Shortcuts
For more convenience, SeqAn defines some shortcuts for often used data types.
Input/Output

MultiFasta | A sequence file mapped in memory as a StringSet of concatenated sequence file fragments.
MultiSeqFile | A sequence file mapped in memory as a StringSet of concatenated sequence file fragments.

Iterators

CharIterator | Iterator for CharString.
Dna5Iterator | Iterator for Dna5String.
DnaIterator | Iterator for DnaString.
IupacIterator | Iterator for IupacString.
PeptideIterator | Iterator for Peptide.
Rna5Iterator | Iterator for Rna5String.
RnaIterator | Iterator for RnaString.
UnicodeIterator | Iterator for UnicodeString.

Modifier

Dna5StringComplement | Modifier for the complement of a Dna5String.
Dna5StringReverse | Modifier for the reverse of a Dna5String.
Dna5StringReverseComplement | Modifier for the reverse complement of a Dna5String.
DnaStringComplement | Modifier for the complement of a DnaString.
DnaStringReverse | Modifier for the reverse of a DnaString.
DnaStringReverseComplement | Modifier for the reverse complement of a DnaString.
ModComplementDna | Modifier specialization type for the complement of Dna alphabet sequences.
ModComplementDna5 | Modifier specialization type for the complement of Dna5 alphabet sequences.
ModComplementRna | Modifier specialization type for the complement of Rna alphabet sequences.
ModComplementRna5 | Modifier specialization type for the complement of Rna5 alphabet sequences.
Rna5StringComplement | Modifier for the complement of a Rna5String.
Rna5StringReverse | Modifier for the reverse of a Rna5String.
Rna5StringReverseComplement | Modifier for the reverse complement of a Rna5String.
RnaStringComplement | Modifier for the complement of a RnaString.
RnaStringReverse | Modifier for the reverse of a RnaString.
RnaStringReverseComplement | Modifier for the reverse complement of a RnaString.

Pattern Matching

MyersUkkonen | Semin-global (query-global, text-local) pattern matching without findBegin() support.
MyersUkkonenBanded | Semin-global (query-global, text-local) pattern matching without findBegin() support.
MyersUkkonenGlobal | Global (query-global, text-global) pattern matching without findBegin() support.
MyersUkkonenGlobalBanded | global (query-global, text-global) pattern matching without findBegin() support.

Scoring

Blosum30 | Blosum30 scoring matrix.
Blosum45 | Blosum45 scoring matrix.
Blosum62 | Blosum62 scoring matrix.
Blosum80 | Blosum80 scoring matrix.
EditDistanceScore | Edit distance scoring scheme.
Pam120 | Pam120 scoring matrix.
Pam200 | Pam200 scoring matrix.
Pam250 | Pam250 scoring matrix.
Pam40 | Pam40 scoring matrix.
SimpleScore | Simple scoring scheme.
Vtml200 | Vtml200 scoring matrix.

Strings

CharString | A string of char.
Dna5String | A string of Dna5.
DnaString | A string of Dna.
IupacString | A string of Iupac.
Peptide | A string of AminoAcid.
Rna5String | A string of Rna5.
RnaString | A string of Rna.
UnicodeString | A string of wchar_t.

SeqAn - Sequence Analysis Library - www.seqan.de

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