Class Specialization
Block String
String optimized for push_back, top, and pop (Stack behaviour).

ContainerConcept

String

Block String

String<TValue, Block<size> >
Include Headers
seqan/sequence.h
Parameters

TValue | The value type, that is the type of the items/characters stored in the string. Remarks: Use Value to get the value type for a given class.
size | A positive integer that specifies the number of values in each allocated block. Remarks: Size should be a power of 2, e.g., 1024.

Specialization of
String
Implements
ContainerConcept
Metafunctions

DefaultOverflowExplicit | The default overflow strategy for explicit resize. (String)
DefaultOverflowImplicit | The default overflow strategy for implicit resize. (String)
Infix | Infix sequence type. (String)
IsSequence | Determines whether a container stores its elements in sequential order. (String)
Iterator | Type of iterator objects that are used to traverse the container.
Motif | The string type of the finder. (String)
Position | Type of an object that represents a position in a container. (String)
Prefix | Prefix sequence type. (String)
SAValue | The default alphabet type of a suffix array, i.e. the type to store a position of a string or string set. (String)
Spec | The spec of a class. (String)
Suffix | Suffix sequence type. (String)
Value | Type of the items in the container or behind an iterator. (String)

Member Functions

String | Constructor (String)

Functions

append | Concatenate two containers. (String)
appendSeqs | Appends all sequences stored in files of directory to a StringSet. (String)
appendValue | Appends a value to a container.
assign | Assigns one object to another object. (String)
assignCroppedSeqId | Extracts the sequence id up to the first whitespace of a sequence file fragment. (String)
assignQual | Extracts the quality values of a sequence file fragment. (String)
assignQualId | Extracts the quality value id of a sequence file fragment. (String)
assignSeq | Extracts the sequence part of a sequence file fragment. (String)
assignSeqId | Extracts the sequence id of a sequence file fragment. (String)
assignValue | Assigns value to item. (ContainerConcept)
back | The last item in container. (ContainerConcept)
bamRecordToAlignment | Convert BamAlignmentRecord to an Align object. (String)
begin | The begin of a container. (String)
beginPosition | Begin position of object in host. (String)
buildAlignmentGraph | Builds an Alignment Graph from a set of input alignments. (String)
calculateCovariance | Calculates the covariance for the number of word occurrences for two words in a sequence of length n, given a background model. (String)
calculateOverlapIndicator | Calculate word overlaps: epsilon(word1,word2)= 1 where word2[j]=word1[j+p] for all j=1...(k-p) (String)
calculatePeriodicity | Calculate word periodicity (indicator for overlaps) (String)
calculateProbability | Calculates the probability of a sequence given a Bernoulli model (String of background frequencies) (String)
calculateVariance | Calculates the variance for the number of word occurrences of a word in a sequence of length n given a background model. (String)
canParseString | Test whether an automaton can parse a string completely. (String)
capacity | The maximal length. (String)
clear | Resets an object. (String)
collectLeaves | Returns all leaves underneath a given vertex. (String)
complement | Complement a sequence or a StringSet in-place. (String)
countKmers | Counts kmers in a sequence. Optionally, a background model is returned. (String)
createLfTable | Creates the LF table (String)
createOracle | Creates a factor oracle. (String)
createOracleOnReverse | Creates a factor oracle for the reversed string. (String)
createPrefixSumTable | Creates the prefix sum table (String)
createRankDictionary | This functions creates the dictionary. (String)
createRightArrayBinaryTree | Computes the wavelet tree structure of a text. (String)
createSentinelRankDictionary | This functions creates the dictionary structure. (String)
createSuffixTrie | Creates a trie of all suffixes of a text. (String)
createTrie | Creates a trie. (String)
createTrieOnReverse | Creates a trie for all reversed keywords. (String)
determineConsensusSeq | Determines the consensus pattern of a given profile. (String)
empty | Test a container for being empty. (String)
end | The end of a container. (String)
endPosition | End position of object in host. (String)
erase | Erases a part of a container (String)
eraseBack | Deletes the last item of a container and reduces its size by 1. The container must have a size greater than or equal to 1. (String)
extendSeed | Extends a seed. (String)
findIntervals | Find all intervals that contain the query point or overlap with the query interval. (String)
findIntervalsExcludeTouching | Find all intervals that contain the query point, exclude intervals that touch the query, i.e. where the query point equals the start or end point. (String)
findRepeats | Search for repeats in a text. (String)
front | The first item in container. (ContainerConcept)
getDistanceMatrix | Computes a pairwise distance matrix from an alignment graph. (String)
getObjectId | A value that identifies the underlying sequence. (String)
getSuccessor | Gets the successor for a given vertex and an edge label. For an automaton a single character is required whereas for a word graph getSuccessor takes a string. (String)
getValue | Access to the value. (ContainerConcept)
globalAlignmentScore | Computes the best global pairwise alignment score. (String)
goDown | Iterates down one edge or a path in a tree. (String)
heaviestIncreasingSubsequence | Computes the heaviest increasing subsequence. (String)
infix | Creates infix object. (String)
infixWithLength | Creates infix object. (String)
integrateAlign | Integrates an alignment into another by copying the gaps. (String)
iter | Iterator to item at given position. (String)
length | The number of items/characters. (String)
longestCommonSubsequence | Computes the longest common subsequence. (String)
longestIncreasingSubsequence | Computes the longest increasing subsequence. (String)
moveValue | Assigns value to item. (ContainerConcept)
njTree | Computes a guide tree from a distance matrix. (String)
parseString | Parses a string one character at a time and moves accordingly in the automaton. (String)
position | Position of an iterator. (ContainerConcept)
prefix | Creates prefix object. (String)
readFasta | Read first sequence from a FASTA file. (String)
readRecord | Read the next sequence record from SequenceStream. (String)
readRegion | Load the infix of a sequence from a FaiIndex. (String)
readSequence | Load a whole sequence from an FaiIndex. (String)
replace | Replaces a part of a container with another container. (String)
reserve | Increases the capacity.
resize | Resizes a container. If the new length exceeds the old length the new elements are filled with copies of value. (String)
resizeSpace | Makes free space in container (String)
reverseComplement | Reverse and complement a sequence or a StringSet in-place. (String)
setHaystack | Sets the haystack of a Finder object. (String)
setHost | Sets the host of an object. (String)
setNeedle | Sets the needle of a Pattern object and optionally induces preprocessing. (String)
shapeToString | Converts a given shape into a sequence of '1' (relevant position) and '0' (irrelevant position). (String)
shareResources | Determines whether two sequences share the same resource. (String)
stringSetLimits | Retrieves a string of delimiter positions of a StringSet which is needed for local<->global position conversions. (String)
stringToShape | Takes a shape given as a string of '1' (relevant position) and '0' (irrelevant position) and converts it into a Shape object. (String)
stringToStringSet | Transform a String into a StringSet containing this String. (String)
suffix | Creates suffix object. (String)
swap | Swaps the contents of two values. (String)
toCString | Access sequence as c-style string. (String)
toLower | Convert characters in sequence or StringSet to lower case in-place. (String)
topologicalSort | Performs a topological sort on a directed acyclic graph (DAG). (String)
toUpper | Convert characters in sequence or StringSet to lower case in-place. (String)
unhash | Inverse of the hash function; for ungapped shapes. (String)
upgmaTree | Computes a guide tree from a distance matrix. (String)
value | Reference to the value. (String)
writeRecord | Write one sequence record from to a SequenceStream object. (String)

Example Programs
ModView, ModReverse, Nested Modifiers
SeqAn - Sequence Analysis Library - www.seqan.de

Page built @2014/10/13 16:13:00