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

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/taxtree__tool__job_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/packages/pkg_alignment/taxtree_tool_job.cpp Source File

=

;

(seqs.size() == 0) {

(

);

tinit_ok = taxon1.

();

* scope = seqs[0].scope.GetPointer();

*

= it->object.GetPointer();

seq_id =

*

(object);

seq_loc =

*

(object);

handle_valid =

;

handle_valid =

;

(seq_loc && seq_loc->

()) {

handle_valid =

;

handles.push_back(canonical_seq_id_h);

}

(std::exception&) {

*

= it->object.GetPointer();

seq_id =

*

(object);

seq_loc =

*

(object);

(seq_loc && seq_loc->

()) {

(tax_it != bio2tax.

()) {

tax_id = (*tax_it).second;

( seq_id && seq_id->

() ) {

gi = seq_id->

();

gi = scope->

(canonical_seq_id_h);

(seq_id && seq_id->

())

gi = seq_id->

();

tax_id_list.push_back(tax_id);

taxbv[tax_id] =

;

seq2tax[canonical_seq_id_h] =

(tax_id, seqid_label);

(

<< seqid_label);

(tax_id_list.size() == 0) {

);

(tax_id_list.size() == 1) {

tax_ids_join = tax_id_list;

);

(tax_ids_join.size() == 0) {

);

tax_load_ok =

;

(vector<int>, it, tax_ids_join) {

tax_load_ok |= taxon2.

(tax_id);

);

TTaxon1Conv conv_func;

conv_func(*btc, tax_tree_iter);

max_tax_id = conv_func.GetMaxNodeId();

TTaxon1Conv::TTaxon1Visitor::TNodeList& node_list = btc->

().Set();

(TSeqId2Tax, mit, seq2tax) {

seqid_str = mit->first.AsString();

tax_id = mit->second.tax_id;

&

= mit->second.label;

cnode->SetId(max_tax_id);

cnode->SetParent(tax_id);

TTaxon1Conv::TTaxon1Visitor::TCNodeFeatureSet& fset = cnode->SetFeatures();

cfeat(

TTaxon1Conv::TTaxon1Visitor::TCNodeFeature);

cfeat->SetValue(seqid_str);

fset.Set().push_back(cfeat);

cfeat(

TTaxon1Conv::TTaxon1Visitor::TCNodeFeature);

cfeat->SetValue(

);

fset.Set().push_back(cfeat);

cfeat(

TTaxon1Conv::TTaxon1Visitor::TCNodeFeature);

cfeat->SetValue(tax_id_str);

fset.Set().push_back(cfeat);

node_list.push_back(cnode);

item->

().SetOther().Set(*btc);

project_item_label(

);

project_item_label +=

;

item->

(project_item_label);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

Things for representing and manipulating bio trees.

void AddProjectItem(objects::CProjectItem &item)

const string & GetLastError() const

bool GetTaxId4GI(TGi gi, TTaxId &tax_id_out)

vector< TTaxId > TTaxIdList

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

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

CRef< ITreeIterator > GetTreeIterator(EIteratorMode mode=eIteratorMode_Default)

const_iterator end() const

const_iterator find(const key_type &key) const

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

#define NCBI_THROW(exception_class, err_code, message)

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

CTaxTreeToolParams m_Params

TConstScopedObjects & SetObjects()

virtual void x_CreateProjectItems()

override this function in derived classes and populate m_Items.

CTaxTreeToolJob(const CTaxTreeToolParams &params)

CTaxTreeToolJob.

static void GetLabel(const CObject &obj, string *label, ELabelType type=eDefault)

string m_Descr

mutex to sync our internals

vector< SConstScopedObject > TConstScopedObjects

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

TTaxId GetTaxId(const CBioseq_Handle &handle)

return the tax-id associated with a given sequence.

vector< TTaxId > TTaxIds

Get taxonomy ids of sequences Return -1 for sequences that aren't found Return 0 for sequences that d...

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TGi GetGi(const CSeq_id_Handle &idh, TGetFlags flags=0)

Get GI of a sequence Returns ZERO_GI if the sequence is not found or if it doesn't have GI.

TTaxIds GetTaxIds(const TSeq_id_Handles &idhs, TGetFlags flags=0)

vector< CSeq_id_Handle > TSeq_id_Handles

Bulk retrieval methods Common argument typedef - vector of requested ids.

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

CConstRef< CSeq_id > GetNonLocalIdOrNull(void) const

Find a non-local ID if present, consulting assembly details if all IDs for the overall sequence are l...

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string SizetToString(size_t value, TNumToStringFlags flags=0, int base=10)

Convert size_t to string.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static const char label[]

@ BM_GAP

GAP compression is ON.

void SetNodes(TNodes &value)

Assign a value to Nodes data member.

void SetTreetype(const TTreetype &value)

Assign a value to Treetype data member.

void SetLabel(const TLabel &value)

Assign a value to Label data member.

void SetItem(TItem &value)

Assign a value to Item data member.

TGi GetGi(void) const

Get the variant data.

bool IsGi(void) const

Check if variant Gi is selected.

Compressed bitset (entry point to bm.h)

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

Sequence information record.

STaxSeqInfo(int tax, string l)

string label

sequence label

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