GeneralizedSuffixTree

Abstract Value Members

abstract def bulkMultipleCommonSubsequence(): Iterator[(Int, Repr)]

Efficiently computes an iterator over the multiple common subsequences from this generalized suffix tree.
Efficiently computes an iterator over the multiple common subsequences from this generalized suffix tree.
Pre-processing of this algorithm has a linear-time complexity. It is fully described in section 9.7 "A linear-time solution to the multiple common substring problem" of Dan Gusfield's book "Algorithms on Strings, Trees, and Sequences" (1997).
returns
An iterator over the sequences along with their frequencies
abstract def contains(pattern: Repr): Boolean

Determines if a pattern is contained in the suffix tree
abstract def find(pattern: Repr): List[(SequenceID, Int)]

Determines the occurrences of a pattern in this suffix tree
Determines the occurrences of a pattern in this suffix tree
returns
A list of pairs containing the sequence ID and the position of the given sequence as a starting index (starting from 0, else an empty list
abstract def findLongestCommonSubsequences(pattern: Repr): Seq[(Int, Int, Set[(SequenceID, Int)])]

Determines the longest common subsequences between a given pattern and the generalized suffix tree.
Determines the longest common subsequences between a given pattern and the generalized suffix tree.
For instance, given a suffix tree containing sequences:
- Scala|is|awesome|! (sequence 0)
- Programming|is|awesome|. (sequence 1)
- Scala|is|cool|! (sequence 2) And given a pattern: |Well|,|Scala|is|...|cool|!
It will return:
- (2, 4, Set((0, 0), (2, 0))) i.e. the position of subpattern Scala|is in sequences 0 and 2
- (5, 7, Set((2, 2))) i.e. the position of subpattern cool|! in sequence 2
returns
an empty list if the longest common subsequence does not exist, else a list of triple containing the starting index (inclusive, starting from 0), the end index (exclusive) and the set of sequence IDs containing this subsequence along with the starting position of the (sub)pattern in the sequence (starting from 0).
abstract def fullSequences(): Iterator[Repr]

Computes an iterator over the full sequences of this generalized suffix tree
abstract def getSequenceBy(id: SequenceID): Repr

Retrieves a sequence by a given ID
abstract def multipleCommonSubsequence(): CommonSubsequences[Repr]

Computes the multiple common subsequence from this generalized suffix tree.
Computes the multiple common subsequence from this generalized suffix tree.
This method is NOT efficient for large tree, see bulkMultipleCommonSubsequence instead.
Pre-processing of this algorithm has a linear-time complexity. It is fully described in section 9.7 "A linear-time solution to the multiple common substring problem" of Dan Gusfield's book "Algorithms on Strings, Trees, and Sequences" (1997).
abstract def nSuffixes(): Int

Number of suffixes in this generalized suffix tree
abstract def size(): Int

Number of sequences in this suffix tree
abstract def suffixes(): Iterator[Repr]

Computes an iterator over the suffixes of this generalized suffix tree

Concrete Value Members

final def !=(arg0: Any): Boolean

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final def ##(): Int

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final def ==(arg0: Any): Boolean

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final def asInstanceOf[T0]: T0

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def clone(): AnyRef

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final def eq(arg0: AnyRef): Boolean

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def equals(arg0: Any): Boolean

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def finalize(): Unit

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@throws( classOf[java.lang.Throwable] )
final def getClass(): Class[_]

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def hashCode(): Int

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final def isInstanceOf[T0]: Boolean

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final def ne(arg0: AnyRef): Boolean

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final def notify(): Unit

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final def notifyAll(): Unit

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def toString(): String

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final def wait(): Unit

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Related Docs: object GeneralizedSuffixTree | package gstlib

trait GeneralizedSuffixTree[Alphabet, Repr] extends AnyRef

Abstract Value Members

abstract def bulkMultipleCommonSubsequence(): Iterator[(Int, Repr)]

abstract def contains(pattern: Repr): Boolean

abstract def find(pattern: Repr): List[(SequenceID, Int)]

abstract def findLongestCommonSubsequences(pattern: Repr): Seq[(Int, Int, Set[(SequenceID, Int)])]

abstract def fullSequences(): Iterator[Repr]

abstract def getSequenceBy(id: SequenceID): Repr

abstract def multipleCommonSubsequence(): CommonSubsequences[Repr]

abstract def nSuffixes(): Int

abstract def size(): Int

abstract def suffixes(): Iterator[Repr]

Concrete Value Members

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: Any): Boolean

final def asInstanceOf[T0]: T0

def clone(): AnyRef

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

def finalize(): Unit

final def getClass(): Class[_]

def hashCode(): Int

final def isInstanceOf[T0]: Boolean

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

final def synchronized[T0](arg0: ⇒ T0): T0

def toString(): String

final def wait(): Unit

final def wait(arg0: Long, arg1: Int): Unit

final def wait(arg0: Long): Unit

Inherited from AnyRef

Inherited from Any

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