Search Toolkit Book for CFastaOstream
FASTA-format output; see also ReadFasta in <objtools/readers/fasta.hpp> More...
#include <objmgr/util/sequence.hpp>
Inheritance diagram for CFastaOstream:
Collaboration diagram for CFastaOstream:
Classes | |
| struct | SGapModText |
| This indicates the text of the modifiers of a gap. More... | |
Public Types | |
| enum | EFlags : long { fAssembleParts = 1 << 0 , fInstantiateGaps = 1 << 1 , fSuppressRange = 1 << 2 , fReverseStrand = 1 << 3 , fKeepGTSigns = 1 << 4 , fMapMasksUp = 1 << 5 , fMapMasksDown = 1 << 6 , fNoExpensiveOps = 1 << 7 , fShowModifiers = 1 << 8 , fNoDupCheck = 1 << 9 , fShowGapModifiers = 1 << 10 , fKeepUnknGapNomLen = 1 << 11 , fShowGapsOfSizeZero = 1 << 12 , fEnableGI = 1 << 13 , fHideGenBankPrefix = 1 << 14 , fHTMLEncode = 1 << 15 , fIgnoreOriginalID = 1 << 16 , eAssembleParts = fAssembleParts , eInstantiateGaps = fInstantiateGaps , fUseAutoDef = 1 << 17 , fBaseFirstUnused = 1 << 18 , fDoNotUseAutoDef = 1 << 19 , fShowGnlAndAcc = 1 << 20 } |
| enum | EGapMode { eGM_one_dash , eGM_dashes , eGM_letters , eGM_count } |
| How to represent gaps with fInstantiateGaps enabled, as it is by default. More... | |
| enum | EMaskType { eSoftMask = 1 , eHardMask = 2 } |
| Which residues to mask out in subsequent output. More... | |
| typedef long | TFlags |
| binary OR of EFlags More... | |
Public Member Functions | |
| CFastaOstream (CNcbiOstream &out) | |
| virtual | ~CFastaOstream () |
| virtual void | Write (const CSeq_entry_Handle &handle, const CSeq_loc *location=0) |
| Unspecified locations designate complete sequences; non-empty custom titles override the usual title determination logic. More... | |
| virtual void | Write (const CBioseq_Handle &handle, const CSeq_loc *location=0, const string &custom_title=kEmptyStr) |
| virtual void | WriteTitle (const CBioseq_Handle &handle, const CSeq_loc *location=0, const string &custom_title=kEmptyStr) |
| virtual void | WriteSequence (const CBioseq_Handle &handle, const CSeq_loc *location=0, CSeq_loc::EOpFlags merge_flags=CSeq_loc::fMerge_AbuttingOnly) |
| void | Write (const CSeq_entry &entry, const CSeq_loc *location=0, bool no_scope=false) |
| These versions may set up a temporary object manager scope In the common case of a raw bioseq, no scope is needed. More... | |
| void | Write (const CBioseq &seq, const CSeq_loc *location=0, bool no_scope=false, const string &custom_title=kEmptyStr) |
| void | WriteTitle (const CBioseq &seq, const CSeq_loc *location=0, bool no_scope=false, const string &custom_title=kEmptyStr) |
| virtual bool | SkipBioseq (const CBioseq &) |
| Used only by Write(CSeq_entry[_Handle], ...); permissive by default. More... | |
| virtual bool | SkipBioseq (const CBioseq_Handle &handle) |
| Delegates to the non-handle version by default for compatibility with older code; newer code should override this version. More... | |
| CConstRef< CSeq_loc > | GetMask (EMaskType type) const |
| void | SetMask (EMaskType type, CConstRef< CSeq_loc > location) |
| TSeqPos | GetWidth (void) const |
| Other parameters... More... | |
| void | SetWidth (TSeqPos width) |
| TFlags | GetAllFlags (void) const |
| void | SetAllFlags (TFlags flags) |
| void | SetFlag (EFlags flag) |
| void | ResetFlag (EFlags flag) |
| void | SetGapMode (EGapMode mode) |
| EGapMode | GetGapMode (void) const |
Static Public Member Functions | |
| static void | GetGapModText (const CSeq_gap &seq_gap, SGapModText &out_gap_mod_text) |
| Given a CSeq_gap object, this outputs the Gap information. More... | |
Protected Member Functions | |
| virtual void | x_WriteSeqIds (const CBioseq &bioseq, const CSeq_loc *location) |
| virtual void | x_WriteAsFasta (const CBioseq &bioseq) |
| virtual void | x_GetBestId (CConstRef< CSeq_id > &gi_id, CConstRef< CSeq_id > &best_id, bool &hide_prefix, const CBioseq &bioseq) |
| virtual void | x_WriteSeqTitle (const CBioseq_Handle &handle, const string &custom_title) |
| virtual void | x_WriteBuffer (const char *buf, unsigned int count) |
Protected Attributes | |
| CNcbiOstream & | m_Out |
| unique_ptr< sequence::CDeflineGenerator > | m_Gen |
| TFlags | m_Flags |
Private Types | |
| typedef AutoPtr< char, ArrayDeleter< char > > | TCharBuf |
| typedef map< TSeqPos, int > | TMSMap |
Private Member Functions | |
| sequence::CDeflineGenerator::TUserFlags | x_GetTitleFlags (void) const |
| CConstRef< CSeq_loc > | x_MapMask (CSeq_loc_Mapper &mapper, const CSeq_loc &mask, const CSeq_id *base_seq_id, CScope *scope) |
| void | x_GetMaskingStates (TMSMap &masking_states, const CSeq_id *base_seq_id, const CSeq_loc *location, CScope *scope) |
| void | x_WriteSequence (const CSeqVector &vec, const TMSMap &masking_state) |
Detailed Description
FASTA-format output; see also ReadFasta in <objtools/readers/fasta.hpp>
Definition at line 770 of file sequence.hpp.
The documentation for this class was generated from the following files:
- include/objmgr/util/sequence.hpp
- src/objmgr/util/sequence.cpp
