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java.lang.Objectjbil.sequence.Trie
jbil.sequence.FactorTrie
public class FactorTrie
A factor trie is a trie representing all factors of a given length of a set of sequences.
| Constructor Summary | |
|---|---|
FactorTrie(Alphabet alphabet,
int factorLength)
Creates an empty factor trie. |
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FactorTrie(Sequence baseSequence,
int factorLength)
Creates a factor trie representing the factors of a given sequence. |
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| Method Summary | |
|---|---|
void |
addBaseSequence(Sequence baseSequence)
Adds a base sequence to the factor trie, i.e., add all factors of the adequate size of this sequence to the trie. |
Pair<java.lang.Integer,java.lang.Integer> |
countOccurrences(Sequence pattern,
int beginIndex,
int endIndex,
int offset)
Counts the number of occurrences of the patterns pattern[beginIndex..endIndex-2] and pattern[beginIndex..endIndex-1] respectively, as prefixes of the words represented by the subtries rooted at nodes at a given height. |
void |
removeBaseSequence(Sequence baseSequence)
Removes one occurrence of a base sequence from the factor trie, that is, removes one occurrence of each factor of the appropriate length of this base sequence from the factor trie. |
| Methods inherited from class jbil.sequence.Trie |
|---|
addSequence, addSequence, countOccurrences, deleteSequence, deleteSequence, getAlphabet, getHeight, getSequenceList, print, reset, sequenceCount |
| Methods inherited from class java.lang.Object |
|---|
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
| Constructor Detail |
|---|
public FactorTrie(Alphabet alphabet,
int factorLength)
alphabet - The base alphabet.factorLength - The length of the represented factors.
public FactorTrie(Sequence baseSequence,
int factorLength)
baseSequence - The base sequence whose factors are to be represented.factorLength - The length of the represented factors.| Method Detail |
|---|
public void addBaseSequence(Sequence baseSequence)
baseSequence - The new base sequence.public void removeBaseSequence(Sequence baseSequence)
baseSequence - The base sequence whose factors are to be removed.
public Pair<java.lang.Integer,java.lang.Integer> countOccurrences(Sequence pattern,
int beginIndex,
int endIndex,
int offset)
Trie
countOccurrences in interface KMerCountercountOccurrences in class Triepattern - The base pattern.beginIndex - The start position of the subpattern to be counted.endIndex - The end position (not inclusive) of the subpattern to be counted.offset - The height of the nodes at which the search must begin.
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