NCBI C++ ToolKit
Typedefs | Functions | Variables
comment_item.cpp File Reference
#include <ncbi_pch.hpp>
#include <sstream>
#include <corelib/ncbistd.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seq/Seq_hist.hpp>
#include <objects/seq/Seq_hist_rec.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/seq/MolInfo.hpp>
#include <objects/seq/seq_macros.hpp>
#include <objects/seqfeat/BioSource.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqfeat/SubSource.hpp>
#include <objects/seqfeat/OrgName.hpp>
#include <objects/seqfeat/OrgMod.hpp>
#include <objects/general/User_object.hpp>
#include <objects/general/User_field.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/general/Date.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/general/general_macros.hpp>
#include <objects/misc/sequence_util_macros.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objmgr/util/sequence.hpp>
#include <objtools/format/formatter.hpp>
#include <objtools/format/text_ostream.hpp>
#include <objtools/format/items/comment_item.hpp>
#include <objtools/format/context.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objtools/alnmgr/alnmap.hpp>
#include <objmgr/util/objutil.hpp>
+ Include dependency graph for comment_item.cpp:

Go to the source code of this file.

Go to the SVN repository for this file.

Typedefs

typedef CConstRef< CSeq_alignTAln
 
typedef list< CRef< CSeq_align > > TAlnList
 
typedef list< CConstRef< CSeq_align > > TAlnConstList
 
typedef multimap< CAlnMap::TRange, TAlnTAlnMap
 

Functions

void x_CollectSegments (TAlnConstList &seglist, const TAlnList &aln_list)
 
void x_CollectSegments (TAlnConstList &seglist, const CSeq_align &aln)
 
static void s_GetAssemblyInfo (const CBioseqContext &ctx, string &s, const CUser_object &uo)
 
static bool s_GetEncodeValues (string &chromosome, string &assembly_date, string &ncbi_annotation, CBioseqContext &ctx)
 
static string s_HtmlizeStructuredCommentData (const bool is_html, const string &label_str, const string &data_str, const char *provider, const char *status, bool has_name, const char *organism, const char *source, const char *category, const char *accession)
 
static void s_GetStrForStructuredComment (const CUser_object::TData &data, list< string > &out_lines, int &out_prefix_len, const bool is_first, const bool is_html)
 
string s_CreateHistCommentString (const string &prefix, const string &suffix, const CSeq_hist_rec &hist, CBioseqContext &ctx)
 
static string s_GetOriginalID (CBioseqContext &ctx)
 

Variables

static const string kRefSeq = "REFSEQ"
 
static const string kRefSeqInformation = "REFSEQ INFORMATION"
 
static const string kRefSeqLink = "<a href=\"https://www.ncbi.nlm.nih.gov/RefSeq/\">REFSEQ</a>"
 
static const string kRefSeqInformationLink = "<a href=\"https://www.ncbi.nlm.nih.gov/RefSeq/\">REFSEQ INFORMATION</a>"
 

Typedef Documentation

◆ TAln

Definition at line 260 of file comment_item.cpp.

◆ TAlnConstList

typedef list< CConstRef< CSeq_align > > TAlnConstList

Definition at line 262 of file comment_item.cpp.

◆ TAlnList

typedef list< CRef< CSeq_align > > TAlnList

Definition at line 261 of file comment_item.cpp.

◆ TAlnMap

Definition at line 263 of file comment_item.cpp.

Function Documentation

◆ s_CreateHistCommentString()

string s_CreateHistCommentString ( const string prefix,
const string suffix,
const CSeq_hist_rec hist,
CBioseqContext ctx 
)

◆ s_GetAssemblyInfo()

static void s_GetAssemblyInfo ( const CBioseqContext ctx,
string s,
const CUser_object uo 
)
static

◆ s_GetEncodeValues()

static bool s_GetEncodeValues ( string chromosome,
string assembly_date,
string ncbi_annotation,
CBioseqContext ctx 
)
static

◆ s_GetOriginalID()

static string s_GetOriginalID ( CBioseqContext ctx)
static

◆ s_GetStrForStructuredComment()

static void s_GetStrForStructuredComment ( const CUser_object::TData data,
list< string > &  out_lines,
int out_prefix_len,
const bool  is_first,
const bool  is_html 
)
static

◆ s_HtmlizeStructuredCommentData()

static string s_HtmlizeStructuredCommentData ( const bool  is_html,
const string label_str,
const string data_str,
const char *  provider,
const char *  status,
bool  has_name,
const char *  organism,
const char *  source,
const char *  category,
const char *  accession 
)
static

◆ x_CollectSegments() [1/2]

void x_CollectSegments ( TAlnConstList seglist,
const CSeq_align aln 
)

◆ x_CollectSegments() [2/2]

void x_CollectSegments ( TAlnConstList seglist,
const TAlnList aln_list 
)

Definition at line 283 of file comment_item.cpp.

References ITERATE.

Referenced by CCommentItem::GetStringForTPA(), and x_CollectSegments().

Variable Documentation

◆ kRefSeq

const string kRefSeq = "REFSEQ"
static

◆ kRefSeqInformation

const string kRefSeqInformation = "REFSEQ INFORMATION"
static

Definition at line 79 of file comment_item.cpp.

Referenced by CCommentItem::GetStringForRefTrack().

◆ kRefSeqInformationLink

const string kRefSeqInformationLink = "<a href=\"https://www.ncbi.nlm.nih.gov/RefSeq/\">REFSEQ INFORMATION</a>"
static

Definition at line 81 of file comment_item.cpp.

Referenced by CCommentItem::GetStringForRefTrack().

◆ kRefSeqLink

const string kRefSeqLink = "<a href=\"https://www.ncbi.nlm.nih.gov/RefSeq/\">REFSEQ</a>"
static
Modified on Sat Jun 22 10:45:27 2024 by modify_doxy.py rev. 669887