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CAlignFormatUtil::SSeqURLInfo Struct Reference

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Structure that holds information needed for creation seqID URL in descriptions and alignments. More...

#include <objtools/align_format/align_format_util.hpp>

+ Collaboration diagram for CAlignFormatUtil::SSeqURLInfo:

Public Member Functions

 SSeqURLInfo (string usurl, string bt, bool isnuc, string db, string rid_in, int qn, TGi gi_in, string acc, int lnk, int blrk, bool alnLink, bool nw, CRange< TSeqPos > range=CRange< TSeqPos >(0, 0), bool flp=false, TTaxId txid=INVALID_TAX_ID, bool addCssInf=false, string seqSegs="", string resUrl="", bool useTmpl=false, bool advView=false)
 Constructor. More...
 

Public Attributes

string user_url
 user url TOOL_URL from .ncbirc More...
 
string blastType
 blast type refer to blobj->adm->trace->created_by More...
 
bool isDbNa
 bool indicating if the database is nucleotide or not More...
 
string database
 name of the database More...
 
string rid
 blast RID More...
 
int queryNumber
 the query number More...
 
TGi gi
 gi to use More...
 
string accession
 accession More...
 
int linkout
 linkout flag More...
 
int blast_rank
 index of the current alignment More...
 
bool isAlignLink
 bool indicating if link is in alignment section More...
 
bool new_win
 bool indicating if click of the url will open a new window More...
 
CRange< TSeqPosseqRange
 sequence range More...
 
bool flip
 flip sequence in case of opposite strands More...
 
TTaxId taxid
 taxid More...
 
bool addCssInfo
 bool indicating that css info should be added More...
 
string segs
 string containing align segments in the the following format seg1Start-seg1End,seg2Start-seg2End More...
 
string resourcesUrl
 URL(s) to other resources from .ncbirc. More...
 
bool useTemplates
 bool indicating that templates should be used when contsructing links More...
 
bool advancedView
 bool indicating that advanced view design option should be used when contsructing links More...
 
string seqUrl
 sequence URL created More...
 
string defline
 sequence defline More...
 
bool hasTextSeqID
 

Detailed Description

Structure that holds information needed for creation seqID URL in descriptions and alignments.

Definition at line 387 of file align_format_util.hpp.

Constructor & Destructor Documentation

◆ SSeqURLInfo()

CAlignFormatUtil::SSeqURLInfo::SSeqURLInfo ( string  usurl,
string  bt,
bool  isnuc,
string  db,
string  rid_in,
int  qn,
TGi  gi_in,
string  acc,
int  lnk,
int  blrk,
bool  alnLink,
bool  nw,
CRange< TSeqPos range = CRange<TSeqPos>(0,0),
bool  flp = false,
TTaxId  txid = INVALID_TAX_ID,
bool  addCssInf = false,
string  seqSegs = "",
string  resUrl = "",
bool  useTmpl = false,
bool  advView = false 
)
inline

Constructor.

Definition at line 413 of file align_format_util.hpp.

Member Data Documentation

◆ accession

string CAlignFormatUtil::SSeqURLInfo::accession

◆ addCssInfo

bool CAlignFormatUtil::SSeqURLInfo::addCssInfo

bool indicating that css info should be added

Definition at line 403 of file align_format_util.hpp.

Referenced by CAlignFormatUtil::GetFullIDLink().

◆ advancedView

bool CAlignFormatUtil::SSeqURLInfo::advancedView

bool indicating that advanced view design option should be used when contsructing links

Definition at line 407 of file align_format_util.hpp.

Referenced by CShowBlastDefline::x_FillDeflineAndId(), and CDisplaySeqalign::x_InitSeqUrl().

◆ blast_rank

int CAlignFormatUtil::SSeqURLInfo::blast_rank

index of the current alignment

Definition at line 397 of file align_format_util.hpp.

Referenced by s_MapCommonUrlParams().

◆ blastType

string CAlignFormatUtil::SSeqURLInfo::blastType

blast type refer to blobj->adm->trace->created_by

Definition at line 389 of file align_format_util.hpp.

Referenced by CAlignFormatUtil::GetGraphiscLink(), and CAlignFormatUtil::SetCustomLinksTypes().

◆ database

string CAlignFormatUtil::SSeqURLInfo::database

name of the database

Definition at line 391 of file align_format_util.hpp.

Referenced by CAlignFormatUtil::GetAlignedRegionsURL().

◆ defline

string CAlignFormatUtil::SSeqURLInfo::defline

sequence defline

Definition at line 409 of file align_format_util.hpp.

Referenced by CAlignFormatUtil::GetFullIDLink(), and CDisplaySeqalign::x_HTMLSeqIDLink().

◆ flip

bool CAlignFormatUtil::SSeqURLInfo::flip

flip sequence in case of opposite strands

Definition at line 401 of file align_format_util.hpp.

◆ gi

TGi CAlignFormatUtil::SSeqURLInfo::gi

◆ hasTextSeqID

bool CAlignFormatUtil::SSeqURLInfo::hasTextSeqID

◆ isAlignLink

bool CAlignFormatUtil::SSeqURLInfo::isAlignLink

bool indicating if link is in alignment section

Definition at line 398 of file align_format_util.hpp.

Referenced by s_MapCommonUrlParams().

◆ isDbNa

bool CAlignFormatUtil::SSeqURLInfo::isDbNa

bool indicating if the database is nucleotide or not

Definition at line 390 of file align_format_util.hpp.

Referenced by CAlignFormatUtil::GetAlignedRegionsURL(), CAlignFormatUtil::GetGiLinksList(), CAlignFormatUtil::GetGraphiscLink(), and s_MapCommonUrlParams().

◆ linkout

int CAlignFormatUtil::SSeqURLInfo::linkout

linkout flag

Definition at line 396 of file align_format_util.hpp.

◆ new_win

bool CAlignFormatUtil::SSeqURLInfo::new_win

bool indicating if click of the url will open a new window

Definition at line 399 of file align_format_util.hpp.

◆ queryNumber

int CAlignFormatUtil::SSeqURLInfo::queryNumber

the query number

Definition at line 393 of file align_format_util.hpp.

Referenced by CAlignFormatUtil::GetAlignedRegionsURL().

◆ resourcesUrl

string CAlignFormatUtil::SSeqURLInfo::resourcesUrl

◆ rid

string CAlignFormatUtil::SSeqURLInfo::rid

◆ segs

string CAlignFormatUtil::SSeqURLInfo::segs

string containing align segments in the the following format seg1Start-seg1End,seg2Start-seg2End

Definition at line 404 of file align_format_util.hpp.

Referenced by CAlignFormatUtil::GetAlignedRegionsURL(), and CDisplaySeqalign::x_InitAlignLinks().

◆ seqRange

CRange<TSeqPos> CAlignFormatUtil::SSeqURLInfo::seqRange

sequence range

Definition at line 400 of file align_format_util.hpp.

Referenced by CAlignFormatUtil::GetGraphiscLink(), and CDisplaySeqalign::x_InitAlignLinks().

◆ seqUrl

string CAlignFormatUtil::SSeqURLInfo::seqUrl

◆ taxid

TTaxId CAlignFormatUtil::SSeqURLInfo::taxid

◆ user_url

string CAlignFormatUtil::SSeqURLInfo::user_url

user url TOOL_URL from .ncbirc

Definition at line 388 of file align_format_util.hpp.

Referenced by s_MapURLLink().

◆ useTemplates

bool CAlignFormatUtil::SSeqURLInfo::useTemplates

bool indicating that templates should be used when contsructing links

Definition at line 406 of file align_format_util.hpp.

Referenced by CShowBlastDefline::x_FillDeflineAndId(), CDisplaySeqalign::x_HTMLSeqIDLink(), and CDisplaySeqalign::x_InitSeqUrl().


The documentation for this struct was generated from the following file:
Modified on Fri Mar 01 10:05:44 2024 by modify_doxy.py rev. 669887