NCBI C++ ToolKit
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align_format_util.hpp File Reference
#include <corelib/ncbistre.hpp>
#include <corelib/ncbireg.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/blastdb/Blast_def_line_set.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/scoremat/PssmWithParameters.hpp>
#include <objmgr/bioseq_handle.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objtools/alnmgr/alnvec.hpp>
#include <objtools/align_format/format_flags.hpp>
#include <util/math/matrix.hpp>
#include <algo/blast/core/blast_stat.h>
#include <objtools/align_format/ilinkoutdb.hpp>
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Go to the source code of this file.

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Classes

class  CAlignFormatUtil
 This class contains misc functions for displaying BLAST results. More...
 
struct  CAlignFormatUtil::SBlastError
 Error info structure. More...
 
struct  CAlignFormatUtil::SDbInfo
 Blast database info. More...
 
struct  CAlignFormatUtil::SSeqURLInfo
 Structure that holds information needed for creation seqID URL in descriptions and alignments. More...
 
struct  CAlignFormatUtil::SLinkoutInfo
 
struct  CAlignFormatUtil::SSeqAlignSetCalcParams
 Structure that holds information for all hits of one subject in Seq Align Set. More...
 

Macros

#define DIM(static_array)   (sizeof(static_array)/sizeof(*static_array))
 Calculates the dimensions of a static array. More...
 

Typedefs

typedef SStaticPair< const char *, const char * > TTagUrl
 create map source of all static URL's using previously defined pairs this map should be in alphabetical order!!! More...
 
typedef CStaticArrayMap< string, stringTTagUrlMap
 

Enumerations

enum  { ePMatrixSize = 23 }
 protein matrix define More...
 

Functions

 DEFINE_STATIC_ARRAY_MAP (TTagUrlMap, sm_TagUrlMap, s_TagUrls)
 

Variables

static const char kClassInfo [] = "class=\"info\""
 blast related url More...
 
static const char kDefaultProtocol [] = "https:"
 
static const char kEntrezUrl [] = "<a title=\"Show report for <@acc@>\" <@cssInf@>href=\"<@protocol@>//www.ncbi.nlm.nih.gov/<@db@>/<@acc@>?report=genbank&log$=<@log@>&blast_rank=<@blast_rank@>&RID=<@rid@>\" <@target@>>"
 entrez More...
 
static const char kEntrezTMUrl [] = "<@protocol@>//www.ncbi.nlm.nih.gov/<@db@>/<@acc@>?report=genbank&log$=<@log@>&blast_rank=<@blast_rank@>&RID=<@rid@>"
 
static const char kWGSUrl [] = "<@protocol@>//www.ncbi.nlm.nih.gov/nuccore/<@wgsacc@>"
 
static const char kTraceUrl [] = "<a title=\"Show report for <@val@>\" <@cssInf@>href=\"<@protocol@>//www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=retrieve&dopt=fasta&val=<@val@>&RID=<@rid@>\">"
 trace db More...
 
static const char kGenomeButton []
 genome button More...
 
static const char kUnigeneUrl []
 unigene More...
 
static const char kUnigeneImg [] = "<img border=0 height=16 width=16 src=\"images/U.gif\" alt=\"UniGene info linked to <@label@>\">"
 
static const string kUnigeneDispl = "<div><@lnk@>-<span class=\"rlLink\">clustered expressed sequence tags</span></div>"
 
static const char kStructureUrl [] = "<a href=\"<@protocol@>//www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?from=blast&blast_rep_id=<@label@>&query_id=<@queryID@>&command=view+annotations;set+annotation+cdd;set+annotation+site;set+view+detailed+view;select+chain+<@label@>;show+selection&log$=<@log@>&blast_rank=<@blast_rank@>&RID=<@rid@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>"
 structure More...
 
static const char kStructureAlphaFoldUrl [] = "<a href=\"<@protocol@>//www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?from=blast&blast_rep_id=<@label@>&query_id=<@queryID@>&command=view+annotations;set+annotation+cdd;set+annotation+site;set+view+detailed+view;select+chain+!A;show+selection&log$=<@log@>&blast_rank=<@blast_rank@>&RID=<@rid@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>"
 
static const char kStructureImg [] = "<img border=0 height=16 width=16 src=\"<@protocol@>//www.ncbi.nlm.nih.gov/Structure/cblast/str_link.gif\" alt=\"Structure related to <@label@>\">"
 
static const string kStructureDispl = "<div><@lnk@>-<span class=\"rlLink\">3D structure displays</span></div>"
 
static const char kStructure_Overview []
 structure overview More...
 
static const char kGeoUrl [] = "<a href=\"<@protocol@>//www.ncbi.nlm.nih.gov/geoprofiles/?term=genbank[Platform+Reporter+Type]+AND+<@label@>[Reporter+Identifier]&RID=<@rid@>&log$=geo<@log@>&blast_rank=<@blast_rank@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>"
 Geo. More...
 
static const char kGeoImg [] = "<img border=0 height=16 width=16 src=\"images/E.gif\" alt=\"GEO profiles info linked to <@label@>\">"
 
static const string kGeoDispl = "<div><@lnk@>-<span class=\"rlLink\">microarray expression data</span></div>"
 
static const char kGeneUrl []
 Gene. More...
 
static const char kGeneTerm [] = "term=<@label@><@uid@>&"
 
static const char kGeneImg [] = "<img border=0 height=16 width=16 src=\"images/G.gif\" alt=\"Gene info linked to <@label@>\">"
 
static const string kGeneDispl = "<div><@lnk@>-<span class=\"rlLink\">associated gene details</span></div>"
 
static const char kBioAssayProtURL [] = "<a href=\"<@protocol@>//www.ncbi.nlm.nih.gov/entrez?db=pcassay&term=<@gi@>[PigGI]&RID=<@rid@>&log$=pcassay<@log@>&blast_rank=<@blast_rank@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>"
 Bioassay for proteins. More...
 
static const char kBioAssayProtImg [] = "<img border=0 height=16 width=16 src=\"images/Bioassay.gif\" alt=\"PubChem BioAssay Info linked to <@label@>\">"
 
static const char kBioAssayNucURL [] = "<a href=\"<@protocol@>//www.ncbi.nlm.nih.gov/entrez?db=pcassay&term=<@gi@>[RNATargetGI]&RID=<@rid@>&log$=pcassay<@log@>&blast_rank=<@blast_rank@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>"
 Bioassay for nucleotides. More...
 
static const char kBioAssayNucImg [] = "<img border=0 height=16 width=16 src=\"images/Bioassay.gif\" alt=\"PubChem BioAssay Info linked to <@label@>\">"
 
static const string kBioAssayDispl = "<div><@lnk@>-<span class=\"rlLink\">bioactivity screening</span></div>"
 
static const char kMapviwerUrl [] = "<a href=\"<@protocol@>//www.ncbi.nlm.nih.gov/mapview/map_search.cgi?direct=on&gbgi=<@gi@>&THE_BLAST_RID=<@rid@>&log$=map<@log@>&blast_rank=<@blast_rank@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>"
 mapviewer linkout More...
 
static const char kMapviwerImg [] = "<img border=0 height=16 width=16 src=\"images/M.gif\" alt=\"Genome view with mapviewer linked to <@label@>\">"
 
static const string kMapviwerDispl = "<div><@lnk@>-<span class=\"rlLink\">aligned genomic context</span></div>"
 
static const string kMapviewBlastHitUrl = "<@protocol@>//www.ncbi.nlm.nih.gov/mapview/maps.cgi?maps=blast_set"
 mapviewer linkout More...
 
static const string kMapviewBlastHitParams = "<a href=\"<@user_url@>&db=<@db@>&na=<@is_na@>&gnl=<@gnl@>&gi=<@gi@>&term=<@gi@>[gi]&taxid=<@taxid@>&RID=<@rid@>&QUERY_NUMBER=<@query_number@>&log$=nucl<@log@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>"
 
static const char kReprMicrobialGenomesUrl [] = "<a href=\"<@protocol@>//www.ncbi.nlm.nih.gov/genome?term=<@label@>[<@uid@>]&RID=<@rid@>&log$=map<@log@>&blast_rank=<@blast_rank@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>"
 Repr microbial Genome linkout. More...
 
static const char kReprMicrobialGenomesImg [] = "<img border=0 height=16 width=16 src=\"images/L.gif\" alt=\"View genome information for <@label@>\">"
 
static const string kReprMicrobialGenomesDispl = "<div><@lnk@>-<span class=\"rlLink\">Genomic Sequence</span></div>"
 
static const char kGenomeDataViewerNucUrl [] = "<span class=\"adNew\">New</span><a href=\"<@protocol@>//www.ncbi.nlm.nih.gov/genome/gdv/browser/?context=blast&id=<@label@>&alignid=<@queryID@>&from=<@from@>&to=<@to@>&rid=<@rid@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>"
 
static const char kGenomeDataViewerProtUrl [] = "<span class=\"adNew\">New</span><a href=\"<@protocol@>//www.ncbi.nlm.nih.gov/genome/gdv/browser/?context=Protein&acc=<@label@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>"
 
static const char kGenomeDataViewerNuclTranscriptUrl [] = "<span class=\"adNew\">New</span><a href=\"<@protocol@>//www.ncbi.nlm.nih.gov/genome/gdv/browser/?context=nucleotide&acc=<@label@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>"
 
static const char kGenomeDataViewerImg [] = "<div class=\"gdv\">V</div>"
 
static const string kGenomeDataViewerDispl = "<div><@lnk@>-<span class=\"rlLink\">aligned genomic context</span></div>"
 
static const char kIdenticalProteinsUrl [] = "<a href=\"<@protocol@>//www.ncbi.nlm.nih.gov/ipg/<@label@>\" title=\"View proteins identical to <@label@>\" <@lnkTarget@>><@lnk_displ@></a>"
 
static const string kIdenticalProteinsDispl = "<div><@lnk@>-<span class=\"rlLink\">Identical proteins to <@label@></span></div>"
 
static const char kDownloadUrl [] = "/blast/dumpgnl.cgi"
 dumpgnl More...
 
static const char kDownloadLink [] = "<a href=\"<@download_url@>&segs=<@segs@>\"><@lnk_displ@></a>"
 
static const char kDownloadImg [] = "<img border=0 height=16 width=16 src=\"images/D.gif\" alt=\"Download subject sequence <@label@> spanning the HSP\">"
 
static const char kSeqViewerUrl [] = "<@protocol@>//www.ncbi.nlm.nih.gov/<@dbtype@>/<@seqid@>?report=graph&rid=<@rid@>[<@seqid@>]&<@seqViewerParams@>&v=<@from@>:<@to@>&appname=ncbiblast&link_loc=<@link_loc@>"
 
static const string kSeqViewerParams = "tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other alignments,annots:NG Alignments|Refseq Alignments|Gnomon Alignments|Unnamed,shown:false]"
 
static const char kSeqViewerUrlNonGi [] = "<@protocol@>//www.ncbi.nlm.nih.gov/projects/sviewer/?RID=<@rid@>&id=<@firstSeqID@>&<@seqViewerParams@>&v=<@from@>:<@to@>&appname=ncbiblast&link_loc=<@link_loc@>"
 
static const char kCustomLinkTemplate [] = "<a href=\"<@custom_url@>\" class=\"<@custom_cls@>\" target=\"<@custom_trg@>\" title=\"<@custom_title@>\"><@custom_lnk_displ@></a>"
 
static const char kCustomLinkTitle [] ="Show <@custom_report_type@> report for <@seqid@>"
 
static const char kGenericLinkTemplate [] = "<a title=\"Show report for <@seqid@>\" href=\"<@url@>\" ><@seqid@></a>"
 
static const char kGenericLinkMouseoverTmpl [] = "<span class=\"jig-ncbipopper\" data-jigconfig=\"destText:'<@defline@>'\"><a onclick=\"window.open(this.href,'<@target@>')\" href=\"<@url@>\" ><@seqid@></a></span>"
 
static const char kEntrezSubseqUrl [] = "<a href=\"<@protocol@>//www.ncbi.nlm.nih.gov/<@db@>/<@gi@>?report=gbwithparts&from=<@from@>&to=<@to@>&RID=<@rid@>\">"
 Sub-sequence. More...
 
static const char kEntrezSubseqTMUrl [] = "<@protocol@>//www.ncbi.nlm.nih.gov/<@db@>/<@gi@>?report=gbwithparts&from=<@from@>&to=<@to@>&RID=<@rid@>"
 
static const char kLinkoutOrderStr [] = "G,U,E,S,B,R,M,V,T"
 Default linkout order. More...
 
static const char kBl2seqUrl [] = "<a href=\"blast.ncbi.nlm.nih.gov/Blast.cgi?QUERY=<@query@>&SUBJECTS=<@subject@>&PROGRAM=tblastx&EXPECT=10&CMD=request&SHOW_OVERVIEW=on&OLD_BLAST=false&NEW_VIEW=on\">Get TBLASTX alignments</a>"
 
static const char k_GetSeqSubmitForm_0 []
 
static const char k_GetSeqSubmitForm_1 []
 
static const char k_GetSeqSelectForm []
 
static const char k_GetTreeViewForm []
 
static const char kGeneInfoUrl []
 
static const char kGetTreeViewCgi [] = "<@protocol@>//www.ncbi.nlm.nih.gov/blast/treeview/blast_tree_view.cgi"
 
static const char kEntrezQueryCgi [] = "<@protocol@>//www.ncbi.nlm.nih.gov/entrez/query.fcgi"
 
static const char kTraceCgi [] = "<@protocol@>//www.ncbi.nlm.nih.gov/Traces/trace.cgi"
 
static const char kMapSearchCgi [] = "<@protocol@>//www.ncbi.nlm.nih.gov/mapview/map_search.cgi"
 
static const char kCBlastCgi [] = "<@protocol@>//www.ncbi.nlm.nih.gov/Structure/cblast/cblast.cgi"
 
static const char kEntrezViewerCgi [] = "<@protocol@>//www.ncbi.nlm.nih.gov/entrez/viewer.fcgi"
 
static const char kBl2SeqWBlastCgi [] = "<@protocol@>//www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi"
 
static const char kEntrezSitesCgi [] = "<@protocol@>//www.ncbi.nlm.nih.gov/sites/entrez"
 
static const TTagUrl s_TagUrls []
 
const int k_NumAsciiChar = 128
 Number of ASCII characters for populating matrix columns. More...
 
const char k_PSymbol []
 Residues. More...
 

Macro Definition Documentation

◆ DIM

#define DIM (   static_array)    (sizeof(static_array)/sizeof(*static_array))

Calculates the dimensions of a static array.

Definition at line 330 of file align_format_util.hpp.

Typedef Documentation

◆ TTagUrl

typedef SStaticPair<const char*, const char*> TTagUrl

create map source of all static URL's using previously defined pairs this map should be in alphabetical order!!!

Definition at line 285 of file align_format_util.hpp.

◆ TTagUrlMap

Definition at line 323 of file align_format_util.hpp.

Enumeration Type Documentation

◆ anonymous enum

anonymous enum

protein matrix define

Enumerator
ePMatrixSize 

Definition at line 334 of file align_format_util.hpp.

Function Documentation

◆ DEFINE_STATIC_ARRAY_MAP()

DEFINE_STATIC_ARRAY_MAP ( TTagUrlMap  ,
sm_TagUrlMap  ,
s_TagUrls   
)

Variable Documentation

◆ k_GetSeqSelectForm

const char k_GetSeqSelectForm[]
static
Initial value:
= "<FORM><input \
type=\"button\" value=\"Select all\" onClick=\"handleCheckAll('select', \
'getSeqAlignment%d', 'getSeqGi')\"></form></td><td><FORM><input \
type=\"button\" value=\"Deselect all\" onClick=\"handleCheckAll('deselect', \
'getSeqAlignment%d', 'getSeqGi')\"></form>"

Definition at line 248 of file align_format_util.hpp.

◆ k_GetSeqSubmitForm_0

const char k_GetSeqSubmitForm_0[]
static
Initial value:
= "<FORM method=\"post\" \
action=\"//www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?SUBMIT=y\" \
name=\"%s%d\"><input type=button value=\"Get selected sequences\" \
onClick=\"finalSubmit(%d, 'getSeqAlignment%d', 'getSeqGi', '%s%d', %d)\"><input \
type=\"hidden\" name=\"db\" value=\"\"><input type=\"hidden\" name=\"term\" \
value=\"\"><input type=\"hidden\" name=\"doptcmdl\" value=\"docsum\"><input \
type=\"hidden\" name=\"cmd\" value=\"search\"></form>"

Definition at line 232 of file align_format_util.hpp.

◆ k_GetSeqSubmitForm_1

const char k_GetSeqSubmitForm_1[]
static
Initial value:
= "<FORM method=\"POST\" \
action=\"//www.ncbi.nlm.nih.gov/Traces/trace.cgi\" \
name=\"%s%d\"><input type=button value=\"Get selected sequences\" \
onClick=\"finalSubmit(%d, 'getSeqAlignment%d', 'getSeqGi', '%s%d', %d)\"><input \
type=\"hidden\" name=\"val\" value=\"\"><input \
type=\"hidden\" name=\"cmd\" value=\"retrieve\"></form>"

Definition at line 239 of file align_format_util.hpp.

◆ k_GetTreeViewForm

const char k_GetTreeViewForm[]
static
Initial value:
= "<FORM method=\"post\" \
action=\"//www.ncbi.nlm.nih.gov/blast/treeview/blast_tree_view.cgi?request=page&rid=%s&queryID=%s&distmode=on\" \
name=\"tree%s%d\" target=\"trv%s\"> \
<input type=button value=\"Distance tree of results\" onClick=\"extractCheckedSeq('getSeqAlignment%d', 'getSeqGi', 'tree%s%d')\"> \
<input type=\"hidden\" name=\"sequenceSet\" value=\"\"><input type=\"hidden\" name=\"screenWidth\" value=\"\"></form>"

Definition at line 255 of file align_format_util.hpp.

◆ k_NumAsciiChar

const int k_NumAsciiChar = 128

Number of ASCII characters for populating matrix columns.

Definition at line 339 of file align_format_util.hpp.

Referenced by CAlignFormatUtil::GetAsciiProteinMatrix(), and CDisplaySeqalign::~CDisplaySeqalign().

◆ k_PSymbol

const char k_PSymbol[]
extern

Residues.

Definition at line 87 of file align_format_util.cpp.

Referenced by CAlignFormatUtil::GetAsciiProteinMatrix().

◆ kBioAssayDispl

const string kBioAssayDispl = "<div><@lnk@>-<span class=\"rlLink\">bioactivity screening</span></div>"
static

Definition at line 154 of file align_format_util.hpp.

Referenced by s_GetLinkoutUrl().

◆ kBioAssayNucImg

const char kBioAssayNucImg[] = "<img border=0 height=16 width=16 src=\"images/Bioassay.gif\" alt=\"PubChem BioAssay Info linked to <@label@>\">"
static

Definition at line 151 of file align_format_util.hpp.

Referenced by s_GetLinkoutUrl().

◆ kBioAssayNucURL

const char kBioAssayNucURL[] = "<a href=\"<@protocol@>//www.ncbi.nlm.nih.gov/entrez?db=pcassay&term=<@gi@>[RNATargetGI]&RID=<@rid@>&log$=pcassay<@log@>&blast_rank=<@blast_rank@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>"
static

Bioassay for nucleotides.

Definition at line 150 of file align_format_util.hpp.

◆ kBioAssayProtImg

const char kBioAssayProtImg[] = "<img border=0 height=16 width=16 src=\"images/Bioassay.gif\" alt=\"PubChem BioAssay Info linked to <@label@>\">"
static

Definition at line 146 of file align_format_util.hpp.

Referenced by s_GetLinkoutUrl().

◆ kBioAssayProtURL

const char kBioAssayProtURL[] = "<a href=\"<@protocol@>//www.ncbi.nlm.nih.gov/entrez?db=pcassay&term=<@gi@>[PigGI]&RID=<@rid@>&log$=pcassay<@log@>&blast_rank=<@blast_rank@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>"
static

Bioassay for proteins.

Definition at line 144 of file align_format_util.hpp.

◆ kBl2seqUrl

const char kBl2seqUrl[] = "<a href=\"blast.ncbi.nlm.nih.gov/Blast.cgi?QUERY=<@query@>&SUBJECTS=<@subject@>&PROGRAM=tblastx&EXPECT=10&CMD=request&SHOW_OVERVIEW=on&OLD_BLAST=false&NEW_VIEW=on\">Get TBLASTX alignments</a>"
static

Definition at line 226 of file align_format_util.hpp.

Referenced by CDisplaySeqalign::x_DisplayBl2SeqLink().

◆ kBl2SeqWBlastCgi

const char kBl2SeqWBlastCgi[] = "<@protocol@>//www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi"
static

Definition at line 278 of file align_format_util.hpp.

◆ kCBlastCgi

const char kCBlastCgi[] = "<@protocol@>//www.ncbi.nlm.nih.gov/Structure/cblast/cblast.cgi"
static

Definition at line 274 of file align_format_util.hpp.

◆ kClassInfo

const char kClassInfo[] = "class=\"info\""
static

blast related url

class info

Definition at line 66 of file align_format_util.hpp.

◆ kCustomLinkTemplate

const char kCustomLinkTemplate[] = "<a href=\"<@custom_url@>\" class=\"<@custom_cls@>\" target=\"<@custom_trg@>\" title=\"<@custom_title@>\"><@custom_lnk_displ@></a>"
static

Definition at line 205 of file align_format_util.hpp.

Referenced by s_MapCustomLink().

◆ kCustomLinkTitle

const char kCustomLinkTitle[] ="Show <@custom_report_type@> report for <@seqid@>"
static

Definition at line 206 of file align_format_util.hpp.

Referenced by CAlignFormatUtil::GetGiLinksList().

◆ kDefaultProtocol

const char kDefaultProtocol[] = "https:"
static

Definition at line 68 of file align_format_util.hpp.

◆ kDownloadImg

const char kDownloadImg[] = "<img border=0 height=16 width=16 src=\"images/D.gif\" alt=\"Download subject sequence <@label@> spanning the HSP\">"
static

Definition at line 195 of file align_format_util.hpp.

Referenced by CDisplaySeqalign::x_GetDumpgnlLink().

◆ kDownloadLink

const char kDownloadLink[] = "<a href=\"<@download_url@>&segs=<@segs@>\"><@lnk_displ@></a>"
static

Definition at line 193 of file align_format_util.hpp.

Referenced by CDisplaySeqalign::x_GetDumpgnlLink().

◆ kDownloadUrl

const char kDownloadUrl[] = "/blast/dumpgnl.cgi"
static

◆ kEntrezQueryCgi

const char kEntrezQueryCgi[] = "<@protocol@>//www.ncbi.nlm.nih.gov/entrez/query.fcgi"
static

Definition at line 268 of file align_format_util.hpp.

◆ kEntrezSitesCgi

const char kEntrezSitesCgi[] = "<@protocol@>//www.ncbi.nlm.nih.gov/sites/entrez"
static

Definition at line 280 of file align_format_util.hpp.

◆ kEntrezSubseqTMUrl

const char kEntrezSubseqTMUrl[] = "<@protocol@>//www.ncbi.nlm.nih.gov/<@db@>/<@gi@>?report=gbwithparts&from=<@from@>&to=<@to@>&RID=<@rid@>"
static

Definition at line 218 of file align_format_util.hpp.

◆ kEntrezSubseqUrl

const char kEntrezSubseqUrl[] = "<a href=\"<@protocol@>//www.ncbi.nlm.nih.gov/<@db@>/<@gi@>?report=gbwithparts&from=<@from@>&to=<@to@>&RID=<@rid@>\">"
static

Sub-sequence.

Definition at line 215 of file align_format_util.hpp.

◆ kEntrezTMUrl

const char kEntrezTMUrl[] = "<@protocol@>//www.ncbi.nlm.nih.gov/<@db@>/<@acc@>?report=genbank&log$=<@log@>&blast_rank=<@blast_rank@>&RID=<@rid@>"
static

Definition at line 74 of file align_format_util.hpp.

Referenced by CAlignFormatUtil::GetGiLinksList().

◆ kEntrezUrl

const char kEntrezUrl[] = "<a title=\"Show report for <@acc@>\" <@cssInf@>href=\"<@protocol@>//www.ncbi.nlm.nih.gov/<@db@>/<@acc@>?report=genbank&log$=<@log@>&blast_rank=<@blast_rank@>&RID=<@rid@>\" <@target@>>"
static

entrez

Definition at line 71 of file align_format_util.hpp.

◆ kEntrezViewerCgi

const char kEntrezViewerCgi[] = "<@protocol@>//www.ncbi.nlm.nih.gov/entrez/viewer.fcgi"
static

Definition at line 276 of file align_format_util.hpp.

◆ kGeneDispl

const string kGeneDispl = "<div><@lnk@>-<span class=\"rlLink\">associated gene details</span></div>"
static

Definition at line 140 of file align_format_util.hpp.

Referenced by s_GetLinkoutUrl().

◆ kGeneImg

const char kGeneImg[] = "<img border=0 height=16 width=16 src=\"images/G.gif\" alt=\"Gene info linked to <@label@>\">"
static

Definition at line 138 of file align_format_util.hpp.

Referenced by s_GetLinkoutUrl().

◆ kGeneInfoUrl

const char kGeneInfoUrl[]
static
Initial value:
=
"<@protocol@>//www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=%d&RID=%s&log$=geneexplicit%s&blast_rank=%d"

Definition at line 262 of file align_format_util.hpp.

◆ kGenericLinkMouseoverTmpl

const char kGenericLinkMouseoverTmpl[] = "<span class=\"jig-ncbipopper\" data-jigconfig=\"destText:'<@defline@>'\"><a onclick=\"window.open(this.href,'<@target@>')\" href=\"<@url@>\" ><@seqid@></a></span>"
static

Definition at line 209 of file align_format_util.hpp.

Referenced by CAlignFormatUtil::GetFullIDLink().

◆ kGenericLinkTemplate

const char kGenericLinkTemplate[] = "<a title=\"Show report for <@seqid@>\" href=\"<@url@>\" ><@seqid@></a>"
static

Definition at line 208 of file align_format_util.hpp.

Referenced by CAlignFormatUtil::GetFullIDLink().

◆ kGeneTerm

const char kGeneTerm[] = "term=<@label@><@uid@>&"
static

Definition at line 136 of file align_format_util.hpp.

Referenced by s_GetLinkoutUrl().

◆ kGeneUrl

const char kGeneUrl[]
static
Initial value:
= "<a class=\"gene\" term=\"<@uid@>\" href=\"<@protocol@>//www.ncbi.nlm.nih.gov/gene?<@termParam@>RID=<@rid@>&log$=gene<@log@>&blast_rank=<@blast_rank@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>\
<input type=\"hidden\" value=\"<@label@>\" />"

Gene.

Definition at line 134 of file align_format_util.hpp.

◆ kGenomeButton

const char kGenomeButton[]
static
Initial value:
= "<table border=0 width=600 cellpadding=8>\
<tr valign=\"top\"><td><a href=\
\"//www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=%d&RID=%s&CLIENT=\
%s&QUERY_NUMBER=%d\"><img border=0 src=\"html/GenomeView.gif\"></a></td>\
<td>Show positions of the BLAST hits in the %s genome \
using the Entrez Genomes MapViewer</td></tr></table><p>"

genome button

Definition at line 87 of file align_format_util.hpp.

◆ kGenomeDataViewerDispl

const string kGenomeDataViewerDispl = "<div><@lnk@>-<span class=\"rlLink\">aligned genomic context</span></div>"
static

Definition at line 185 of file align_format_util.hpp.

Referenced by s_GetLinkoutUrl().

◆ kGenomeDataViewerImg

const char kGenomeDataViewerImg[] = "<div class=\"gdv\">V</div>"
static

Definition at line 183 of file align_format_util.hpp.

Referenced by s_GetLinkoutUrl().

◆ kGenomeDataViewerNuclTranscriptUrl

const char kGenomeDataViewerNuclTranscriptUrl[] = "<span class=\"adNew\">New</span><a href=\"<@protocol@>//www.ncbi.nlm.nih.gov/genome/gdv/browser/?context=nucleotide&acc=<@label@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>"
static

Definition at line 181 of file align_format_util.hpp.

◆ kGenomeDataViewerNucUrl

const char kGenomeDataViewerNucUrl[] = "<span class=\"adNew\">New</span><a href=\"<@protocol@>//www.ncbi.nlm.nih.gov/genome/gdv/browser/?context=blast&id=<@label@>&alignid=<@queryID@>&from=<@from@>&to=<@to@>&rid=<@rid@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>"
static

Definition at line 179 of file align_format_util.hpp.

◆ kGenomeDataViewerProtUrl

const char kGenomeDataViewerProtUrl[] = "<span class=\"adNew\">New</span><a href=\"<@protocol@>//www.ncbi.nlm.nih.gov/genome/gdv/browser/?context=Protein&acc=<@label@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>"
static

Definition at line 180 of file align_format_util.hpp.

◆ kGeoDispl

const string kGeoDispl = "<div><@lnk@>-<span class=\"rlLink\">microarray expression data</span></div>"
static

Definition at line 129 of file align_format_util.hpp.

Referenced by s_GetLinkoutUrl().

◆ kGeoImg

const char kGeoImg[] = "<img border=0 height=16 width=16 src=\"images/E.gif\" alt=\"GEO profiles info linked to <@label@>\">"
static

Definition at line 127 of file align_format_util.hpp.

Referenced by s_GetLinkoutUrl().

◆ kGeoUrl

const char kGeoUrl[] = "<a href=\"<@protocol@>//www.ncbi.nlm.nih.gov/geoprofiles/?term=genbank[Platform+Reporter+Type]+AND+<@label@>[Reporter+Identifier]&RID=<@rid@>&log$=geo<@log@>&blast_rank=<@blast_rank@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>"
static

Geo.

Definition at line 123 of file align_format_util.hpp.

◆ kGetTreeViewCgi

const char kGetTreeViewCgi[] = "<@protocol@>//www.ncbi.nlm.nih.gov/blast/treeview/blast_tree_view.cgi"
static

Definition at line 266 of file align_format_util.hpp.

◆ kIdenticalProteinsDispl

const string kIdenticalProteinsDispl = "<div><@lnk@>-<span class=\"rlLink\">Identical proteins to <@label@></span></div>"
static

Definition at line 188 of file align_format_util.hpp.

Referenced by s_AddOtherRelatedInfoLinks().

◆ kIdenticalProteinsUrl

const char kIdenticalProteinsUrl[] = "<a href=\"<@protocol@>//www.ncbi.nlm.nih.gov/ipg/<@label@>\" title=\"View proteins identical to <@label@>\" <@lnkTarget@>><@lnk_displ@></a>"
static

Definition at line 187 of file align_format_util.hpp.

Referenced by s_AddOtherRelatedInfoLinks().

◆ kLinkoutOrderStr

const char kLinkoutOrderStr[] = "G,U,E,S,B,R,M,V,T"
static

◆ kMapSearchCgi

const char kMapSearchCgi[] = "<@protocol@>//www.ncbi.nlm.nih.gov/mapview/map_search.cgi"
static

Definition at line 272 of file align_format_util.hpp.

◆ kMapviewBlastHitParams

const string kMapviewBlastHitParams = "<a href=\"<@user_url@>&db=<@db@>&na=<@is_na@>&gnl=<@gnl@>&gi=<@gi@>&term=<@gi@>[gi]&taxid=<@taxid@>&RID=<@rid@>&QUERY_NUMBER=<@query_number@>&log$=nucl<@log@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>"
static

Definition at line 167 of file align_format_util.hpp.

Referenced by s_GetLinkoutUrl().

◆ kMapviewBlastHitUrl

const string kMapviewBlastHitUrl = "<@protocol@>//www.ncbi.nlm.nih.gov/mapview/maps.cgi?maps=blast_set"
static

mapviewer linkout

Definition at line 166 of file align_format_util.hpp.

Referenced by s_GetLinkoutUrl().

◆ kMapviwerDispl

const string kMapviwerDispl = "<div><@lnk@>-<span class=\"rlLink\">aligned genomic context</span></div>"
static

Definition at line 162 of file align_format_util.hpp.

Referenced by s_GetLinkoutUrl().

◆ kMapviwerImg

const char kMapviwerImg[] = "<img border=0 height=16 width=16 src=\"images/M.gif\" alt=\"Genome view with mapviewer linked to <@label@>\">"
static

Definition at line 160 of file align_format_util.hpp.

Referenced by s_GetLinkoutUrl().

◆ kMapviwerUrl

const char kMapviwerUrl[] = "<a href=\"<@protocol@>//www.ncbi.nlm.nih.gov/mapview/map_search.cgi?direct=on&gbgi=<@gi@>&THE_BLAST_RID=<@rid@>&log$=map<@log@>&blast_rank=<@blast_rank@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>"
static

mapviewer linkout

Definition at line 158 of file align_format_util.hpp.

Referenced by s_GetLinkoutUrl().

◆ kReprMicrobialGenomesDispl

const string kReprMicrobialGenomesDispl = "<div><@lnk@>-<span class=\"rlLink\">Genomic Sequence</span></div>"
static

Definition at line 176 of file align_format_util.hpp.

Referenced by s_GetLinkoutUrl().

◆ kReprMicrobialGenomesImg

const char kReprMicrobialGenomesImg[] = "<img border=0 height=16 width=16 src=\"images/L.gif\" alt=\"View genome information for <@label@>\">"
static

Definition at line 174 of file align_format_util.hpp.

Referenced by s_GetLinkoutUrl().

◆ kReprMicrobialGenomesUrl

const char kReprMicrobialGenomesUrl[] = "<a href=\"<@protocol@>//www.ncbi.nlm.nih.gov/genome?term=<@label@>[<@uid@>]&RID=<@rid@>&log$=map<@log@>&blast_rank=<@blast_rank@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>"
static

Repr microbial Genome linkout.

Definition at line 172 of file align_format_util.hpp.

◆ kSeqViewerParams

const string kSeqViewerParams = "tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other alignments,annots:NG Alignments|Refseq Alignments|Gnomon Alignments|Unnamed,shown:false]"
static

Definition at line 198 of file align_format_util.hpp.

Referenced by CAlignFormatUtil::GetGraphiscLink().

◆ kSeqViewerUrl

const char kSeqViewerUrl[] = "<@protocol@>//www.ncbi.nlm.nih.gov/<@dbtype@>/<@seqid@>?report=graph&rid=<@rid@>[<@seqid@>]&<@seqViewerParams@>&v=<@from@>:<@to@>&appname=ncbiblast&link_loc=<@link_loc@>"
static

Definition at line 197 of file align_format_util.hpp.

Referenced by CAlignFormatUtil::GetGraphiscLink().

◆ kSeqViewerUrlNonGi

const char kSeqViewerUrlNonGi[] = "<@protocol@>//www.ncbi.nlm.nih.gov/projects/sviewer/?RID=<@rid@>&id=<@firstSeqID@>&<@seqViewerParams@>&v=<@from@>:<@to@>&appname=ncbiblast&link_loc=<@link_loc@>"
static

Definition at line 200 of file align_format_util.hpp.

Referenced by CAlignFormatUtil::GetGraphiscLink().

◆ kStructure_Overview

const char kStructure_Overview[]
static
Initial value:
= "<a href=\"<@protocol@>//www.ncbi.nlm.nih.\
gov/Structure/cblast/cblast.cgi?blast_RID=%s&blast_rep_gi=%d&hit=%d&%s\
&blast_view=%s&hsp=0&taxname=%s&client=blast\">Related Structures</a>"

structure overview

Definition at line 116 of file align_format_util.hpp.

Referenced by s_DisplayStructureOverview().

◆ kStructureAlphaFoldUrl

const char kStructureAlphaFoldUrl[] = "<a href=\"<@protocol@>//www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?from=blast&blast_rep_id=<@label@>&query_id=<@queryID@>&command=view+annotations;set+annotation+cdd;set+annotation+site;set+view+detailed+view;select+chain+!A;show+selection&log$=<@log@>&blast_rank=<@blast_rank@>&RID=<@rid@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>"
static

Definition at line 107 of file align_format_util.hpp.

Referenced by s_GetLinkoutUrl().

◆ kStructureDispl

const string kStructureDispl = "<div><@lnk@>-<span class=\"rlLink\">3D structure displays</span></div>"
static

Definition at line 113 of file align_format_util.hpp.

Referenced by s_GetLinkoutUrl().

◆ kStructureImg

const char kStructureImg[] = "<img border=0 height=16 width=16 src=\"<@protocol@>//www.ncbi.nlm.nih.gov/Structure/cblast/str_link.gif\" alt=\"Structure related to <@label@>\">"
static

Definition at line 111 of file align_format_util.hpp.

Referenced by s_GetLinkoutUrl().

◆ kStructureUrl

const char kStructureUrl[] = "<a href=\"<@protocol@>//www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?from=blast&blast_rep_id=<@label@>&query_id=<@queryID@>&command=view+annotations;set+annotation+cdd;set+annotation+site;set+view+detailed+view;select+chain+<@label@>;show+selection&log$=<@log@>&blast_rank=<@blast_rank@>&RID=<@rid@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>"
static

structure

Definition at line 106 of file align_format_util.hpp.

Referenced by s_GetLinkoutUrl().

◆ kTraceCgi

const char kTraceCgi[] = "<@protocol@>//www.ncbi.nlm.nih.gov/Traces/trace.cgi"
static

Definition at line 270 of file align_format_util.hpp.

◆ kTraceUrl

const char kTraceUrl[] = "<a title=\"Show report for <@val@>\" <@cssInf@>href=\"<@protocol@>//www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=retrieve&dopt=fasta&val=<@val@>&RID=<@rid@>\">"
static

trace db

Definition at line 83 of file align_format_util.hpp.

◆ kUnigeneDispl

const string kUnigeneDispl = "<div><@lnk@>-<span class=\"rlLink\">clustered expressed sequence tags</span></div>"
static

Definition at line 102 of file align_format_util.hpp.

Referenced by s_GetLinkoutUrl().

◆ kUnigeneImg

const char kUnigeneImg[] = "<img border=0 height=16 width=16 src=\"images/U.gif\" alt=\"UniGene info linked to <@label@>\">"
static

Definition at line 100 of file align_format_util.hpp.

Referenced by s_GetLinkoutUrl().

◆ kUnigeneUrl

const char kUnigeneUrl[]
static
Initial value:
= "<a class=\"gene\" term=\"<@uid@>\" href=\"<@protocol@>//www.ncbi.nlm.nih.gov/unigene/?<@termParam@>RID=<@rid@>&log$=unigene<@log@>&blast_rank=<@blast_rank@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>\
<input type=\"hidden\" value=\"<@label@>\" />"

unigene

Definition at line 96 of file align_format_util.hpp.

◆ kWGSUrl

const char kWGSUrl[] = "<@protocol@>//www.ncbi.nlm.nih.gov/nuccore/<@wgsacc@>"
static

Definition at line 77 of file align_format_util.hpp.

◆ s_TagUrls

const TTagUrl s_TagUrls[]
static

Definition at line 286 of file align_format_util.hpp.

Modified on Tue Jul 23 17:57:26 2024 by modify_doxy.py rev. 669887