NCBI C++ ToolKit
Classes | Macros
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>
+ Include dependency graph for showalign.hpp:
+ This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Go to the SVN repository for this file.

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::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);
friend class CRef
Definition: ncbiobj.hpp:629

Definition at line 89 of file showalign.hpp.

Modified on Mon Jun 17 05:08:59 2024 by modify_doxy.py rev. 669887