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33 #ifndef __process_fasta__hpp__ 34 #define __process_fasta__hpp__FASTA-format output; see also ReadFasta in <objtools/readers/fasta.hpp>
void ProcessInitialize(const CArgs &args)
virtual void SeqEntryInitialize(CRef< CSeq_entry > &se)
void ProcessInitialize(const CArgs &args)
virtual void SeqEntryInitialize(CRef< CSeq_entry > &se)
CRef< CSeq_entry > m_entry
unsigned int m_objectcount
#define ERR_POST(message)
Error posting with file, line number information but without error codes.
void Error(CExceptionArgs_Base &args)
virtual const char * what(void) const noexcept
Standard report (includes full backlog).
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 ...
void SetFlag(EFlags flag)
void SetAllFlags(TFlags flags)
EGapMode
How to represent gaps with fInstantiateGaps enabled, as it is by default.
void SetGapMode(EGapMode mode)
@ fNoExpensiveOps
don't try too hard to find titles
@ fShowModifiers
show key-value pair modifiers (e.g. "[organism=Homo sapiens]")
@ fInstantiateGaps
honor specifed gap mode; on by default
@ fKeepGTSigns
don't convert '>' to '_' in title
@ fNoDupCheck
skip check for duplicate sequence IDs
@ fEnableGI
Use this flag to enable GI output in the defline.
@ fAssembleParts
assemble FAR delta sequences; on by dflt
@ eGM_letters
Multiple inline Ns or Xs as appropriate (default).
@ eGM_count
>?N or >?unk100, as appropriate.
@ eGM_dashes
Multiple inline dashes.
@ eGM_one_dash
A single dash, followed by a line break.
#define VISIT_ALL_BIOSEQS_WITHIN_SEQENTRY(Itr, Var)
VISIT_ALL_BIOSEQS_WITHIN_SEQENTRY.
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