public class SuffixArrayMotifFinder 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.Modifier and Type | Class and Description |
---|---|
static class |
SuffixArrayMotifFinder.SuffixArrayFindResults |
MotifFinder.EmptyFindResults, MotifFinder.UncompressedFindResults
Modifier and Type | Field and Description |
---|---|
private SuffixArray |
sa |
(package private) static long |
serialVersionUID |
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 |
---|
SuffixArrayMotifFinder(java.lang.String sequence,
int geneLength)
Calls
super(String, int) . |
SuffixArrayMotifFinder(java.lang.String seqID,
java.lang.String sequence,
int geneLength)
Calls
super(String, String, int) . |
Modifier and Type | Method and Description |
---|---|
java.lang.Object |
clone()
Returns a deep copy of this suffix array motif finder, with the exception that the new suffix array uses the same array and string,
which never get changed.
|
FindResults |
createFindResults(Motif motif) |
MotifFinder |
createNewInstance(java.lang.String seqID,
java.lang.String sequence,
int geneLength)
|
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 |
readObject(java.io.ObjectInputStream in)
Calls in.defaultReadObject() and reconstructs sa.
|
private void |
writeObject(java.io.ObjectOutputStream out)
Calls out.defaultWriteObject() and serializes sa.a so that sa can be restored.
|
areOnSameGene, count, count, count, count, countGenes, createFindResults, createNewInstance, find, 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
static final long serialVersionUID
private transient SuffixArray sa
public SuffixArrayMotifFinder(java.lang.String sequence, int geneLength)
super(String, int)
.public SuffixArrayMotifFinder(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 java.lang.Object clone()
clone
in class MotifFinder
public FindResults createFindResults(Motif motif)
public MotifFinder createNewInstance(java.lang.String seqID, java.lang.String sequence, int geneLength)
createNewInstance
in class MotifFinder
public 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 readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException