Class Specialization
External String
String that is stored in external memory.
External String
String<TValue, External<> >
String<TValue, External<TConfig> >
Include Headers
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.
A structure to configure the external string.
The External String enables to access sequences larger than the available internal memory (RAM) by using external memory (e.g. Hard disk, Network storage, ...) via a File object. Sequences of nearly arbitrary size can be accessed even larger than the logically addressable memory, i.e. they can in particular contain more than 2^32 elements on a 32bit system (see Tag.ExternalConfigLarge). See the String constructor for more details.
This String also supports fast appending and removing of values at the end (see Block String, appendValue)
The External String implements a LRU mechanism to swap out pages. The External String's Iterator detects a forward or backward iteration and asynchronously prefetches pages that certainly will be accessed and automatically swaps out pages that certainly won't be accessed any more in the iteration process.
The String is implemented like a virtual memory manager. It divides its character sequence into pages of a fixed length (e.g. 1MB) and maintains a page table with information for each page (e.g. resides in memory or was swapped out, is dirty and needs to be saved, ...). Besides the page table the String also contains a size-limited list of page frames. A page frame is reserved internal memory for a page. When accessing values of a page that is stored in external memory, the page is loaded to a page frame first. In case that there is no page frame free, another page is swapped out before to free a page frame.
Specialization of
DefaultOverflowExplicitThe default overflow strategy for explicit resize. (String)
DefaultOverflowImplicitThe default overflow strategy for implicit resize. (String)
InfixInfix sequence type. (String)
IsSequenceDetermines whether a container stores its elements in sequential order. (String)
MotifThe string type of the finder. (String)
PositionType of an object that represents a position in a container. (String)
PrefixPrefix sequence type. (String)
SAValueThe default alphabet type of a suffix array, i.e. the type to store a position of a string or string set. (String)
SpecThe spec of a class. (String)
SuffixSuffix sequence type. (String)
ValueType of the items in the container or behind an iterator. (String)
Member Functions
StringConstructor (String)
appendConcatenate two containers. (String)
appendSeqsAppends all sequences stored in files of directory to a StringSet. (String)
assignAssigns one object to another object. (String)
assignCroppedSeqIdExtracts the sequence id up to the first whitespace of a sequence file fragment. (String)
assignQualExtracts the quality values of a sequence file fragment. (String)
assignQualIdExtracts the quality value id of a sequence file fragment. (String)
assignSeqExtracts the sequence part of a sequence file fragment. (String)
assignSeqIdExtracts the sequence id of a sequence file fragment. (String)
assignValueAssigns value to item. (ContainerConcept)
backThe last item in container. (ContainerConcept)
bamRecordToAlignmentConvert BamAlignmentRecord to an Align object. (String)
beginThe begin of a container. (String)
beginPositionBegin position of object in host. (String)
buildAlignmentGraphBuilds an Alignment Graph from a set of input alignments. (String)
calculateCovarianceCalculates the covariance for the number of word occurrences for two words in a sequence of length n, given a background model. (String)
calculateOverlapIndicatorCalculate word overlaps: epsilon(word1,word2)= 1 where word2[j]=word1[j+p] for all j=1...(k-p) (String)
calculatePeriodicityCalculate word periodicity (indicator for overlaps) (String)
calculateProbabilityCalculates the probability of a sequence given a Bernoulli model (String of background frequencies) (String)
calculateVarianceCalculates the variance for the number of word occurrences of a word in a sequence of length n given a background model. (String)
canParseStringTest whether an automaton can parse a string completely. (String)
capacityThe maximal length. (String)
clearResets an object. (String)
closeCloses a file.
collectLeavesReturns all leaves underneath a given vertex. (String)
complementComplement a sequence or a StringSet in-place. (String)
countKmersCounts kmers in a sequence. Optionally, a background model is returned. (String)
createLfTableCreates the LF table (String)
createOracleCreates a factor oracle. (String)
createOracleOnReverseCreates a factor oracle for the reversed string. (String)
createPrefixSumTableCreates the prefix sum table (String)
createRankDictionaryThis functions creates the dictionary. (String)
createRightArrayBinaryTreeComputes the wavelet tree structure of a text. (String)
createSentinelRankDictionaryThis functions creates the dictionary structure. (String)
createSuffixTrieCreates a trie of all suffixes of a text. (String)
createTrieCreates a trie. (String)
createTrieOnReverseCreates a trie for all reversed keywords. (String)
determineConsensusSeqDetermines the consensus pattern of a given profile. (String)
emptyTest a container for being empty. (String)
endThe end of a container. (String)
endPositionEnd position of object in host. (String)
eraseErases a part of a container (String)
eraseBackDeletes 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)
extendSeedExtends a seed. (String)
findIntervalsFind all intervals that contain the query point or overlap with the query interval. (String)
findIntervalsExcludeTouchingFind 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)
findRepeatsSearch for repeats in a text. (String)
flushWaits for all open requests to complete.
frontThe first item in container. (ContainerConcept)
getDistanceMatrixComputes a pairwise distance matrix from an alignment graph. (String)
getObjectIdA value that identifies the underlying sequence. (String)
getSuccessorGets 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)
getValueAccess to the value. (ContainerConcept)
globalAlignmentScoreComputes the best global pairwise alignment score. (String)
goDownIterates down one edge or a path in a tree. (String)
heaviestIncreasingSubsequenceComputes the heaviest increasing subsequence. (String)
infixCreates infix object. (String)
infixWithLengthCreates infix object. (String)
integrateAlignIntegrates an alignment into another by copying the gaps. (String)
iterIterator to item at given position. (String)
lengthThe number of items/characters. (String)
longestCommonSubsequenceComputes the longest common subsequence. (String)
longestIncreasingSubsequenceComputes the longest increasing subsequence. (String)
moveValueAssigns value to item. (ContainerConcept)
njTreeComputes a guide tree from a distance matrix. (String)
openOpens a file, stream, or persistent string.
openTempOpens a temporary file.
parseStringParses a string one character at a time and moves accordingly in the automaton. (String)
positionPosition of an iterator. (ContainerConcept)
prefixCreates prefix object. (String)
readFastaRead first sequence from a FASTA file. (String)
readRecordRead the next sequence record from SequenceStream. (String)
readRegionLoad the infix of a sequence from a FaiIndex. (String)
readSequenceLoad a whole sequence from an FaiIndex. (String)
replaceReplaces a part of a container with another container. (String)
reserveIncreases the capacity. (String)
resizeResizes a container. If the new length exceeds the old length the new elements are filled with copies of value. (String)
resizeSpaceMakes free space in container (String)
reverseComplementReverse and complement a sequence or a StringSet in-place. (String)
setHaystackSets the haystack of a Finder object. (String)
setHostSets the host of an object. (String)
setNeedleSets the needle of a Pattern object and optionally induces preprocessing. (String)
shapeToStringConverts a given shape into a sequence of '1' (relevant position) and '0' (irrelevant position). (String)
shareResourcesDetermines whether two sequences share the same resource. (String)
stringSetLimitsRetrieves a string of delimiter positions of a StringSet which is needed for local<->global position conversions. (String)
stringToShapeTakes a shape given as a string of '1' (relevant position) and '0' (irrelevant position) and converts it into a Shape object. (String)
stringToStringSetTransform a String into a StringSet containing this String. (String)
suffixCreates suffix object. (String)
swapSwaps the contents of two values. (String)
toCStringAccess sequence as c-style string. (String)
toLowerConvert characters in sequence or StringSet to lower case in-place. (String)
topologicalSortPerforms a topological sort on a directed acyclic graph (DAG). (String)
toUpperConvert characters in sequence or StringSet to lower case in-place. (String)
unhashInverse of the hash function; for ungapped shapes. (String)
upgmaTreeComputes a guide tree from a distance matrix. (String)
valueReference to the value. (String)
writeRecordWrite one sequence record from to a SequenceStream object. (String)
SeqAn - Sequence Analysis Library -

Page built @2013/07/11 09:12:38