extends MotifFinder
SuffixArray
as its internal representation of a biological sequence, allowing access to the number of occurrences of a
given motif and the indices of these occurrences in the sequence.MotifFinder.EmptyFindResults, MotifFinder.UncompressedFindResults
Modifier and Type | Field and Description |
---|---|
private int |
cacheRetrievalCountForCount |
private int |
cacheRetrievalCountForFind |
private int |
cacheStorageCountForCount |
private int |
cacheStorageCountForFind |
private int |
countCallCount |
private int |
countCallNegativeCount |
private int |
countCallPositiveCount |
private int |
findCallCount |
private int |
findCallNegativeCount |
private int |
findCallPositiveCount |
private Stopwatch |
globalTimer |
private java.lang.String[] |
motifFinderClassNames |
private MotifFinder[] |
motifFinders |
private static long |
serialVersionUID |
private static boolean |
useSoftCache |
BIPARTITE_INIT_CACHE_SIZE, BIPARTITE_INIT_LEN, BIPARTITE_INIT_N_COUNT_MAX, BIPARTITE_INIT_N_COUNT_MIN, checkMotifFinderResults, countCache, DEFAULT_MAX_HASH_LENGTH, discardOverlaps, doPersisting, ExtraGeneMotifFinderIdentifier, extraGeneSoftCache, geneLength, geneStarts, genomeSoftCache, groupSoftCache, maxHashLength, NO_WILDCARD_OPTIMIZATION, rand, seqID, sequence, simpleFindCache, TemporaryMotifFinderIdentifier, UNEQUAL_GENE_LENGTHS, wildcardOptimizationCutoff
Constructor and Description |
---|
ComparatorMotifFinder(java.lang.String sequence,
int geneLength)
Calls
super(String, int) . |
ComparatorMotifFinder(java.lang.String seqID,
java.lang.String sequence,
int geneLength)
Calls
super(String, String, int) . |
Modifier and Type | Method and Description |
---|---|
int |
count(Motif m,
int k)
Returns the number of times that any motif with a hamming distance from m of up to k occurs in the sequence; not implemented.
|
int |
count(java.lang.String pattern)
Returns the number of times that pattern occurs in the sequence.
|
MotifFinder |
createNewInstance(java.lang.String seqID,
java.lang.String sequence,
int geneLength)
|
int[] |
find(Motif m,
int k)
Returns the indices of where any motif with a hamming distance from m of up to k occurs in the sequence; not implemented.
|
int[] |
find(java.lang.String pattern)
Returns an unsorted array of the indices of where pattern occurs in the sequence.
|
FindResults |
findResults(java.lang.String pattern) |
static java.lang.String |
getUsedMemoryInMb() |
protected void |
initializeDataStructure()
Initializes the internal suffix array.
|
static void |
main(java.lang.String[] args) |
private void |
reportStatus() |
areOnSameGene, clone, count, count, countGenes, createFindResults, createNewInstance, find, find, findResults, findResults, getAveragePercentageLengthVariation, getAvgGeneLength, getBaseCount, getCountCacheSize, getDiscardOverlaps, getEndIndexOf, getFindCacheSize, getFindResults, getGeneCount, getGeneIDOf, getGeneSequence, getInternalGeneLength, getPositionInGene, getSequence, getSequenceLength, getWildcardOptimizationCutoff, hasUniformGeneLengths, initialize, isCachingOn, loadBipartiteCaches, resetExtraGeneSoftCache, setDiscardOverlaps, setWildcardOptimization, simpleFind, strandCount, strandCount, toString, turnOffCaching, turnOnCaching, turnOnCaching, turnOnCaching, wildcardFind
private static final long serialVersionUID
private static transient boolean useSoftCache
private final transient int cacheRetrievalCountForCount
private final transient int cacheRetrievalCountForFind
private final transient int cacheStorageCountForCount
private final transient int cacheStorageCountForFind
private transient int countCallCount
private transient int countCallNegativeCount
private transient int countCallPositiveCount
private transient int findCallCount
private transient int findCallNegativeCount
private transient int findCallPositiveCount
private final transient Stopwatch globalTimer
private final java.lang.String[] motifFinderClassNames
private final MotifFinder[] motifFinders
public ComparatorMotifFinder(java.lang.String sequence, int geneLength)
super(String, int)
.public ComparatorMotifFinder(java.lang.String seqID, java.lang.String sequence, int geneLength)
super(String, String, int)
.public static java.lang.String getUsedMemoryInMb()
public static void main(java.lang.String[] args)
public int count(Motif m, int k)
count
in class MotifFinder
java.lang.IllegalArgumentException
- Because this method hasn't been implementedpublic int count(java.lang.String pattern)
count
in class MotifFinder
public MotifFinder createNewInstance(java.lang.String seqID, java.lang.String sequence, int geneLength)
createNewInstance
in class MotifFinder
public int[] find(Motif m, int k)
find
in class MotifFinder
java.lang.IllegalArgumentException
- Because this method hasn't been implementedpublic int[] find(java.lang.String pattern)
find
in class MotifFinder
public FindResults findResults(java.lang.String pattern)
findResults
in class MotifFinder
protected void initializeDataStructure()
initializeDataStructure
in class MotifFinder
private void reportStatus()