include/objtools/align_format/showalign.hpp File Reference

#include <corelib/ncbireg.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/blastdb/Blast_def_line_set.hpp>
#include <objects/seqfeat/SeqFeatData.hpp>
#include <objects/seq/seqlocinfo.hpp>
#include <objtools/alnmgr/alnvec.hpp>
#include <objtools/readers/getfeature.hpp>
#include <objtools/blast/gene_info_reader/gene_info_reader.hpp>
#include <objtools/align_format/align_format_util.hpp>
#include <objmgr/object_manager.hpp>
#include <cgi/cgictx.hpp>

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Classes
struct	SSeqIdKey
	Auxiliary type to embed a CConstRef<objects::CSeq_id> in STL containers that require operator< to be defined. More...
class	CDisplaySeqalign
struct	CDisplaySeqalign::FeatureInfo
	structure for store feature display info More...
struct	CDisplaySeqalign::SInsertInformation
	internal insert information aln_start. More...
struct	CDisplaySeqalign::SAlnInfo
	store alnvec and score info More...
struct	CDisplaySeqalign::SAlnFeatureInfo
	store feature information More...
struct	CDisplaySeqalign::SAlnSeqlocInfo
	store seqloc info More...
Defines
#define	BLAST_DEFAULT_MATRIX   "BLOSUM62"
	Example:.

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Define Documentation

#define BLAST_DEFAULT_MATRIX   "BLOSUM62"

Example:. CRef<objects::CSeq_align_set> aln_set = ... CRef<objects::CScope> scope = ... int display_option = 0; display_option += CDisplaySeqalign::eShowGi; display_option += CDisplaySeqalign::eHtml; ....... CDisplaySeqalign ds(*aln_set, *scope); ds.SetAlignOption(display_option); ds.DisplaySeqalign(stdout); Definition at line 88 of file showalign.hpp.

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