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NCBI C++ ToolKit: include/objtools/align_format/align_format_util.hpp Source File

name = definition = date =

;

(

usurl,

bt,

isnuc,

db,

rid_in,

qn,

txid =

,

addCssInf =

,

seqSegs =

,

resUrl =

,

useTmpl =

,

advView =

)

: user_url(usurl),blastType(bt), isDbNa(isnuc),

(db),rid(rid_in),

queryNumber(qn), gi(gi_in), accession(acc), linkout(lnk),blast_rank(blrk),isAlignLink(alnLink),

new_win(nw),seqRange(range),flip(flp),taxid (txid),addCssInfo(addCssInf),segs(seqSegs),

resourcesUrl(resUrl),useTemplates(useTmpl),advancedView(advView){}

(

rid_in,

cdd_rid_in,

entrez_term_in,

is_na_in,

database_in,

query_number_in,

user_url_in,

preComputedResID_in,

linkoutOrder_in,

structure_linkout_as_group_in =

,

for_alignment_in =

) {

cdd_rid = cdd_rid_in;

entrez_term = entrez_term_in;

query_number = query_number_in;

user_url = user_url_in;

preComputedResID = preComputedResID_in;

linkoutOrder = linkoutOrder_in;

structure_linkout_as_group = structure_linkout_as_group_in;

for_alignment = for_alignment_in;

(

rid_in,

cdd_rid_in,

entrez_term_in,

is_na_in,

database_in,

query_number_in,

user_url_in,

preComputedResID_in,

linkoutOrder_in,

* linkoutdb_in,

mv_build_name_in,

structure_linkout_as_group_in =

,

for_alignment_in =

) {

(rid_in,cdd_rid_in,entrez_term_in,is_na_in,

database_in,query_number_in, user_url_in,preComputedResID_in,

structure_linkout_as_group_in, for_alignment_in);

linkoutdb = linkoutdb_in;

mv_build_name = mv_build_name_in;

eNonGenomicFirst = 1,

eLinkTypeDefault = 0,

eLinkTypeMapViewer = (1 << 0),

eLinkTypeSeqViewer = (1 << 1),

eDownLoadSeq = (1 << 2),

eLinkTypeGenLinks = (1 << 3),

eLinkTypeTraceLinks = (1 << 4),

eLinkTypeSRALinks = (1 << 5),

eLinkTypeSNPLinks = (1 << 6),

eLinkTypeGSFastaLinks = (1 << 7)

eSpacePosToCenter = (1 << 0),

eSpacePosAtLineStart = (1 << 1),

eSpacePosAtLineEnd = (1 << 2),

eAddEOLAtLineStart = (1 << 3),

eAddEOLAtLineEnd = (1 << 4)

BlastPrintError(list<SBlastError>& error_return,

PrintTildeSepLines(

,

line_len,

FillScanModeBlastDbInfo(vector<SDbInfo>& retval,

is_protein,

numSeqs,

numLetters,

&

);

GetBlastDbInfo(vector<SDbInfo>& retval,

& blastdb_names,

is_protein,

dbfilt_algorithm,

is_remote =

);

PrintDbReport(

vector<SDbInfo>& dbinfo_list,

PrintKAParameters(

,

k,

h,

GetSeqDescrString(

objects::CBioseq& cbs);

AcknowledgeBlastQuery(

objects::CBioseq& cbs,

line_len,

html,

tabular=

,

AcknowledgeBlastSubject(

objects::CBioseq& cbs,

line_len,

html,

tabular=

);

GetAsciiProteinMatrix(

* matrix_name,

x_AcknowledgeBlastSequence(

objects::CBioseq& cbs,

&

,

& rid

);

PrintPhiInfo(

num_patterns,

& pattern,

list<TGi>& use_this_gi);

list<string>& use_this_seq);

list<TGi>& use_this_gi,

& comp_adj_method);

list<string>& use_this_seq,

& comp_adj_method);

MatchSeqInUseThisSeqList(list<string> &use_this_seq,

textSeqIDToMatch);

IsGiList(list<string> &use_this_seq);

list<TGi> StringGiToNumGiList(list<string> &use_this_seq);

GetGnlID(

objects::CDbtag& dtg);

GetScoreString(

evalue,

total_bit_score,

& bit_score_str,

& total_bit_score_str,

& raw_score_str);

PruneSeqalign(

objects::CSeq_align_set& source_aln,

objects::CSeq_align_set& new_aln,

GetSubjectsNumber(

objects::CSeq_align_set& source_aln,

PruneSeqalignAll(

objects::CSeq_align_set& source_aln,

objects::CSeq_align_set& new_aln,

GetAlignLengths(objects::CAlnVec& salv,

& align_length,

& num_gaps,

& num_gap_opens);

ExtractSeqalignSetFromDiscSegs(objects::CSeq_align_set& target,

objects::CSeq_align_set&

);

GetTaxidForSeqid(

objects::CSeq_id&

, objects::CScope& scope);

GetFrame (

start,

strand,

objects::CBioseq_Handle& handle);

objects::CSeq_align_set&

);

BuildUserUrl(

objects::CBioseq::TId& ids,

taxid,

user_url,

,

db_is_na,

rid,

query_number,

for_alignment);

BuildSRAUrl(

objects::CBioseq::TId& ids,

user_url);

do_translation);

GetAlignmentLength(

objects::CSeq_align& aln,

do_translation);

do_translation);

SortHitByPercentIdentityDescendingEx

SortHspByPercentIdentityDescending

SortHitByScoreDescending

objects::CScope& scope,

* linkoutdb,

& mv_build_name);

do_translation, objects::CScope& scope,

sort_method,

* linkoutdb,

& mv_build_name);

objects::CSeq_align_set&

,

objects::CScope& scope,

& mv_build_name);

objects::CScope& scope,

objects::CSeq_align_set& aln_set,

nuc_to_nuc_translation,

& mv_build_name);

nuc_to_nuc_translation,

list< CRef<objects::CSeq_align_set> >

SortOneSeqalignForSortableFormat(

objects::CSeq_align_set&

,

nuc_to_nuc_translation,

GetPercentMatch(

numerator,

denominator);

GetPercentIdentity(

numerator,

denominator);

percentIdentLow,

percentIdentHigh);

percentIdentLow,

percentIdentHigh);

percentIdentLow,

percentIdentHigh,

queryCoverageLow,

queryCoverageHigh);

vector <string> &seqList);

RemoveSeqsOfAccessionTypeFromSeqInUse(list<string> &use_this_seq, objects::CSeq_id::EAccessionInfo accesionType);

objects::CScope& scope,

* linkoutdb,

& mv_build_name);

list<string> GetLinkoutUrl(

linkout,

objects::CBioseq::TId& ids,

& cdd_rid,

& entrez_term,

structure_linkout_as_group,

preComputedResID);

<

, vector < objects::CBioseq::TId > > &linkout_map,

& mv_build_name);

<

, vector <objects::CBioseq::TId > > &linkout_map,

& mv_build_name);

& cdd_rid,

& entrez_term,

structure_linkout_as_group,

& linkoutOrder,

&preComputedResID,

& mv_build_name);

& cdd_rid,

& entrez_term,

structure_linkout_as_group,

& linkoutOrder,

&preComputedResID,

& mv_build_name,

getIdentProteins);

GetSeqLinkoutInfo(objects::CBioseq::TId& cur_id,

& mv_build_name,

GetMasterCoverage(

objects::CSeq_align_set& alnset);

GetSeqAlignCoverageParams(

objects::CSeq_align_set& alnset,

*masterCoverage,

*flip);

GetURLFromRegistry(

url_name,

index = -1);

GetURLDefault(

url_name,

index = -1);

MapTemplate(

inpString,

tmplParamName,

templParamVal);

MapTemplate(

inpString,

tmplParamName,

templParamVal);

MapSpaceTemplate(

inpString,

tmplParamName,

templParamVal,

maxParamLength,

spacesFormatFlag = eSpacePosAtLineEnd);

MapTagToHTML(

tag_name);

MapTagToConstString(

tag_name,

flag = eMapToURL);

AddSpaces(

paramVal,

maxParamLength,

spacesFormatFlag = eSpacePosToCenter);

GetProtocol(

);

MapProtocol(

url_link);

objects::CSeq_id&

,

objects::CScope &scope);

objects::CBioseq::TId* ids);

GetFullIDLink(

*seqUrlInfo,

objects::CBioseq::TId* ids);

objects::CSeq_id&

,

objects::CScope &scope);

SetCustomLinksTypes(

*seqUrlInfo,

customLinkTypesInp);

list <string> GetCustomLinksList(

*seqUrlInfo,

objects::CSeq_id&

,

objects::CScope &scope,

customLinkTypes = eLinkTypeDefault);

list<string> GetGiLinksList(

*seqUrlInfo,

hspRange =

);

GetGraphiscLink(

*seqUrlInfo,

hspRange =

);

list<string> GetSeqLinksList(

*seqUrlInfo,

hspRange =

);

GetFASTALinkURL(

*seqUrlInfo,

objects::CSeq_id&

,

objects::CScope &scope);

GetAlignedRegionsURL(

*seqUrlInfo,

objects::CSeq_id&

,

objects::CScope &scope);

objects::CScope & scope);

GetSeqAlignSetCalcPercentIdent(

objects::CSeq_align_set& aln,

do_translation);

objects::CSeq_id& aln_id,

list<TGi>& use_this_gi,

objects::CSeq_id& aln_id,

list<TGi>& use_this_gi,

objects::CSeq_id& aln_id,

list<TGi>& use_this_gi);

objects::CSeq_id& aln_id,

list<string>& use_this_seq,

*textSeqID =

);

(

&accession,

&wgsProj);

IsWGSPattern(

&wgsAccession);

unique_ptr<CNcbiRegistry>

;

GetUniqSeqCoverage(objects::CSeq_align_set & alnset);

(

objects::CBioseq_Handle & bh);

(

objects::CSeq_id&

);

x_WrapOutputLine(

,

line_len,

html =

);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

const int k_NumAsciiChar

Number of ASCII characters for populating matrix columns.

const char k_PSymbol[]

Residues.

Definitions and prototypes used by blast_stat.c to calculate BLAST statistics.

This class contains misc functions for displaying BLAST results.

static void GetAlnScores(const objects::CSeq_align &aln, int &score, double &bits, double &evalue, int &sum_n, int &num_ident, list< TGi > &use_this_gi, int &comp_adj_method)

Extract score info from blast alingment Second version that fetches compositional adjustment integer.

static const char * kNoHitsFound

The string containing the message that no hits were found.

static string GetIDUrl(SSeqURLInfo *seqUrlInfo, const objects::CSeq_id &id, objects::CScope &scope)

Create URL for seqid.

static CRef< objects::CSeq_id > GetDisplayIds(const objects::CBioseq_Handle &handle, const objects::CSeq_id &aln_id, list< string > &use_this_seq, TGi *gi=NULL, TTaxId *taxid=NULL, string *textSeqID=NULL)

Scan the the list of blast deflines and find seqID to be use in display.

static void GetUseThisSequence(const objects::CSeq_align &aln, list< string > &use_this_seq)

Extract use_this_seq info from blast alingment.

static bool IsMixedDatabase(const objects::CSeq_align_set &alnset, objects::CScope &scope, ILinkoutDB *linkoutdb, const string &mv_build_name)

static list< string > GetFullLinkoutUrl(const list< CRef< objects::CBlast_def_line > > &bdl, const string &rid, const string &cdd_rid, const string &entrez_term, bool is_na, bool structure_linkout_as_group, bool for_alignment, int cur_align, string &linkoutOrder, TTaxId taxid, string &database, int query_number, string &user_url, string &preComputedResID, ILinkoutDB *linkoutdb, const string &mv_build_name)

Get linkout membership for for the list of blast deflines.

static string GetIDUrlGen(SSeqURLInfo *seqUrlInfo, const objects::CBioseq::TId *ids)

Create URL for seqid that goes to entrez or trace.

static string GetIDUrl(SSeqURLInfo *seqUrlInfo, const objects::CBioseq::TId *ids)

Create URL for seqid.

static void GetAlnScores(const objects::CSeq_align &aln, int &score, double &bits, double &evalue, int &sum_n, int &num_ident, list< string > &use_this_seq)

Extract score info from blast alingment.

static list< string > GetFullLinkoutUrl(objects::CBioseq::TId &cur_id, const string &rid, const string &cdd_rid, const string &entrez_term, bool is_na, bool structure_linkout_as_group, bool for_alignment, int cur_align, string &linkoutOrder, TTaxId taxid, string &database, int query_number, string &user_url, string &preComputedResID, ILinkoutDB *linkoutdb, const string &mv_build_name, bool getIdentProteins)

Get linkout membership for one seqID.

static void GetAlnScores(const objects::CSeq_align &aln, int &score, double &bits, double &evalue, int &sum_n, int &num_ident, list< TGi > &use_this_gi)

Extract score info from blast alingment.

static CRef< objects::CSeq_id > GetDisplayIds(const objects::CBioseq_Handle &handle, const objects::CSeq_id &aln_id, list< TGi > &use_this_gi, TGi &gi)

Scan the the list of blast deflines and find seqID to be use in display.

static bool m_geturl_debug_flag

static list< string > GetFullLinkoutUrl(objects::CBioseq::TId &cur_id, SLinkoutInfo &linkoutInfo, bool getIdentProteins)

static string GetIDUrlGen(SSeqURLInfo *seqUrlInfo, const objects::CSeq_id &id, objects::CScope &scope)

Create URL for seqid that goes to entrez or trace.

static CRef< objects::CSeq_align_set > FilterSeqalignByScoreParams(objects::CSeq_align_set &source_aln, double evalueLow, double evalueHigh, double percentIdentLow, double percentIdentHigh, int queryCoverageLow, int queryCoverageHigh)

static bool MatchSeqInSeqList(TGi cur_gi, CRef< objects::CSeq_id > &seqID, list< string > &use_this_seq, bool *isGiList=NULL)

Matches text seqID or gi with the list of seqIds or gis.

static CRef< objects::CSeq_align_set > SortSeqalignForSortableFormat(objects::CSeq_align_set &aln_set, bool nuc_to_nuc_translation, int hit_order, int hsp_order)

static CRef< objects::CSeq_id > GetDisplayIds(const objects::CBioseq_Handle &handle, const objects::CSeq_id &aln_id, list< TGi > &use_this_gi, TGi &gi, TTaxId &taxid)

Scan the the list of blast deflines and find seqID to be use in display.

static list< string > GetFullLinkoutUrl(const list< CRef< objects::CBlast_def_line > > &bdl, SLinkoutInfo &linkoutInfo)

static bool GetTextSeqID(const list< CRef< objects::CSeq_id > > &ids, string *textSeqID=NULL)

static void GetUseThisSequence(const objects::CSeq_align &aln, list< TGi > &use_this_gi)

Extract use_this_gi info from blast alingment.

static string GetSeqIdString(const objects::CBioseq &cbs, bool believe_local_id=true)

Returns a full '|'-delimited Seq-id string for a Bioseq.

static CRef< objects::CSeq_align_set > SortSeqalignForSortableFormat(CCgiContext &ctx, objects::CScope &scope, objects::CSeq_align_set &aln_set, bool nuc_to_nuc_translation, int db_order, int hit_order, int hsp_order, ILinkoutDB *linkoutdb, const string &mv_build_name)

static double GetPercentIdentity(const objects::CSeq_align &aln, objects::CScope &scope, bool do_translation)

calculate the percent identity for a seqalign

static void GetAlnScores(const objects::CSeq_align &aln, int &score, double &bits, double &evalue, int &sum_n, int &num_ident, list< string > &use_this_seq, int &comp_adj_method)

Extract score info from blast alingment Second version that fetches compositional adjustment integer.

static CRef< objects::CSeq_align_set > FilterSeqalignByScoreParams(objects::CSeq_align_set &source_aln, double evalueLow, double evalueHigh, double percentIdentLow, double percentIdentHigh)

function for Filtering seqalign by expect value and percent identity

static TGi GetDisplayIds(const list< CRef< objects::CBlast_def_line > > &bdl, const objects::CSeq_id &aln_id, list< TGi > &use_this_gi)

static unique_ptr< CNcbiRegistry > m_Reg

static void GetBdlLinkoutInfo(const list< CRef< objects::CBlast_def_line > > &bdl, map< int, vector< objects::CBioseq::TId > > &linkout_map, ILinkoutDB *linkoutdb, const string &mv_build_name)

Create map that holds all linkouts for the list of blast deflines and corresponding seqIDs.

static bool GetTextSeqID(CConstRef< objects::CSeq_id > seqID, string *textSeqID=NULL)

static void GetBdlLinkoutInfo(objects::CBioseq::TId &cur_id, map< int, vector< objects::CBioseq::TId > > &linkout_map, ILinkoutDB *linkoutdb, const string &mv_build_name)

Create map that holds all linkouts for one seqID.

static bool MatchSeqInSeqList(CConstRef< objects::CSeq_id > &alnSeqID, list< string > &use_this_seq, vector< string > &seqList)

Matches string of seqIDs (gis or text seqID)

static string GetSeqIdString(const list< CRef< objects::CSeq_id > > &ids, bool believe_local_id)

Returns a full '|'-delimited Seq-id string for a a list of seq-ids.

std::ofstream out("events_result.xml")

main entry point for tests

static bool InitConfig(const CArgs &args, Parser &config)

@ eSubjectStart

Start of alignment in subject.

const size_t kDfltArgNumAlignments

Default number of alignments to display in the traditional BLAST report.

static const char * str(char *buf, int n)

SStrictId_Tax::TId TTaxId

Taxon id type.

EDiagSev

Severity level for the posted diagnostics.

string GetLabel(const CSeq_id &id)

NCBI_XOBJUTIL_EXPORT string GetTitle(const CBioseq_Handle &hnd, TGetTitleFlags flags=0)

int64_t Int8

8-byte (64-bit) signed integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

#define NCBI_ALIGN_FORMAT_EXPORT

static const char label[]

ENa_strand

strand of nucleic acid

Declares the ILinkoutDB interface.

use only n Cassandra database for the lookups</td > n</tr > n< tr > n< td > yes</td > n< td > do not use tables BIOSEQ_INFO and BLOB_PROP in the Cassandra database

static CRef< CSeq_align > CreateDensegFromDendiag(CSeq_align const &aln)

const CharType(& source)[N]

Process information in the NCBI Registry, including working with configuration files.

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

double lambda(size_t dimMatrix_, const Int4 *const *scoreMatrix_, const double *q_)

static PCRE2_SIZE * offsets

static bool SortHspByMasterStartAscending(const SHspInfo *info1, const SHspInfo *info2)

Structure to hold the Gumbel parameters (for FSC).

SDbInfo()

Default constructor.

string filt_algorithm_name

Filtering algorithm ID used in BLAST search.

string filt_algorithm_options

Filtering algorithm options used in BLAST search.

void Init(string rid_in, string cdd_rid_in, string entrez_term_in, bool is_na_in, string database_in, int query_number_in, string user_url_in, string preComputedResID_in, string linkoutOrder_in, bool structure_linkout_as_group_in=false, bool for_alignment_in=true)

CRange< TSeqPos > subjRange

bool structure_linkout_as_group

void Init(string rid_in, string cdd_rid_in, string entrez_term_in, bool is_na_in, string database_in, int query_number_in, string user_url_in, string preComputedResID_in, string linkoutOrder_in, ILinkoutDB *linkoutdb_in, string mv_build_name_in, bool structure_linkout_as_group_in=false, bool for_alignment_in=true)

Structure that holds information for all hits of one subject in Seq Align Set.

CConstRef< objects::CSeq_id > id

CRange< TSeqPos > subjRange

list< string > use_this_seq

int master_covered_length

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

bool flip

flip sequence in case of opposite strands

string user_url

user url TOOL_URL from .ncbirc

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.

string blastType

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

CRange< TSeqPos > seqRange

sequence range

string database

name of the database

string defline

sequence defline

bool new_win

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

bool addCssInfo

bool indicating that css info should be added

bool useTemplates

bool indicating that templates should be used when contsructing links

int queryNumber

the query number

string accession

accession

string segs

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

int blast_rank

index of the current alignment

bool advancedView

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

string seqUrl

sequence URL created

bool isAlignLink

bool indicating if link is in alignment section

bool isDbNa

bool indicating if the database is nucleotide or not

string resourcesUrl

URL(s) to other resources from .ncbirc.

static bool IsWGSAccession(const string &acc, const CTextseq_id &id, TAllowSeqType allow_seq_type)

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