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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/taxFormat_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/align_format/taxFormat.cpp Source File

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cit = kMapTagToString.find(tag_name);

( cit != kMapTagToString.end()) {

mappedStr = cit->second;

displayOption,

connectToTaxServer,

lineLength)

: m_SeqalignSetRef(&seqalign),

m_DisplayOption(displayOption),

m_ConnectToTaxServer(connectToTaxServer),

m_LineLength(lineLength)

(m_ConnectToTaxServer) {

displayOption,

connectToTaxServer,

lineLength)

: m_AccessionTaxidList(accessionTaxidList),

m_DisplayOption(displayOption),

m_ConnectToTaxServer(connectToTaxServer),

m_LineLength(lineLength)

(

= 0;

< it->second.seqInfoList.size();

++) {

* seqInfo = it->second.seqInfoList[

];

(seqInfo)

seqInfo;

useTaxid =

;

(taxid == currTaxid) {

(taxid != currTaxid) {

((*m_TreeTaxInfoMap).count(taxid) != 0 ) {

((*m_TreeTaxInfoMap).count(taxid) != 0 ) {

(*m_TreeTaxInfoMap)[taxid].depth =

;

((*m_TreeTaxInfoMap).count(taxid) != 0 ) {

(

j = 0; j <

.size(); j++) {

(!lineage.empty()) lineage +=

;

cerr << header <<

<< tax_node->

() <<

<< tax_node->

() <<

<<

<<

<< lineage << endl;

orgReportData;

prevTaxid,nextTaxid, hidePrevTaxid, hideNextTaxid, hideTop;

kDisabled =

;

hidePrevTaxid = kDisabled;

hideNextTaxid = kDisabled;

(i < m_BlastResTaxInfo->orderedTaxids.size() - 1) {

orgReportSeqInfo;

(

j = 0; j < seqsForTaxID.

.size(); j++) {

orgReportSeqInfo += orgReportTableRow;

oneOrgInfo = orgHeader + orgReportSeqInfo;

orgReportData += oneOrgInfo;

orgReportTxtTableCaption =

(

);

orgEValueTxtTableHeader =

(

);

<< orgReportData;

lngReportTableRow;

= 0;

(

= 0;

< alnSeqTaxInfo.

.size();

++) {

lngReportRows += lngReportTableRow;

lngReportRows += lngReportTableRow;

<< lngReportData;

taxReportRows;

(

= 0;

< taxTreeTaxids.size();

++) {

taxid = taxTreeTaxids[

];

taxReportTableRow;

lineage,parentTaxid;

(

= 0;

< taxInfo.

.size();

++) {

(!lineage.empty()) lineage +=

;

(

== taxInfo.

.size() - 1) {

taxReportRows += taxReportTableRow;

<< taxReportData;

vector <TTaxId> taxidsToRoot;

tax_load_ok =

;

(

= 0;

< alignTaxids.size();

++) {

tax_id = alignTaxids[

];

(!tax_load_ok)

;

(tax_node && tax_node->

() != tax_id) {

cerr <<

<< tax_id <<

<< tax_node->

() <<

<< endl;

taxInfo.

= newTaxid;

(

j = 0; j < taxInfo.

.size(); j++) {

seqInfo->

= newTaxid;

(vector<TTaxId>, it, taxidsToRoot) {

(!tax_load_ok)

;

cerr <<

<< title <<

<< endl;

(

= 0;

< taxids.size();

++) {

(

j = 0; j < taxInfo.

.size(); j++) {

(!lineage.empty()) lineage +=

;

cerr <<

<< taxid <<

<< taxInfo.

<<

<< taxInfo.

<<

<<

<< taxInfo.

<<

<< taxInfo.

<<

<< taxInfo.

<<

<< taxInfo.

<<

<< lineage << endl;

list< CRef< CTaxon1_name > > nameList;

((*iter)->CanGetTaxid() && (*iter)->IsSetCde() && (*iter)->GetCde() == blastNameCde) {

vector <TTaxId> lineage =

.lineage;

strTaxidLineage;

(

j = 0; j < lineage.size(); j++) {

(!strTaxidLineage.empty()) strTaxidLineage +=

;

strTaxidLineage;

lineage1 > lineage2;

vector <TTaxId> alignHitLineage;

(

= 0;

< bestHitLinage.size();

++) {

(taxTreeInfo.

.size() - 1 >=

) {

taxid = bestHitLinage[

];

(taxTreeInfo.

[

] == taxid) {

alignHitLineage.push_back(taxid);

alignHitLineage;

cerr <<

<< endl;

taxid = iter->taxid;

name = iter->scientificName;

cerr <<

<< taxid <<

<< name <<

;

(

= 0;

< iter->lineage.size();

++) {

lnTaxid = iter->lineage[

];

list <STaxInfo> alnTaxInfo;

(

= 0;

< alignTaxids.size();

++) {

taxInfo.

= alignHitLineage;

(

= 0;

< iter->lineage.size();

++) {

lnTaxid = iter->lineage[

];

->taxid = taxid;

orgEValueTxtTableHeader =

(

);

SSeqInfo *seqInfo =

SSeqInfo;

total_bit_score_buf, raw_score_buf;

seqInfo->displGi = seqInfo->gi;

seqInfo->dispSeqID = seqInfo->label;

list<string>& use_this_seqid)

SSeqInfo *seqInfo =

;

list<CRef<CSeq_id> > ids = bdl->GetSeqid();

(use_this_seqid.empty() ||

) {

seqInfo =

SSeqInfo();

total_bit_score_buf, raw_score_buf;

(bdl->IsSetTaxid() && bdl->CanGetTaxid()){

taxid = bdl->GetTaxid();

seqInfo->taxid = taxid;

(bdl->IsSetTitle()){

seqInfo->title = bdl->GetTitle();

(seqInfo->title.empty()) {

score, sum_n, num_ident;

subid = &((*iter)->GetSeq_id(1));

(!previousId.

() && subid->

(*previousId))

;

list<string> use_this_seqid;

sum_n, num_ident, use_this_seqid);

( !handle )

;

(dispGI ==

&& dispSeqID.empty()){

(dispGI ==

&& !dispSeqID.empty()) {

dispSeqID = seqInfo->

;

std::list<std::pair<std::string,TTaxId> >::iterator at_it;

seqsForTaxID.

= taxid;

taxid = accTaxidPair.second;

accession = accTaxidPair.first;

seqInfo->

= accession;

seqInfo->

= taxid;

seqsForTaxID.

= taxid;

seqsForTaxID.

= accession;

reportTableRow;

reportTableRow;

txtOrgValue = reportTableRow;

numHits = (numHits > 0) ? numHits : taxInfo.

;

(

= 0;

<

;

++) {

reportTableRow;

static CRef< CScope > m_Scope

User-defined methods of the data storage class.

static string GetProtocol(void)

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.

@ eAddEOLAtLineEnd

add EOL at the beginning of the string

@ eAddEOLAtLineStart

add spaces at the end of the string

static string AddSpaces(string paramVal, size_t maxParamLength, int spacesFormatFlag=eSpacePosToCenter)

Calculate the number of spaces and add them to paramVal.

static void GetScoreString(double evalue, double bit_score, double total_bit_score, int raw_score, string &evalue_str, string &bit_score_str, string &total_bit_score_str, string &raw_score_str)

format evalue and bit_score

static string MapTemplate(string inpString, string tmplParamName, Int8 templParamVal)

Replace template tags by real data.

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_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 TGi GetGiForSeqIdList(const list< CRef< objects::CSeq_id > > &ids)

return gi from id list

static string MapSpaceTemplate(string inpString, string tmplParamName, string templParamVal, unsigned int maxParamLength, int spacesFormatFlag=eSpacePosAtLineEnd)

Replace template tags by real data and calculate and add spaces dependent on maxParamLength and space...

static string GetLabel(CConstRef< objects::CSeq_id > id, bool with_version=false)

Return a label for an ID Tries to recreate behavior of GetLabel before a change that prepends "ti|" t...

Class for computing sequences' titles ("definitions").

ITreeIterator::EAction LevelEnd(const ITaxon1Node *tax_node)

CDownwardTreeFiller(CTaxFormat::TSeqTaxInfoMap *treeTaxInfoMap)

vector< TTaxId > m_Lineage

CTaxFormat::TSeqTaxInfoMap * m_TreeTaxInfoMap

void SetDebugMode(bool debug)

virtual ~CDownwardTreeFiller()

ITreeIterator::EAction LevelBegin(const ITaxon1Node *tax_node)

ITreeIterator::EAction Execute(const ITaxon1Node *tax_node)

void x_PrintTaxInfo(string header, const ITaxon1Node *tax_node)

static void GetTaxInfo(TTaxId taxid, SSeqDBTaxInfo &info)

Get taxonomy information.

static CRef< CBlast_def_line_set > ExtractBlastDefline(const CBioseq &bioseq)

Extract a Blast-def-line-set object from a Bioseq retrieved by CSeqDB.

unsigned int m_MaxScoreLength

void x_InitBlastNameTaxInfo(STaxInfo &taxInfo)

CConstRef< objects::CSeq_align_set > m_SeqalignSetRef

reference to seqalign set

string m_TaxBrowserURL

Taxonomy Browser URL.

SBlastResTaxInfo * m_BlastResTaxInfo

SBlastResTaxInfo structure containing information for taxids in alignment, orderedTaxids are ordered ...

bool m_Debug

String containig map of taxids to corresponding accessions.

SBlastResTaxInfo * m_TaxTreeinfo

SBlastResTaxInfo structure containing information for all taxids in common tree, intermediate nodes w...

struct STaxInfo & GetTaxTreeInfo(TTaxId taxid)

Gets info for sequences in taxonomy tree corresponding to taxid.

unsigned int m_MaxAccLength

CNcbiIfstream * m_ConfigFile

CTaxon1 * m_TaxClient

Taxonomy server client.

list< STaxInfo > m_AlnLineageTaxInfo

STaxInfo structure list contaning info for lineage report ordered by linage display order....

CTaxFormat(const objects::CSeq_align_set &seqalign, objects::CScope &scope, unsigned int displayOption=eHtml, bool connectToTaxServer=true, unsigned int lineLength=100)

Constructors.

objects::CScope & m_Scope

void x_InitTaxInfoMapFromAccList(void)

struct STaxInfo & GetAlignTaxInfo(TTaxId taxid)

Gets info for sequences in alignment corresponding to taxid.

void x_InitBlastDBTaxInfo(SSeqInfo *seqInfo)

void x_InitTaxReport(void)

void x_InitTaxFormat(void)

CTaxFormat::SSeqInfo * x_FillTaxDispParams(const CRef< objects::CBlast_def_line > &bdl, const objects::CBioseq_Handle &bsp_handle, double bits, double evalue, list< string > &use_this_seqid)

void x_InitOrgTaxMetaData(void)

~CTaxFormat()

Destructor.

bool m_ConnectToTaxServer

bool isTaxidInAlign(TTaxId taxid)

Checks if there are sequences in alignment with specified taxid.

unsigned int m_DisplayOption

string x_MapSeqTemplate(string seqTemplate, SSeqInfo *seqInfo)

vector< TTaxId > & GetTaxTreeTaxIDs(void)

Gets taxids for sequences in taxonomy tree.

void x_LoadTaxTree(void)

Initializes CTaxon1 *m_TaxClient.

void x_InitLineageMetaData(void)

unsigned int m_MaxDescrLength

vector< TTaxId > m_BestHitLineage

vector of <int> containing taxids for the best hit linage

void x_PrintLineage(void)

unsigned int m_MaxEvalLength

list< pair< string, TTaxId > > m_AccessionTaxidList

void x_InitTaxIdToSeqsMap(void)

string x_MapTaxInfoTemplate(string tableRowTemplate, STaxInfo &taxInfo, unsigned int depth=0)

void x_InitTextFormatInfo(CTaxFormat::SSeqInfo *seqInfo)

STaxFormatTemplates * m_TaxFormatTemplates

void DisplayTaxonomyReport(CNcbiOstream &out)

Displays Taxonomy Report.

vector< TTaxId > & GetAlignTaxIDs(void)

Gets taxids for sequences in alignment.

void x_InitTaxClient(void)

void DisplayOrgReport(CNcbiOstream &out)

Displays Organism Report.

void x_InitLineageReport(void)

string m_Protocol

protocol, default https otherwise get from .ncbirc

unsigned int m_LineLength

void x_InitTaxInfoMap(void)

void DisplayLineageReport(CNcbiOstream &out)

Displays Linage Report.

void x_PrintTaxInfo(vector< TTaxId > taxids, string title)

CRef< ITreeIterator > m_TreeIterator

const string & GetLastError() const

bool GetPopsetJoin(const TTaxIdList &ids_in, TTaxIdList &ids_out)

TTaxId SearchTaxIdByName(const string &orgname, ESearch mode=eSearch_TokenSet, list< CRef< CTaxon1_name > > *name_list_out=NULL)

bool LoadNode(TTaxId tax_id, const ITaxon1Node **ppNode=NULL)

TTaxNameClass GetNameClassId(const string &class_name)

CRef< ITreeIterator > GetTreeIterator(EIteratorMode mode=eIteratorMode_Default)

bool GetBlastName(TTaxId tax_id, string &blast_name_out)

void x_PrintTaxInfo(string header)

CUpwardTreeFiller(CTaxFormat::TSeqTaxInfoMap &seqAlignTaxInfoMap)

void x_InitTreeTaxInfo(void)

ITreeIterator::EAction LevelEnd(const ITaxon1Node *tax_node)

ITreeIterator::EAction LevelBegin(const ITaxon1Node *tax_node)

stack< CTaxFormat::STaxInfo * > m_Nodes

void x_InitTaxInfo(const ITaxon1Node *tax_node)

CTaxFormat::SBlastResTaxInfo * GetTreeTaxInfo(void)

CTaxFormat::STaxInfo * m_Curr

virtual ~CUpwardTreeFiller()

CTaxFormat::SBlastResTaxInfo * m_TreeTaxInfo

SBlastResTaxInfo Map containing information for all taxids in common tree, intermidiate nodes with no...

ITreeIterator::EAction Execute(const ITaxon1Node *tax_node)

void SetDebugMode(bool debug)

CTaxFormat::TSeqTaxInfoMap m_SeqAlignTaxInfoMap

Map containing information for taxids and corresponding sequnces in alignment.

virtual const string & GetName() const =0

virtual const string & GetBlastName() const =0

virtual TTaxId GetTaxId() const =0

EAction TraverseUpward(I4Each &, unsigned levels=kMax_UInt)

EAction TraverseDownward(I4Each &, unsigned levels=kMax_UInt)

container_type::iterator iterator

const_iterator begin() const

const_iterator end() const

iterator_bool insert(const value_type &val)

container_type::value_type value_type

static unsigned char depth[2 *(256+1+29)+1]

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

main entry point for tests

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define TAX_ID_TO(T, tax_id)

SStrictId_Tax::TId TTaxId

Taxon id type.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

TGi FindGi(const container &ids)

Return gi from id list if exists, return 0 otherwise.

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

static int WorstRank(const CRef< CSeq_id > &id)

string GenerateDefline(const CBioseq_Handle &bsh, TUserFlags flags=0)

Main method.

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

bool Empty(void) const THROWS_NONE

Check if CConstRef is empty – not pointing to any object which means having a null value.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

virtual const string & Get(const string &section, const string &name, TFlags flags=0) const

Get the parameter value.

#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.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

C::value_type FindBestChoice(const C &container, F score_func)

Find the best choice (lowest score) for values in a container.

const Tdata & Get(void) const

Get the member data.

list< CRef< CSeq_align > > Tdata

const TId & GetId(void) const

Get the Id member data.

std::false_type tagStrNocase

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

Defines BLAST database access classes.

vector< TTaxId > orderedTaxids

taxids ordered by highest score or common tree top to bottom tarveres??

TSeqTaxInfoMap seqTaxInfoMap

Map containing info for orderedTaxids.

CRef< objects::CSeq_id > seqID

seqID used in defline

TGi displGi

gi for seq that is displayed in alignment section

string label

sequence label

string title

sequnce title

string lineageReportTableRow

Template for displaying lineage report table row.

string lineageReportTableHeader

Template for displaying lineage report table header.

string blastNameLink

Template for displaying blast name link.

string taxIdToSeqsMap

Tempalte for mapping taxids to seqlist.

string orgReportTable

Template for displaying organism report table.

string taxonomyReportOrganismHeader

Template for displaying taxonomy report organism header.

string taxonomyReportTableHeader

Template for displaying taxonomy report table header.

string taxonomyReportTable

Template for displaying taxonomy report table.

string taxonomyReportTableRow

Template for displaying taxonomy report table row.

string orgReportOrganismHeader

Template for organism report organism header.

string orgReportTableRow

Tempalte for displaying organism report table row.

string orgReportTableHeader

Template for displaying organism report table header.

string lineageReportOrganismHeader

Template for displaying lineage report organism header.

string lineageReportTable

Template for displaying lineage report table.

string blastName

blastName

unsigned int numChildren

Number of childre for taxid.

string taxidList

string of "children" taxids containing sequences in alignment separated by comma corresponding to tax...

string commonName

commonName

int blNameTaxid

blastName taxid

unsigned int numOrgs

Number of organism in alignmnet corresponding to taxid and it's children.

string accList

string of accessions separated by comma corresponding to taxid

vector< TTaxId > lineage

vector of taxids containg lineage for taxid

string giList

string of gis separated by comma corresponding to taxid

unsigned int numHits

Number of sequences in alignmnet corresponding to taxid and it's children.

vector< SSeqInfo * > seqInfoList

vector of SSeqInfo corresponding to taxid

unsigned int depth

Depth.

string scientificName

scientificName

string common_name

Common name, such as "noisy night monkey".

string blast_name

A simple category name, such as "birds".

string scientific_name

Scientific name, such as "Aotus vociferans".

static string s_TagToConstString(const string tag_name)

static vector< TTaxId > s_InitAlignHitLineage(vector< TTaxId > bestHitLinage, struct CTaxFormat::STaxInfo &taxTreeInfo)

static string s_TaxidLinageToString(CTaxFormat::STaxInfo const &info)

static bool s_SortByLinageToBestHit(CTaxFormat::STaxInfo const &info1, CTaxFormat::STaxInfo const &info2)

MAKE_CONST_MAP(kMapTagToString, ct::tagStrNocase, ct::tagStrNocase, { { "TAX_BROWSER_URL", "<@protocol@>//www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi"}, {"BLAST_NAME_LINK","<a href=\"<@taxBrowserURL@>?id=<@bl_taxid@>\" target=\"lnktx<@rid@>\" title=\"Show taxonomy info for <@blast_name@> (taxid <@bl_taxid@>)\"><@blast_name@></a>"}, { "ORG_REPORT_TABLE", "<table><caption><h2>Organism Report</h2></caption><tr><th>Accession</th><th>Descr</th><th>Score</th><th>E-value</th></tr><@table_rows@></table><@taxidToSeqsMap@>"}, { "ORG_REPORT_ORG_HEADER", "<tr><th colspan=\"4\"><a href=\"<@taxBrowserURL@>?id=<@taxid@>\" name=\"<@taxid@>\" title=\"Show taxonomy info for <@scientific_name@> (taxid <@taxid@>)\" target=\"lnktx<@rid@>\"><@scientific_name@> <@common_name@> [<@blast_name_link@>] taxid <@taxid@></th></tr>"}, { "ORG_REPORT_ORG_HEADER_NO_TAX_CON", "<tr><th colspan=\"4\"><a href=\"<@taxBrowserURL@>?id=<@taxid@>\" name=\"<@taxid@>\" title=\"Show taxonomy info for <@scientific_name@> (taxid <@taxid@>)\" target=\"lnktx<@rid@>\"><@scientific_name@> <@common_name@> [<@blast_name@>]</th></tr>"}, { "ORG_REPORT_TABLE_HEADER", "<tr><th>Accession</th><th>Description</th><th>Score</th><th>E-value</th></tr>"}, { "ORG_REPORT_TABLE_ROW", "<tr><td><a title=\"Show report for <@acc@>\" target=\"lnktx<@rid@>\" href=\"<@protocol@>//www.ncbi.nlm.nih.gov/protein/<@acc@>?report=fwwwtax&amp;log$=taxrep&amp;RID=<@rid@>\"><@acc@></a></td><td><@descr_abbr@></td><td><@score@></td><td><@evalue@></td></tr>"}, { "TAXID_TO_SEQ_MAP", "<input type=\"hidden\" id=\"txForSeq_<@taxid@>\" value=\"<@giList@>\" />"}, { "LINAGE_REPORT_TABLE", "<table><caption><h2>Linage Report</h2><caption><@table_rows@></table>"}, {"LINAGE_REPORT_TABLE_HEADER", "<tr><th>Organism</th><th>Blast Name</th><th>Score</th><th>Number of Hits</th><th>Description</th></tr>"}, {"LINAGE_REPORT_ORG_HEADER", "<tr><td><@depth@><a href=\"//<@taxBrowserURL@>?id=<@taxid@>\" title=\"Show taxonomy info for <@scientific_name@> (taxid <@taxid@>)\" target=\"lnktx<@rid@>\"><@scientific_name@></a><td><@blast_name_link@></td><td colspan =\"3\"></td></tr>"}, {"LINAGE_REPORT_TABLE_ROW", "<tr><td><@depth@><a href=\"//<@taxBrowserURL@>?id=<@taxid@>\" title=\"Show taxonomy info for <@scientific_name@> (taxid <@taxid@>)\" target=\"lnktx<@rid@>\"><@scientific_name@></a></td><td><@blast_name_link@></td><td><@score@></td><td><a href=\"#<@taxid@>\" title=\"Show organism report for <@scientific_name@>\"><@numhits@></a></td><td><a title=\"Show report for <@acc@> <@descr_abbr@>\" target=\"lnktx<@rid@>\" href=\"<@protocol@>//www.ncbi.nlm.nih.gov/protein/<@acc@>?report=genbank&amp;log$=taxrep&amp;RID=<@rid@>\"><@descr_abbr@></a></td></tr>"}, { "TAXONOMY_REPORT_TABLE", "<table><caption><h2>Taxonomy Report</h2><caption><@table_rows@></table>"}, { "TAXONOMY_REPORT_TABLE_HEADER", "<tr><th>Taxonomy</th><th>Number of hits</th><th>Number of organisms</th><th>Description</th></tr>"}, {"TAXONOMY_REPORT_ORG_HEADER", "<tr><td><@depth@><a href=\"//<@taxBrowserURL@>?id=<@taxid@>\" title=\"Show taxonomy info for <@scientific_name@> (taxid <@taxid@>)\" target=\"lnktx<@rid@>\"><@scientific_name@></a></td><td><@numhits@></td><td><@numOrgs@></td><td><@descr_abbr@></td></tr>"}, { "TAXONOMY_REPORT_TABLE_ROW", "<tr><td><@depth@><a href=\"//<@taxBrowserURL@>?id=<@taxid@>\" title=\"Show taxonomy info for <@scientific_name@> (taxid <@taxid@>)\" target=\"lnktx<@rid@>\"><@scientific_name@></a></td><td><@numhits@></td><td><@numOrgs@></td><td><@descr_abbr@></td></tr>"}, {"ORG_REPORT_TXT_TABLE", "<@org_report_caption@>\n<@acc_hd@><@descr_hd@><@score_hd@><@evalue_hd@>\n<@table_rows@>"}, {"ORG_REPORT_TXT_ORG_HEADER", "<@scientific_name@> <@common_name@> [<@blast_name_link@>] taxid <@taxid@>"}, {"ORG_REPORT_TXT_ORG_HEADER_NO_TAX_CON", "<@scientific_name@> <@common_name@> [<@blast_name@>]"}, {"ORG_REPORT_TXT_TABLE_HEADER", " <@acc_hd@><@descr_hd@><@score_hd@><@evalue_hd@>\n"}, {"ORG_REPORT_TXT_TABLE_ROW", " <@acc@><@descr_text@><@score@><@evalue@>\n"}, {"ORG_REPORT_TXT_TABLE_CAPTION", "Organism Report"}, { "ORG_ACC_TXT_TABLE_HEADER", "Accession"}, { "ORG_DESCR_TXT_TABLE_HEADER", "Description"}, { "ORG_SCORE_TXT_TABLE_HEADER", "Score"}, { "ORG_EVALUE_TXT_TABLE_HEADER", "E-value"}, })

Sequence alignment taxonomy display tool.

const unsigned int kMinLineLength

Example:

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