showalign.hpp File Reference

Sequence alignment display tool. More...

#include <corelib/ncbireg.hpp>
#include <unordered_set>
#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/align_format/align_format_util.hpp>
#include <objmgr/object_manager.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::DomainInfo
	structure for showing domains on the master sequence More...
struct	CDisplaySeqalign::SAlignTemplates
struct	CDisplaySeqalign::SInsertInformation
	internal insert information aln_start. More...
struct	CDisplaySeqalign::SAlnFeatureInfo
	store feature information More...
struct	CDisplaySeqalign::SAlnSeqlocInfo
	store seqloc info More...
struct	CDisplaySeqalign::SAlnRowInfo
struct	CDisplaySeqalign::SAlnDispParams
struct	CDisplaySeqalign::SAlnLinksParams
	Info used to contstruct seq url obtained from processing the whole seq align for particular subject sequnce. More...
struct	CDisplaySeqalign::SAlnInfo
	store alnvec and score info More...

Macros
#define	BLAST_DEFAULT_MATRIX   "BLOSUM62"
	Example: More...

Detailed Description

Sequence alignment display tool.

Definition in file showalign.hpp.

Macro Definition Documentation

BLAST_DEFAULT_MATRIX

#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 89 of file showalign.hpp.