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USING_SCOPE (ncbi) USING_SCOPE (objects) MAKE_CONST_MAP (kMapTagToURL, ct::tagStrNocase, ct::tagStrNocase, { { "BL2SEQ_WBLAST_CGI", "<@protocol@>//www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi" }, { "CBLAST_CGI", "<@protocol@>//www.ncbi.nlm.nih.gov/Structure/cblast/cblast.cgi" }, { "DOWNLOAD_CGI","/blast/dumpgnl.cgi"}, { "ENTREZ_QUERY_CGI", "<@protocol@>//www.ncbi.nlm.nih.gov/entrez/query.fcgi" }, { "ENTREZ_SITES_CGI", "<@protocol@>//www.ncbi.nlm.nih.gov/sites/entrez" }, { "ENTREZ_SUBSEQ_TM", "<@protocol@>//www.ncbi.nlm.nih.gov/<@db@>/<@gi@>?report=gbwithparts&from=<@from@>&to=<@to@>&RID=<@rid@>" }, { "ENTREZ_TM", "<@protocol@>//www.ncbi.nlm.nih.gov/<@db@>/<@acc@>?report=genbank&log$=<@log@>&blast_rank=<@blast_rank@>&RID=<@rid@>" }, { "ENTREZ_VIEWER_CGI", "<@protocol@>//www.ncbi.nlm.nih.gov/entrez/viewer.fcgi" }, { "GENE_INFO", "<@protocol@>//www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=%d&RID=%s&log$=geneexplicit%s&blast_rank=%d" }, { "MAP_SEARCH_CGI", "<@protocol@>//www.ncbi.nlm.nih.gov/mapview/map_search.cgi" }, { "MAPVIEWER_CGI", "https://www.ncbi.nlm.nih.gov/mapview/maps.cgi?maps=blast_set" }, {"SEQVIEW_URL","https://www.ncbi.nlm.nih.gov/<@dbtype@>/<@seqid@>?report=graph&rid=<@rid@>[<@seqid@>]&"}, {"SEQVIEW_URL_NON_GI","https://www.ncbi.nlm.nih.gov/projects/sviewer/?RID=<@rid@>&id=<@firstSeqID@>&"}, { "TRACE_CGI", "<@protocol@>//www.ncbi.nlm.nih.gov/Traces/trace.cgi" }, { "TREEVIEW_CGI", "<@protocol@>//www.ncbi.nlm.nih.gov/blast/treeview/blast_tree_view.cgi"}, { "WGS", "<@protocol@>//www.ncbi.nlm.nih.gov/nuccore/<@wgsacc@>" }, }) MAKE_CONST_MAP (kMapTagToHTML, ct::tagStrNocase, ct::tagStrNocase, { { "BIOASSAY_NUC", "<a href=\"https://www.ncbi.nlm.nih.gov/entrez?db=pcassay&term=<@gi@>[RNATargetGI]&RID=<@rid@>&log$=pcassay<@log@>&blast_rank=<@blast_rank@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>"}, { "BIOASSAY_PROT", "<a href=\"https://www.ncbi.nlm.nih.gov/entrez?db=pcassay&term=<@gi@>[PigGI]&RID=<@rid@>&log$=pcassay<@log@>&blast_rank=<@blast_rank@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>"}, { "BIOASSAY_IMG", "<img border=0 height=16 width=16 src=\"images/Bioassay.gif\" alt=\"PubChem BioAssay Info linked to <@label@>\">"}, { "BIOASSAY_DISPL", "<div><@lnk@>-<span class=\"rlLink\">bioactivity screening</span></div>" }, { "GENE", "<a class=\"gene\" term=\"<@uid@>\" href=\"https://www.ncbi.nlm.nih.gov/gene?<@termParam@>RID=<@rid@>&log$=gene<@log@>&blast_rank=<@blast_rank@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a><input type=\"hidden\" value=\"<@label@>\" />"}, { "GENE_IMG", "<img border=0 height=16 width=16 src=\"images/G.gif\" alt=\"Gene info linked to <@label@>\">"}, { "GENE_DISPL","<div><@lnk@>-<span class=\"rlLink\">associated gene details</span></div>" }, { "GENE_TERM", "term=<@label@><@uid@>&"}, { "GENOME_DATA_VIEWER_NUC", "<span class=\"adNew\">New</span><a href=\"https://www.ncbi.nlm.nih.gov/genome/gdv/browser/?context=blast&id=<@label@>&alignid=<@queryID@>&from=<@from@>&to=<@to@>&rid=<@rid@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>"}, { "GENOME_DATA_VIEWER_PROT", "<span class=\"adNew\">New</span><a href=\"https://www.ncbi.nlm.nih.gov/genome/gdv/browser/?context=Protein&acc=<@label@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>" }, { "GENOME_DATA_VIEWER_TRANSCR", "<span class=\"adNew\">New</span><a href=\"https://www.ncbi.nlm.nih.gov/genome/gdv/browser/?context=nucleotide&acc=<@label@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>" }, { "GENOME_DATA_VIEWER_IMG", "<div class=\"gdv\">V</div>" }, { "GENOME_DATA_VIEWER_DISPL", "<div><@lnk@>-<span class=\"rlLink\">aligned genomic context</span></div>" }, { "GEO", "<a href=\"https://www.ncbi.nlm.nih.gov/geoprofiles/?term=genbank[Platform+Reporter+Type]+AND+<@label@>[Reporter+Identifier]&RID=<@rid@>&log$=geo<@log@>&blast_rank=<@blast_rank@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>" }, { "GEO_IMG", "<img border=0 height=16 width=16 src=\"images/E.gif\" alt=\"GEO profiles info linked to <@label@>\">"}, { "GEO_DISPL", "<div><@lnk@>-<span class=\"rlLink\">microarray expression data</span></div>"}, { "MAPVIEWER", "<a href=\"https://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?direct=on&gbgi=<@gi@>&THE_BLAST_RID=<@rid@>&log$=map<@log@>&blast_rank=<@blast_rank@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>" }, { "MAPVIEWER_GENOME", "<a href=\"<@user_url@>&db=<@db@>&na=<@is_na@>&gnl=<@gnl@>&gi=<@gi@>&term=<@gi@>[gi]&taxid=<@taxid@>&RID=<@rid@>&QUERY_NUMBER=<@query_number@>&log$=nucl<@log@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>" }, { "MAPVIEWER_IMG", "<img border=0 height=16 width=16 src=\"images/M.gif\" alt=\"Genome view with mapviewer linked to <@label@>\">" }, { "MAPVIEWER_DISPL", "<div><@lnk@>-<span class=\"rlLink\">aligned genomic context</span></div>" }, { "REPR_MICROBIAL_GENOMES", "<a href=\"https://www.ncbi.nlm.nih.gov/genome?term=<@label@>[<@uid@>]&RID=<@rid@>&log$=map<@log@>&blast_rank=<@blast_rank@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>"}, { "REPR_MICROBIAL_GENOMES_IMG", "<img border=0 height=16 width=16 src=\"images/L.gif\" alt=\"View genome information for <@label@>\">"}, { "REPR_MICROBIAL_GENOMES_DISPL", "<div><@lnk@>-<span class=\"rlLink\">Genomic Sequence</span></div>"}, { "STRUCTURE_URL", "<a href=\"https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?from=blast&blast_rep_id=<@label@>&query_id=<@queryID@>&command=view+annotations;set+annotation+cdd;set+annotation+site;set+view+detailed+view;select+chain+<@label@>;show+selection&log$=<@log@>&blast_rank=<@blast_rank@>&RID=<@rid@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>" }, { "STRUCTURE_SINGLE_CHAIN_URL", "<a href=\"https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=5FN2&command=select%20sets%20!<@chainID@>;%20show%20selection\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>" }, { "STRUCTURE_IMG", "<img border=0 height=16 width=16 src=\"https://www.ncbi.nlm.nih.gov/Structure/cblast/str_link.gif\" alt=\"Structure related to <@label@>\">" }, { "STRUCTURE_DISPL", "<div><@lnk@>-<span class=\"rlLink\">3D structure displays</span></div>" }, { "STRUCTURE_ALPHA_FOLD", "<a href=\"https://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$=<@log@>&blast_rank=<@blast_rank@>&RID=<@rid@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>" }, { "STRUCTURE_ALPHA_FOLD_NO_RID", "<a href=\"https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?from=blast&blast_rep_id=<@label@>&query_id=<@label@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a>" }, { "UNIGEN", "<a class=\"gene\" term=\"<@uid@>\" href=\"https://www.ncbi.nlm.nih.gov/unigene/?<@termParam@>RID=<@rid@>&log$=unigene<@log@>&blast_rank=<@blast_rank@>\"<@lnkTitle@><@lnkTarget@>><@lnk_displ@></a><input type=\"hidden\" value=\"<@label@>\" />" }, { "UNIGEN_IMG", "<img border=0 height=16 width=16 src=\"images/U.gif\" alt=\"UniGene info linked to <@label@>\">" }, { "UNIGEN_DISPL", "<div><@lnk@>-<span class=\"rlLink\">clustered expressed sequence tags</span></div>" }, { "BL2SEQ", "<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>" }, { "ENTREZ", "<a title=\"Show report for <@acc@>\" <@cssInf@>href=\"https://www.ncbi.nlm.nih.gov/<@db@>/<@acc@>?report=genbank&log$=<@log@>&blast_rank=<@blast_rank@>&RID=<@rid@>\" <@target@>>" }, { "ENTREZ_SUBSEQ", "<a href=\"https://www.ncbi.nlm.nih.gov/<@db@>/<@gi@>?report=gbwithparts&from=<@from@>&to=<@to@>&RID=<@rid@>\">" }, { "STRUCTURE_OVW", "<a href=\"https://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>" }, { "TRACE", "<a title=\"Show report for <@val@>\" <@cssInf@>href=\"https://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=retrieve&dopt=fasta&val=<@val@>&RID=<@rid@>\">" }, {"CUSTOM_LINK_TEMPLATE","<a href=\"<@custom_url@>\" class=\"<@custom_cls@>\" target=\"<@custom_trg@>\" title=\"<@custom_title@>\"><@custom_lnk_displ@></a>"}, {"CUSTOM_LINK_TITLE","Show <@custom_report_type@> report for <@seqid@>"}, {"GENERIC_LINK_TEMPLATE","<a title=\"Show report for <@seqid@>\" href=\"<@url@>\" ><@seqid@></a>"}, {"GENERIC_LINK_MOUSE_OVER","<span class=\"jig-ncbipopper\" data-jigconfig=\"destText:'<@defline@>'\"><a onclick=\"window.open(this.href,'<@target@>')\" href=\"<@url@>\" ><@seqid@></a></span>"}, {"DOWNLOAD_LINK", "<a href=\"<@download_url@>&segs=<@segs@>\"><@lnk_displ@></a>" }, {"DOWNLOAD_LINK_IMG", "<img border=0 height=16 width=16 src=\"images/D.gif\" alt=\"Download subject sequence <@label@> spanning the HSP\">" }, {"IDENTICAL_PROTEINS_URL","<a href=\"https://www.ncbi.nlm.nih.gov/ipg/<@label@>\" title=\"View proteins identical to <@label@>\" <@lnkTarget@>><@lnk_displ@></a>"}, {"IDENTICAL_PROTEINS_DISPL","<div><@lnk@>-<span class=\"rlLink\">Identical proteins to <@label@></span></div>"}, }) MAKE_CONST_MAP (kMapTagToString, ct::tagStrNocase, ct::tagStrNocase, { {"CLASS_INFO","class=\"info\""}, {"LINKOUT_ORDER","G,U,E,S,B,R,M,V,T"}, {"SEQVIEW_COMMON_PARAMS","<@seqViewerParams@>&v=<@from@>:<@to@>&appname=ncbiblast&link_loc=<@link_loc@>"}, {"SEQVIEW_PARAMS", "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]"}, }) template<class container > bool s_GetBlastScore (const container &scoreList, int &score, double &bits, double &evalue, int &sum_n, int &num_ident, list< TGi > &use_this_gi, int &comp_adj_method) Get blast score information. More...Definition at line 2673 of file align_format_util.cpp.
References CSeq_id::eContent, FindBestChoice(), CSeq_id::GetLabel(), CAlignFormatUtil::GetTextSeqID(), label, CAlignFormatUtil::MapTagToHTML(), CAlignFormatUtil::MapTemplate(), NStr::NumericToString(), s_MapLinkoutGenParam(), CSeq_id::WorstRank(), and ZERO_GI.
Referenced by s_GetFullLinkoutUrl().
◆ s_CalcAlnPercentIdent() ◆ s_FillDbInfoLocally()Initialize database statistics with data obtained from local BLAST databases.
Definition at line 376 of file align_format_util.cpp.
References dbname(), CSeqDB::eNucleotide, CSeqDB::eProtein, CSeqDB::GetDate(), CSeqDB::GetDBNameList(), CSeqDB::GetMaskAlgorithmDetails(), CSeqDB::GetNumSeqs(), CSeqDB::GetTitle(), CSeqDB::GetTotalLength(), and info.
Referenced by CAlignFormatUtil::GetBlastDbInfo().
◆ s_FixMinusStrandRange() ◆ s_GetBestIDForURL()Definition at line 1903 of file align_format_util.cpp.
References CSeq_id::AsFastaString(), CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Other, CConstRef< C, Locker >::Empty(), FindBestChoice(), GetSeq_idByType(), NULL, NStr::URLEncode(), CSeq_id_Base::Which(), and CSeq_id::WorstRank().
Referenced by CAlignFormatUtil::BuildUserUrl(), and s_GetFullLinkoutUrl().
◆ s_GetBlastScore() [1/2]template<class container >
bool s_GetBlastScore ( const container & scoreList, double & evalue, double & bitScore, double & totalBitScore, int & percentCoverage, double & percentIdent, int & hspNum, double & totalLen, int & rawScore, int & sum_n, list< TGi > & use_this_gi ) ◆ s_GetBlastScore() [2/2]template<class container >
bool s_GetBlastScore ( const container & scoreList, int & score, double & bits, double & evalue, int & sum_n, int & num_ident, list< TGi > & use_this_gi, int & comp_adj_method ) ◆ s_GetFullLinkoutUrl()Definition at line 2700 of file align_format_util.cpp.
References CAlignFormatUtil::SLinkoutInfo::cur_align, eBioAssay, eGenomeDataViewer, eGenomicSeq, eMapviewer, eTranscript, FindBestChoice(), FindGi(), CAlignFormatUtil::SLinkoutInfo::for_alignment, CAlignFormatUtil::GetLabel(), CAlignFormatUtil::SLinkoutInfo::gnl, i, CAlignFormatUtil::SLinkoutInfo::is_na, label, CAlignFormatUtil::SLinkoutInfo::linkoutOrder, NStr::NumericToString(), CAlignFormatUtil::SLinkoutInfo::rid, s_AddOtherRelatedInfoLinks(), s_GetBestIDForURL(), s_GetLinkoutUrl(), s_GetTaxName(), s_LinkLetterToType(), NStr::Split(), CAlignFormatUtil::SLinkoutInfo::taxid, CAlignFormatUtil::SLinkoutInfo::taxName, CSeq_id::WorstRank(), and ZERO_GI.
◆ s_GetLinkoutUrl()Definition at line 2227 of file align_format_util.cpp.
References CAlignFormatUtil::SLinkoutInfo::cur_align, CAlignFormatUtil::SLinkoutInfo::database, CSeq_id_Base::e_Pdb, eBioAssay, eGene, eGenomeDataViewer, eGenomicSeq, eGeo, eMapviewer, eReprMicrobialGenomes, eStructure, eTranscript, eUnigene, NStr::Find(), CAlignFormatUtil::SLinkoutInfo::for_alignment, CRange_Base::GetFrom(), CRange_Base::GetTo(), CAlignFormatUtil::GetURLDefault(), CAlignFormatUtil::SLinkoutInfo::gnl, NStr::IntToString(), CAlignFormatUtil::SLinkoutInfo::is_na, CAlignFormatUtil::MapTagToHTML(), CAlignFormatUtil::MapTemplate(), NPOS, NStr::NumericToString(), CAlignFormatUtil::SLinkoutInfo::query_number, CAlignFormatUtil::SLinkoutInfo::queryID, NStr::Replace(), CAlignFormatUtil::SLinkoutInfo::rid, s_MapLinkoutGenParam(), NStr::Split(), NStr::SplitInTwo(), CAlignFormatUtil::SLinkoutInfo::subjRange, CAlignFormatUtil::SLinkoutInfo::taxid, CAlignFormatUtil::SLinkoutInfo::taxName, NStr::URLEncode(), CAlignFormatUtil::SLinkoutInfo::user_url, CSeq_id_Base::Which(), ZERO_GI, and ZERO_TAX_ID.
Referenced by CAlignFormatUtil::GetLinkoutUrl(), and s_GetFullLinkoutUrl().
◆ s_GetSeqIdByType() ◆ s_GetSRASeqMetadata()Definition at line 1845 of file align_format_util.cpp.
References CDbtag_Base::CanGetDb(), CDbtag_Base::CanGetTag(), CSeq_id_Base::e_General, CConstRef< C, Locker >::Empty(), CSeq_id_Base::GetGeneral(), GetSeq_idByType(), CObject_id_Base::GetStr(), CDbtag_Base::GetTag(), CObject_id_Base::IsStr(), NcbiEmptyString, and NStr::Split().
Referenced by CAlignFormatUtil::BuildSRAUrl(), and s_MapURLLink().
◆ s_GetTaxName() ◆ s_isAlnInFilteringRange() static bool s_isAlnInFilteringRange ( double evalue, double percentIdent, int queryCover, double evalueLow, double evalueHigh, double percentIdentLow, double percentIdentHigh, int queryCoverLow, int queryCoverHigh ) static ◆ s_LinkLetterToType() ◆ s_MapCommonUrlParams() ◆ s_MapCustomLink() ◆ s_MapLinkoutGenParam() ◆ s_MapURLLink() ◆ s_MergeRangeList() ◆ s_NumGiToStringGiList() ◆ s_ProcessAlignSet() ◆ s_UseThisSeqToTextSeqID() ◆ USING_SCOPE() [1/2] ◆ USING_SCOPE() [2/2] ◆ k_PSymbol ◆ kScope ◆ kTranslationRetroSearch is an open source project built by @garambo | Open a GitHub Issue
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