Go to the SVN repository for this file.
33 #ifndef __process_prosplign__hpp__ 34 #define __process_prosplign__hpp__ 62 m_out= args[
"o"] ? &(args[
"o"].AsOutputFile()) : &cout;
88 if(bioseq.
IsNa()) {
96 if(bioseq.
IsAa()) {
spliced protein to genomic alignment
CRef< objects::CSeq_align > FindAlignment(objects::CScope &scope, const objects::CSeq_id &protein, const objects::CSeq_loc &genomic, CProSplignOutputOptions output_options=CProSplignOutputOptions())
Aligns protein to a region on genomic sequence.
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).
#define MSerial_AsnText
I/O stream manipulators â.
TInst_Length GetInst_Length(void) const
CRef< CSeq_loc > GetRangeSeq_loc(TSeqPos start, TSeqPos stop, ENa_strand strand=eNa_strand_unknown) const
Return CSeq_loc referencing the given range and strand on the bioseq If start == 0,...
void Reset(void)
Reset reference object.
IO_PREFIX::ostream CNcbiOstream
Portable alias for ostream.
#define FOR_EACH_SEQID_ON_BIOSEQ(Itr, Var)
FOR_EACH_SEQID_ON_BIOSEQ EDIT_EACH_SEQID_ON_BIOSEQ.
#define VISIT_ALL_BIOSEQS_WITHIN_SEQENTRY(Itr, Var)
VISIT_ALL_BIOSEQS_WITHIN_SEQENTRY.
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