Shortcuts
For more convenience, SeqAn defines some shortcuts for often used data types.
Input/Output
AutoSeqStreamFormatA TagSelector for SeqStreamFormats, the list of the currently implemented Sequence-Formats (in RecordReader/Stream-IO)
MultiFastaA sequence file mapped in memory as a StringSet of concatenated sequence file fragments.
MultiSeqFileA sequence file mapped in memory as a StringSet of concatenated sequence file fragments.
SeqStreamFormatsA Tag list of the currently implemented Sequence-Formats (in RecordReader/Stream-IO)
Iterators
CharIteratorIterator for CharString.
Dna5IteratorIterator for Dna5String.
DnaIteratorIterator for DnaString.
IupacIteratorIterator for IupacString.
PeptideIteratorIterator for Peptide.
Rna5IteratorIterator for Rna5String.
RnaIteratorIterator for RnaString.
UnicodeIteratorIterator for UnicodeString.
Modifier
Dna5StringComplementModifier for the complement of a Dna5String.
Dna5StringReverseModifier for the reverse of a Dna5String.
Dna5StringReverseComplementModifier for the reverse complement of a Dna5String.
DnaStringComplementModifier for the complement of a DnaString.
DnaStringReverseModifier for the reverse of a DnaString.
DnaStringReverseComplementModifier for the reverse complement of a DnaString.
ModComplementDnaModifier specialization type for the complement of Dna alphabet sequences.
ModComplementDna5Modifier specialization type for the complement of Dna5 alphabet sequences.
ModComplementRnaModifier specialization type for the complement of Rna alphabet sequences.
ModComplementRna5Modifier specialization type for the complement of Rna5 alphabet sequences.
Rna5StringComplementModifier for the complement of a Rna5String.
Rna5StringReverseModifier for the reverse of a Rna5String.
Rna5StringReverseComplementModifier for the reverse complement of a Rna5String.
RnaStringComplementModifier for the complement of a RnaString.
RnaStringReverseModifier for the reverse of a RnaString.
RnaStringReverseComplementModifier for the reverse complement of a RnaString.
Scoring
Blosum30Blosum30 scoring matrix.
Blosum45Blosum45 scoring matrix.
Blosum62Blosum62 scoring matrix.
Blosum80Blosum80 scoring matrix.
EditDistanceScoreEdit distance scoring scheme.
Pam120Pam120 scoring matrix.
Pam200Pam200 scoring matrix.
Pam250Pam250 scoring matrix.
Pam40Pam40 scoring matrix.
SimpleScoreSimple scoring scheme.
Vtml200Vtml200 scoring matrix.
Searching
MyersUkkonenSemin-global (query-global, text-local) pattern matching without findBegin() support.
MyersUkkonenBandedSemin-global (query-global, text-local) pattern matching without findBegin() support.
MyersUkkonenGlobalGlobal (query-global, text-global) pattern matching without findBegin() support.
MyersUkkonenGlobalBandedglobal (query-global, text-global) pattern matching without findBegin() support.
Strings
CharStringA string of char.
Dna5StringA string of Dna5.
DnaStringA string of Dna.
IupacStringA string of Iupac.
PeptideA string of AminoAcid.
Rna5StringA string of Rna5.
RnaStringA string of Rna.
UnicodeStringA string of wchar_t.
SeqAn - Sequence Analysis Library - www.seqan.de
 

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