RetroSearch Browse

Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cuTaxTree_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/structure/cd_utils/cuTaxTree.cpp Source File

47

orgName(rhs.orgName), rankId(rhs.rankId), rowId(rhs.rowId), cd(rhs.cd), seqName(rhs.seqName),

48

numLeaves(rhs.numLeaves),selectedLeaves(rhs.selectedLeaves)

88

sprintf(name,

"row_%d_of_%s"

, rowInCd,

GetAccession

().c_str());

96 return

node.

rowId

>= 0;

106

m_rowToTaxNode(), m_rankNameToId(), m_failedRows()

123

vector<TaxTreeIterator> nodes;

125 for

(

unsigned int i

= 0;

< nodes.size();

++)

135

nodes.push_back(taxNode);

139 while

(sib != taxNode.

end

())

149 for

(

unsigned int i

= 0;

< rowIDs.size();

++)

167 if

(taxIt->selectedLeaves > 0)

168

rows.push_back(taxIt->rowId);

181 while

(sib != cursor.

end

())

192

cursor->selectedLeaves = 1;

194

cursor->selectedLeaves = 0;

196 else if

(cursor->cd == cd)

199

cursor->selectedLeaves = 1;

201

cursor->selectedLeaves = 0;

207

cursor->selectedLeaves = 1;

209

cursor->selectedLeaves = 0;

249

insert(begin(), *root);

261 for

(

int i

= 0;

< num;

++)

278

cursor->numLeaves = 0;

279

cursor->selectedLeaves = 0;

283 while

(sib != cursor.

end

())

289 if

(cursor != begin())

292

parentIt->numLeaves += cursor->numLeaves;

293

parentIt->selectedLeaves += cursor->selectedLeaves;

299

stack<TaxNode*> lineage;

316 while

(pos != end() && !(*pos == *top) ) {

333

lineage.push(parentTax);

341 while

(!lineage.empty())

343 TaxNode

* topNode = lineage.top();

344

cursor = append_child(cursor,*topNode);

352

vector<RowSource> rss;

356 for

(

unsigned int i

= 0;

< rss.size();

++)

362

append_child(cursor,*subSeqNode);

389 bool

gotGI = aligns.

GetGI

(rowID, gi,

false

);

397 if

(seqEntry->

IsSeq

())

400 if

(localTaxid != taxid)

419 if

(seqDescr.

IsSet

())

421

list< CRef< CSeqdesc > >& descrList = seqDescr.

Set

();

422

list< CRef< CSeqdesc > >::iterator cit = descrList.begin();

424 while

(cit != descrList.end())

426 if

((*cit)->IsSource())

428

cit = descrList.erase(cit);

439

descrList.push_back(

source

);

450

std::ofstream fout(

".\\SeqTree\\ranks"

);

455

fout<<mit->first<<

' '

<<mit->second<<endl;

462

ofstream os(fname.c_str());

475

ofstream os(fname.c_str());

486 if

(number_of_children(cursor) > 1)

488

os <<cursor->taxId<<

","

<<branchingNode->taxId<<

"\n"

;

489

sibling_iterator sib = cursor.begin();

490 while

(sib != cursor.end())

496 else if

(number_of_children(cursor) == 1)

498

sibling_iterator onlychild = child(cursor,0);

503

os<<cursor->seqName<<

","

<<branchingNode->taxId<<

"\n"

;

513 if

(cursor->rowId >= 0)

520 if

(number_of_children(cursor) > 1)

523

sibling_iterator sib = cursor.begin();

524 while

(sib != cursor.end())

530 if

(number_of_children(cursor) > 1)

536 if

(cursor == begin())

539 else if

(number_of_siblings(cursor) > 1)

552 if

(

leaf

->rowId < 0)

556 while

(parentNode != begin())

558 if

(parentNode->rankId == rank)

562

oneBeforeParentNode = parentNode;

563

parentNode = parent(parentNode);

567 return

oneBeforeParentNode;

bool GetGI(int row, TGi &gi, bool ignorePDBs=true) const

bool GetSeqEntryForRow(int row, CRef< CSeq_entry > &seqEntry) const

bool Get_GI_or_PDB_String_FromAlignment(int row, std::string &result) const

const RowSourceTable & GetRowSourceTable() const

bool isCDInScope(CCdCore *cd) const

string GetAccession(int &Version) const

TTaxId SetTaxId(TTaxId tax_id)

@Seq_descr.hpp User-defined methods of the data storage class.

int findEntries(int row, vector< RowSource > &src, bool scopedOnly=false) const

virtual short GetRankID(TTaxId taxId, string &rankName)

virtual TTaxId GetTaxIDFromBioseq(const CBioseq &bioseq, bool lookInBioseq)

virtual TTaxId GetParentTaxID(TTaxId taxid)

virtual TTaxId GetTaxIDForGI(TGi gi)

virtual string GetTaxNameForTaxID(TTaxId taxid)

static bool isSubSeqLeaf(const TaxNode &node)

static TaxNode * makeTaxNode(TTaxId taxID, std::string taxName, short rankId=-1)

static bool isSeqLeaf(const TaxNode &node)

static TaxNode * makeSeqLeaf(int rowID, std::string sequenceName)

static TaxNode * makeSubSeqLeaf(int rowID, CCdCore *cd, int rowInCd)

bool writeToFile(string fname) const

short getRankId(string rankName)

void growAndInsertLineage(stack< TaxNode * > &lineage)

RankNameToId m_rankNameToId

void addTaxToBioseq(CBioseq &bioseq, TTaxId taxid, string &taxName)

bool writeToFileAsTable(string fname) const

TaxTreeData(const AlignmentCollection &ac)

const AlignmentCollection & m_ac

TaxClient * m_taxDataSource

int getAllLeafNodes(const TaxTreeIterator &taxNode, vector< TaxTreeIterator > &nodes) const

vector< int > m_failedRows

void fillLeafCount(const TaxTreeIterator &cursor)

void setSelections(const vector< int > &rowIDs, CCdCore *cd=0)

bool write(std::ostream &os, const iterator &cursor) const

RowToTaxNode m_rowToTaxNode

void addSeqTax(int rowID, string seqName, TTaxId taxid)

TTaxId GetTaxIDForSequence(const AlignmentCollection &aligns, int rowID)

void selectTaxTreeLeaf(const TaxTreeIterator &cursor, bool select, CCdCore *cd=0)

TaxTreeIterator getParentAtRank(int row, string rankName)

void selectTaxNode(TaxTreeIterator &taxNode, bool select)

void insertLineage(TaxTreeIterator &pos, stack< TaxNode * > &lineage)

int getSelections(vector< int > &rows)

bool writeAsTable(std::ostream &os, const iterator &cursor, const iterator &branchingNode) const

void cacheRank(short rank, string rankName)

void deselectAllTaxNodes()

void addRows(const AlignmentCollection &ac)

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

const_iterator find(const key_type &key) const

sibling_iterator end() const

unsigned int number_of_children() const

sibling_iterator begin() const

static void DLIST_NAME() init(DLIST_LIST_TYPE *list)

SStrictId_Tax::TId TTaxId

Taxon id type.

#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.

void SetTaxname(const TTaxname &value)

Assign a value to Taxname data member.

const TSeq & GetSeq(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

TSeq & SetSeq(void)

Select the variant.

bool IsSet(void) const

Check if a value has been assigned to data member.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

Tdata & Set(void)

Assign a value to data member.

const CharType(& source)[N]

#define row(bind, expected)

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4