Shortcuts
For more convenience, SeqAn defines some shortcuts for often used data types.
Input/Output
| A TagSelector for SeqStreamFormats, the list of the currently implemented Sequence-Formats (in RecordReader/Stream-IO) | |
| A sequence file mapped in memory as a StringSet of concatenated sequence file fragments. | |
| A sequence file mapped in memory as a StringSet of concatenated sequence file fragments. | |
| A Tag list of the currently implemented Sequence-Formats (in RecordReader/Stream-IO) |
Iterators
| Iterator for CharString. | |
| Iterator for Dna5String. | |
| Iterator for DnaString. | |
| Iterator for IupacString. | |
| Iterator for Peptide. | |
| Iterator for Rna5String. | |
| Iterator for RnaString. | |
| Iterator for UnicodeString. |
Modifier
| Modifier for the complement of a Dna5String. | |
| Modifier for the reverse of a Dna5String. | |
| Modifier for the reverse complement of a Dna5String. | |
| Modifier for the complement of a DnaString. | |
| Modifier for the reverse of a DnaString. | |
| Modifier for the reverse complement of a DnaString. | |
| Modifier specialization type for the complement of Dna alphabet sequences. | |
| Modifier specialization type for the complement of Dna5 alphabet sequences. | |
| Modifier specialization type for the complement of Rna alphabet sequences. | |
| Modifier specialization type for the complement of Rna5 alphabet sequences. | |
| Modifier for the complement of a Rna5String. | |
| Modifier for the reverse of a Rna5String. | |
| Modifier for the reverse complement of a Rna5String. | |
| Modifier for the complement of a RnaString. | |
| Modifier for the reverse of a RnaString. | |
| Modifier for the reverse complement of a RnaString. |
Scoring
| Blosum30 scoring matrix. | |
| Blosum45 scoring matrix. | |
| Blosum62 scoring matrix. | |
| Blosum80 scoring matrix. | |
| Edit distance scoring scheme. | |
| Pam120 scoring matrix. | |
| Pam200 scoring matrix. | |
| Pam250 scoring matrix. | |
| Pam40 scoring matrix. | |
| Simple scoring scheme. | |
| Vtml200 scoring matrix. |
Searching
| Semin-global (query-global, text-local) pattern matching without findBegin() support. | |
| Semin-global (query-global, text-local) pattern matching without findBegin() support. | |
| Global (query-global, text-global) pattern matching without findBegin() support. | |
| global (query-global, text-global) pattern matching without findBegin() support. |
Strings
| A string of | |
| A string of Dna5. | |
| A string of Dna. | |
| A string of Iupac. | |
| A string of AminoAcid. | |
| A string of Rna5. | |
| A string of Rna. | |
| A string of |
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