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/biotreeconv_8hpp_source.html below:

NCBI C++ ToolKit: include/algo/phy_tree/bio_tree_conv.hpp Source File

1 #ifndef ALGO_PHY_TREE___BIO_TREE_CONV__HPP 2 #define ALGO_PHY_TREE___BIO_TREE_CONV__HPP 55 template

class

TDstTreeNode,

class

TSrcTreeNode,

class

TNodeConvFunc>

78 if

(delta_level == 0) {

85

parent_node->AddNode(pnode);

90 if

(delta_level == 1) {

94

parent_node->AddNode(pnode);

98 if

(delta_level == -1) {

112 unsigned int

uid = src_node.GetValue().GetId();

113

pnode->GetValue().SetId(uid);

116 return

pnode.release();

129 template

class

TDynamicTree,

class

TSrcBioTree,

class

TNodeConvFunc>

131 const

TSrcBioTree& bio_tree,

132

TNodeConvFunc node_conv)

135 typedef typename

TSrcBioTree::TBioTreeNode TSrcTreeNodeType;

136 typedef typename

TDynamicTree::TBioTreeNode TDstTreeNodeType;

142 const

TSrcTreeNodeType *

= bio_tree.GetTreeNode();

157 template

class

TDynamicTree,

class

TTreeNode,

class

TNodeConvFunc>

159 const

TTreeNode* src_tree,

160

TNodeConvFunc node_conv)

164 typedef

TTreeNode TSrcTreeNodeType;

165 typedef typename

TDynamicTree::TBioTreeNode TDstTreeNodeType;

181 template

class

TDynamicTree,

class

TTreeNode,

class

TNodeConvFunc>

183

TNodeConvFunc node_conv,

184

TTreeNode*& dst_node)

186 typedef

TTreeNode TDstTreeNodeType;

187 typedef typename

TDynamicTree::TBioTreeNode TSrcTreeNodeType;

192 const

TSrcTreeNodeType *

= dyn_tree.GetTreeNode();

210 template

class

TBioTreeContainer,

class

TDynamicTree>

219 typedef typename

TNodeList::value_type::element_type

TCNode

;

228 m_NodeList

= &(tree_container->SetNodes().Set());

235 if

(delta_level < 0) {

248

cnode->SetParent(node_parent->GetValue().GetId());

252

TDynamicNodeValueType::TNodeFeaturesType::TFeatureList TFList;

253 const

TFList& flist = v.features.GetFeatureList();

255 if

(!flist.empty()) {

259 ITERATE

(

typename

TFList, it, flist) {

261 const string

fvalue = it->value;

264

cfeat->SetFeatureid(fid);

265

cfeat->SetValue(fvalue);

267

fset.Set().push_back(cfeat);

286 template

class

TBioTreeContainer,

class

TDynamicTree>

288 const

TDynamicTree& dyn_tree)

292 typedef typename

TBioTreeContainer::TFdict TContainerDict;

298

TContainerDict& fd = tree_container.SetFdict();

299 typename

TContainerDict::Tdata& feat_list = fd.Set();

301 typename

TContainerDict::Tdata::value_type::element_type TCFeatureDescr;

305 const string

& fvalue = it->second;

312

feat_list.push_back(d);

319 typedef typename

TDynamicTree::TBioTreeNode TTreeNode;

320 const

TTreeNode *

= dyn_tree.GetTreeNode();

323

func(&tree_container);

334 template

class

TBioTreeContainer,

class

TDynamicTree>

336 const

TBioTreeContainer& tree_container,

337 bool

preserve_node_ids =

false

)

343 typedef typename

TBioTreeContainer::TFdict TContainerDict;

346 const

TContainerDict& fd = tree_container.GetFdict();

347 const typename

TContainerDict::Tdata& feat_list = fd.Get();

349 ITERATE

(

typename

TContainerDict::Tdata, it, feat_list) {

351 const string

& fvalue = (*it)->GetName();

357 typedef typename

TBioTreeContainer::TNodes TCNodeSet;

358 typedef typename

TCNodeSet::Tdata TNodeList;

359 typedef typename

TNodeList::value_type::element_type TCNode;

361 const

TNodeList node_list = tree_container.GetNodes().Get();

363

std::map<TBioTreeNodeId, typename TDynamicTree::TBioTreeNode*> pmap;

365 ITERATE

(

typename

TNodeList, it, node_list) {

371 typedef typename

TDynamicTree::TBioTreeNode TDynamicNodeType;

372 typedef typename

TDynamicNodeType::TValueType TDynamicNodeValueType;

374

TDynamicNodeValueType v;

375 if

(preserve_node_ids) {

379 typedef typename

TCNode::TFeatures TCNodeFeatureSet;

381 if

(cnode->CanGetFeatures()) {

382 const

TCNodeFeatureSet& fset = cnode->GetFeatures();

384 const typename

TCNodeFeatureSet::Tdata& flist = fset.Get();

386 ITERATE

(

typename

TCNodeFeatureSet::Tdata, fit, flist) {

387 unsigned int

fid = (*fit)->GetFeatureid();

388 const string

& fvalue = (*fit)->GetValue();

390

v.features.SetFeature(fid, fvalue);

396 if

(cnode->CanGetParent()) {

398 typename

TDynamicTree::TBioTreeNode* node =

NULL

;

400 typename

TDynamicTree::TBioTreeNode* parent_node = pmap[parent_id];

401 if

(parent_node !=

NULL

) {

402

node = dyn_tree.AddNode(v, parent_node);

403 if

(!preserve_node_ids) {

404

dyn_tree.SetNodeId(node);

413

TDynamicNodeType* dnode =

new

TDynamicNodeType(v);

414

dyn_tree.SetTreeNode(dnode);

415 if

(!preserve_node_ids) {

416

dyn_tree.SetNodeId(dnode);

427 template

class

TBioTreeContainer,

class

TDynamicForest>

429 const

TDynamicForest& dyn_forest)

433 typedef typename

TBioTreeContainer::TFdict TContainerDict;

439

TContainerDict& fd = tree_container.SetFdict();

440 typename

TContainerDict::Tdata& feat_list = fd.Set();

442 typename

TContainerDict::Tdata::value_type::element_type TCFeatureDescr;

446 const string

& fvalue = it->second;

453

feat_list.push_back(d);

459 typedef typename

TDynamicForest::TBioTree::TBioTreeNode TTreeNode;

461

func(&tree_container);

463 for

(

unsigned int i

=0;

<dyn_forest.GetTrees().

size

(); ++

) {

464 const

TTreeNode *

= dyn_forest.GetTrees()[

]->GetTreeNode();

474 template

class

TBioTreeContainer,

class

TDynamicForest>

476 const

TBioTreeContainer& tree_container)

482 typedef typename

TBioTreeContainer::TFdict TContainerDict;

485 const

TContainerDict& fd = tree_container.GetFdict();

486 const typename

TContainerDict::Tdata& feat_list = fd.Get();

488 ITERATE

(

typename

TContainerDict::Tdata, it, feat_list) {

490 const string

& fvalue = (*it)->GetName();

496 typedef typename

TBioTreeContainer::TNodes TCNodeSet;

497 typedef typename

TCNodeSet::Tdata TNodeList;

498 typedef typename

TNodeList::value_type::element_type TCNode;

500 const

TNodeList node_list = tree_container.GetNodes().Get();

502 typename

TDynamicForest::TBioTree* current_tree =

NULL

;

504 ITERATE

(

typename

TNodeList, it, node_list) {

510 typedef typename

TDynamicForest::TBioTree TDynamicTree;

511 typedef typename

TDynamicTree::TBioTreeNode TDynamicNodeType;

512 typedef typename

TDynamicNodeType::TValueType TDynamicNodeValueType;

514

TDynamicNodeValueType v;

517 typedef typename

TCNode::TFeatures TCNodeFeatureSet;

519 if

(cnode->CanGetFeatures()) {

520 const

TCNodeFeatureSet& fset = cnode->GetFeatures();

522 const typename

TCNodeFeatureSet::Tdata& flist = fset.Get();

524 ITERATE

(

typename

TCNodeFeatureSet::Tdata, fit, flist) {

525 unsigned int

fid = (*fit)->GetFeatureid();

526 const string

& fvalue = (*fit)->GetValue();

528

v.features.SetFeature(fid, fvalue);

534 if

(cnode->CanGetParent()) {

535 if

(current_tree !=

NULL

) {

537

current_tree->AddNode(v, parent_id);

544

current_tree =

new typename

TDynamicForest::TBioTree();

545

dyn_forest.AddTree(current_tree);

547

TDynamicNodeType* dnode =

new

TDynamicNodeType(v);

548

current_tree->SetTreeNode(dnode);

578 template

class

TITaxon4Each,

class

TITaxon1Node,

579 class

TITreeIterator,

class

TBioTreeContainer>

583 typedef typename

TITreeIterator::EAction

EAction

;

587 typedef typename

TNodeList::value_type::element_type

TCNode

;

598 m_NodeList

= &(tree_container->SetNodes().Set());

612 if

(uid > (

unsigned int

)

m_MaxUID

) {

616

vector<TTaxId>::size_type psize =

m_Parents

.size();

619

cnode->SetParent(

TAX_ID_TO

(

int

, parent_tax_id));

631

cfeat->SetValue(pNode->GetName());

633

fset.Set().push_back(cfeat);

639

cfeat->SetValue(pNode->GetName());

641

fset.Set().push_back(cfeat);

648

cfeat->SetValue(pNode->GetBlastName());

650

fset.Set().push_back(cfeat);

657 int

v = pNode->GetRank();

660

fset.Set().push_back(cfeat);

667 int

v = pNode->GetDivision();

670

fset.Set().push_back(cfeat);

677 int

v = pNode->GetGC();

680

fset.Set().push_back(cfeat);

687 int

v = pNode->GetMGC();

690

fset.Set().push_back(cfeat);

697 int

v = pNode->IsUncultured();

700

fset.Set().push_back(cfeat);

708

fset.Set().push_back(cfeat);

713 return

TITreeIterator::eOk;

719 m_Parents

.push_back(pParent->GetTaxId());

720 return

TITreeIterator::eOk;

727 return

TITreeIterator::eOk;

742 template

class

TBioTreeContainer>

744 unsigned int

feature_id,

745 const string

& feature_name)

747 typedef typename

TBioTreeContainer::TFdict TContainerDict;

748 typedef typename

TContainerDict::Tdata::value_type::element_type TFeatureDescr;

750

TContainerDict& fd = tree_container.SetFdict();

751 typename

TContainerDict::Tdata& feat_list = fd.Set();

754 ITERATE

(

typename

TContainerDict::Tdata, it, feat_list) {

755 if

( (

unsigned int

)((*it)->GetId()) == feature_id )

760

d->SetId(feature_id);

761

d->SetName(feature_name);

763

feat_list.push_back(d);

768 template

class

TBioTreeContainer,

769 class

TTaxon1,

class

TITaxon1Node,

class

TITreeIterator>

773 typedef typename

TITreeIterator::I4Each

T4Each

;

775

TITreeIterator, TBioTreeContainer>

791 const

TITaxon1Node* tax_node=0;

792 bool

res = tax.LoadSubtree(tax_id, &tax_node);

795

tax_tree_iter->GoNode(tax_node);

797

tax_tree_iter->TraverseDownward(tax_vis);

808

tax_tree_iter->GoRoot();

810

tax_tree_iter->TraverseDownward(tax_vis);

843 template

class

TBioTreeContainer>

849 typedef typename

TBioTreeContainer::TNodes TCNodeSet;

850 typedef typename

TCNodeSet::Tdata TNodeList;

851 typedef typename

TNodeList::value_type::element_type TCNode;

853 const

TNodeList node_list = tree_container.GetNodes().Get();

855 int

number_roots = 0;

857 ITERATE

(

typename

TNodeList, it, node_list) {

861 if

(!cnode->CanGetParent())

866 return

(number_roots > 1);

Things for representing and manipulating bio trees.

Visitor functor to convert dynamic tree nodes to ASN.1 BioTree container.

Taxon1 tree visitor functor.

Visitor functor to convert one tree to another.

#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.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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

Convert int to string.

virtual ~CTaxon1NodeConvertVisitor()

TNodeList::value_type::element_type TCNode

void TreeConvert2Dynamic(TDynamicTree &dyn_tree, const TTreeNode *src_tree, TNodeConvFunc node_conv)

Convert CTreeNode<> to dynamic tree using a node converter.

TCNodeFeatureSet::Tdata TNodeFeatureList

void BioTreeConvert2Dynamic(TDynamicTree &dyn_tree, const TSrcBioTree &bio_tree, TNodeConvFunc node_conv)

Convert biotree to dynamic tree using a node converter.

void BioTreeAddFeatureToDictionary(TBioTreeContainer &tree_container, unsigned int feature_id, const string &feature_name)

void SetupFeatureDictionary(TBioTreeContainer &tree_container)

Add elements to the feature dictionary.

CTaxon1NodeConvertVisitor(TBioTreeContainer *tree_container)

TNodeList::value_type::element_type TCNode

TDynamicNodeType::TValueType TDynamicNodeValueType

TCNode::TFeatures TCNodeFeatureSet

Fun TreeDepthFirstTraverse(TTreeNode &tree_node, Fun func)

Depth-first tree traversal algorithm.

ETreeTraverseCode

Tree traverse code returned by the traverse predicate function.

unsigned int TBioTreeNodeId

Tree node id. Every node has its unique id in the tree.

TSrcTreeNode TSrcTreeNodeType

TCNode::TFeatures TCNodeFeatureSet

ETaxon1ConvFeatures

Feature ids for Bio-Tree.

TNodeConvFunc & m_ConvFunc

void operator()(TBioTreeContainer &tree_container, TTaxon1 &tax, TTaxId tax_id)

TBioTreeContainer::TNodes TCNodeSet

unsigned int TBioTreeFeatureId

Feature Id.

TDstTreeNodeType * MakeNewTreeNode(const TSrcTreeNodeType &src_node)

TNodeFeatureList::value_type::element_type TCNodeFeature

TBioTreeContainer * m_TreeContainer

CTree2TreeFunc(TNodeConvFunc &func)

CTaxon1ConvertToBioTreeContainer()

void BioTreeConvert2Container(TBioTreeContainer &tree_container, const TDynamicTree &dyn_tree)

Convert Dynamic tree to ASN.1 BioTree container.

virtual EAction LevelBegin(const TITaxon1Node *pParent)

TBioTreeFeatureId Register(const string &feature_name)

vector< TTaxId > m_Parents

TNodeFeatureList::value_type::element_type TCNodeFeature

void BioTreeConvertContainer2Dynamic(TDynamicTree &dyn_tree, const TBioTreeContainer &tree_container, bool preserve_node_ids=false)

Convert ASN.1 BioTree container to dynamic tree.

TBioTreeContainer * m_Container

void operator()(TBioTreeContainer &tree_container, CRef< TITreeIterator > tax_tree_iter)

TDstTreeNodeType * m_DstTree

virtual EAction Execute(const TITaxon1Node *pNode)

CTaxon1NodeConvertVisitor< T4Each, TITaxon1Node, TITreeIterator, TBioTreeContainer > TTaxon1Visitor

TDstTreeNode TDstTreeNodeType

TCNodeFeatureSet::Tdata TNodeFeatureList

CBioTreeConvert2ContainerFunc(TBioTreeContainer *tree_container)

TITreeIterator::EAction EAction

TDstTreeNodeType * GetTreeNode()

TCNodeSet::Tdata TNodeList

TBioTreeContainer::TNodes TCNodeSet

const TFeatureDict & GetFeatureDict() const

Get reference on the internal map.

bool BioTreeContainerIsForest(const TBioTreeContainer &tree_container)

Function to determine tree if a given biotree container is a single tree or a forest.

ETreeTraverseCode operator()(const TDynamicNodeType &node, int delta_level)

TDynamicTree::TBioTreeNode TDynamicNodeType

TTreeNode * DynamicConvert2Tree(TDynamicTree &dyn_tree, TNodeConvFunc node_conv, TTreeNode *&dst_node)

Convert dynamic tree to CTreeNode<>, returned CTReeNode<> to be deleted by caller.

vector< TDstTreeNodeType * > m_TreeStack

virtual EAction LevelEnd(const TITaxon1Node *)

void BioTreeForestConvert2Container(TBioTreeContainer &tree_container, const TDynamicForest &dyn_forest)

Convert forest of Dynamic trees to ASN.1 BioTree container.

int GetMaxNodeId() const

Get max node id (available after conversion)

TITreeIterator::I4Each T4Each

void BioTreeConvertContainer2DynamicForest(TDynamicForest &dyn_forest, const TBioTreeContainer &tree_container)

Convert ASN.1 BioTree container to forest of dynamic trees.

TCNodeSet::Tdata TNodeList

ETreeTraverseCode operator()(const TSrcTreeNodeType &node, int delta_level)

@ eTreeTraverse

Keep traversal.

unsigned int

A callback function used to compare two keys in a database.

const struct ncbi::grid::netcache::search::fields::SIZE size

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

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

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/bio__tree__conv_8hpp_source.html below:

NCBI C++ ToolKit: include/algo/phy_tree/bio_tree_conv.hpp Source File

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/biotreeconv_8hpp_source.html below: