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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cuTaxNRCriteria_8cpp_source.html below:

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

52

}

catch

(std::bad_cast) {

58 bool

gotAnswer =

false

;

60 TTaxItemId

prefNodeIdLHS, prefNodeIdRHS, modelOrgIdLHS, modelOrgIdRHS;

61 string

nodeName, orgName;

69 if

(prefNodeIdLHS == badId) {

70 result

= (prefNodeIdRHS == badId) ? 0 : -1;

72

}

else if

(prefNodeIdRHS == badId) {

80 if

(!gotAnswer && prefNodeIdLHS != prefNodeIdRHS) {

90 if

(modelOrgIdLHS == badId) {

91 if

(modelOrgIdRHS == badId) {

96

}

else if

(modelOrgIdRHS == badId) {

98

}

else if

(modelOrgIdLHS != modelOrgIdRHS) {

159 m_name

"Taxonomic Non-redundification Criteria"

;

178 unsigned int

nSubcluster = 0, nMarkedRedundant = 0;

183 if

(!clusterPtr || !

m_id2ItemMap

)

return

nMarkedRedundant;

195 for

(; itemIt != itemItEnd; ++itemIt) {

201 if

(priorityNodeId == -1) priorityNodeId = badId;

210

taxNRItem->

keep

false

;

215 if

(

m_subclusters

.count(priorityNodeId) == 0) ++nSubcluster;

223 if

(report && report->length() > 0) report->append(

"\n"

);

225 return

nMarkedRedundant;

231 string

nodeName, orgName;

246 return

(lhsItem.taxId == rhsItem.

taxId

) ? 0 : (lhsItem.taxId < rhsItem.

taxId

) ? -1 : 1;

TCluster::iterator TClusterIt

TCluster::value_type TClusterVT

TId2Item::value_type TId2ItemVT

static const TItemId INVALID_ITEM_ID

int GetPriorityTaxnode(TTaxId taxid, string &nodeName, TaxClient *taxClient=NULL)

TTaxId GetTaxIdFromClient(const CBioseq &bioseq)

virtual int CompareItems(const CTaxNRItem &lhs, const CTaxNRItem &rhs) const

void InitializeCriteria()

TSubclusterMap m_subclusters

virtual ~CTaxNRCriteria()

CPriorityTaxNodes * m_priorityTaxNodes

TId2TaxidMap::const_iterator TId2TaxidMapCIt

virtual unsigned int Apply(CBaseClusterer::TCluster *&cluster, string *report=NULL)

TTaxId GetTaxIdForId(const CBaseClusterer::TId &id) const

static TaxClient * m_taxClient

static const TTaxItemId INVALID_TAX_ITEM_ID

static int CompareItems(const CTaxNRItem &lhs, const CTaxNRItem &rhs)

virtual int Compare(const CNRItem &rhs) const

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

virtual bool ConnectToTaxServer()

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

const_iterator begin() const

const_iterator end() const

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.

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

Convert int to string.

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

Convert UInt to string.

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.

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