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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/phytree__simplify_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/phy_tree/phytree_format/phytree_simplify.cpp Source File

42 const string

& feature_color,

45

: m_Root(

NULL

), m_Ostr(ostr)

47 Init

(feature_name, feature_color,

tree

);

51 const string

& feature_color,

61 m_Error

"Feature not in feature dictionary"

;

75

CBioTreeDynamic::CBioNode& x_node,

79

m_Ostr

"stack top: "

;

106

CBioTreeDynamic::CBioNode& x_node)

114 if

(x_node.IsLeaf()) {

115

pair<string, string> label_color

119 if

(label_color.first.empty() || label_color.second.empty()) {

120 m_Error

"Leafe node has unset feature, Id: " 128

m_Ostr

"Leaf, m_CurrentGroupName put on stack: " 140

CBioTreeDynamic::CBioNode& x_node)

143

m_Ostr

"x_OnStepDown, Id: " 147 if

(x_node.IsLeaf()) {

152

m_Ostr

"Leaf, m_CurrentGroupName == DIFFERENT_GROUPS" 161 m_Error

"Leafe node has unset feature, Id: " 175

m_Ostr

" group name different, changing stack top to DIFFERENT_GROUPS" 183

m_Ostr

" group name the same, stack top not changed" 193

CBioTreeDynamic::CBioNode& x_node)

200 const

pair<string, string> subtree_label_color =

m_LabelStack

.top();

245 if

(

m_LabelStack

.top().first != subtree_label_color.first)

254 const string

& color_feature,

256

: m_LabelFeatureTag(label_feature),

257

m_ColorFeatureTag(color_feature),

258

m_FoundQueryNode(

false

259

m_FoundSeqFromType(

false

260

m_FoundSeqFromVerifiedMat(

false

261

m_FoundSeqReferenceDB(

false

262

m_FoundSeqKmerBlast(

false

)

266 m_Error

"Feature not in feature dictionary"

;

274

CBioTreeDynamic::CBioNode& node,

321 const

CBioTreeDynamic::CBioNode& node)

const 329 const

CBioTreeDynamic::CBioNode& node)

const 336 const

CBioTreeDynamic::CBioNode& node)

const 343 const

CBioTreeDynamic::CBioNode& node)

const 351 const string

& feature_color,

352 const string

& feature_acc,

357 Init

(feature_name, feature_color, feature_acc,

tree

);

361 const string

& feature_color,

362 const string

& feature_acc,

383

CBioTreeDynamic::CBioNode& x_node,

401

m_Ostr

"Number of blast names ="

<< nodeMap.

size

() << endl;

402 for

(

auto

it = nodeMap.

begin

(); it != nodeMap.

end

(); ++it) {

403

vector <CPhyTreeNodeAnalyzer::TLeafNodeInfo> vecInf = it->second;

404 string

printStr = (vecInf.size() > 1) ?

" nodeIDs: "

" nodeID: "

;

405

m_Ostr

"Blast name: "

<< it->first << printStr;

406 for

(

size_t i

= 0;

< vecInf.size();

++){

407

m_Ostr

<< vecInf[

].nodeID <<

","

;

410

printStr = (vecInf.size() > 1) ?

" Accessions: "

" Accession: "

;

412 for

(

size_t i

= 0;

< vecInf.size();

++){

413

m_Ostr

<< vecInf[

].accession <<

","

;

422

vector <TLeafNodeInfo> vecLeafInfoNode;

425

leafInfoNode.

nodeID

= x_node.GetValue().GetId();

430

vecLeafInfoNode.push_back(leafInfoNode);

441

CBioTreeDynamic::CBioNode& x_node)

448 if

(x_node.IsLeaf()) {

450 m_Error

"Leaf node has unset feature, Id: " 461

CBioTreeDynamic::CBioNode& x_node)

466 if

(x_node.IsLeaf()) {

469 m_Error

"Leaf node has unset feature, Id: " 484 for

(

auto

it = nodeMap2.

begin

(); it != nodeMap2.

end

(); ++it) {

485 if

(mapResult.count(it->first) > 0 ) {

486

vector <TLeafNodeInfo> vecInf2 = it->second;

487

vector <TLeafNodeInfo> vecInf1 = mapResult[it->first];

488

vecInf1.

insert

(vecInf1.end(), vecInf2.begin(), vecInf2.end());

489

mapResult[it->first].

insert

(mapResult[it->first].

end

(), vecInf2.begin(), vecInf2.end());

499

CBioTreeDynamic::CBioNode& x_node)

static string GetFeatureTag(EFeatureID feat)

Get tree feature tag.

static const char * kNodeInfoSeqFromType

Node feature "node-info" value for sequences from type.

@ eNodeInfoId

Used for denoting query nodes.

static const char * kNodeInfoSeqReferenceDB

static const char * kNodeInfoQuery

Node feature "node-info" value for query nodes.

static const char * kNodeInfoSeqKmerBlast

static const char * kNodeInfoSeqFromVerifiedMat

bool x_IsSeqReferenceDB(const CBioTreeDynamic::CBioNode &node) const

CPhyTreeLabelTracker(const string &label, const string &color, CBioTreeDynamic &tree)

bool m_FoundSeqFromVerifiedMat

bool x_IsSeqKmerBlast(const CBioTreeDynamic::CBioNode &node) const

bool x_IsQuery(const CBioTreeDynamic::CBioNode &node) const

ETreeTraverseCode operator()(CBioTreeDynamic::CBioNode &node, int delta)

bool m_FoundSeqReferenceDB

bool x_IsSeqFromVerifiedMat(const CBioTreeDynamic::CBioNode &node) const

bool x_IsSeqFromType(const CBioTreeDynamic::CBioNode &node) const

TLabelColorMap m_LabelsColors

void x_InitLeafNodeStack(CBioTreeDynamic::CBioNode &x_node)

void x_PrintNodeMap(TLeafNodeInfoMap nodeMap)

stack< TLeafNodeInfoMap > m_InfoStack

CLabeledNodes m_LabeledNodes

ETreeTraverseCode x_OnStepLeft(CBioTreeDynamic::CBioNode &x_node)

TLeafNodeInfoMap x_CombineNodeMaps(TLeafNodeInfoMap nodeMap1, TLeafNodeInfoMap nodeMap2)

ETreeTraverseCode operator()(CBioTreeDynamic::CBioNode &node, int delta)

string m_LabelFeatureName

CPhyTreeNodeAnalyzer(const string &feature_name, const string &feature_acc, const string &feature_color, CBioTreeDynamic &tree, CNcbiOfstream *ostr=NULL)

string m_ColorFeatureName

ETreeTraverseCode x_OnStepRight(CBioTreeDynamic::CBioNode &x_node)

void Init(const string &feature_name, const string &feature_color, const string &feature_acc, CBioTreeDynamic &tree)

ETreeTraverseCode x_OnStepDown(CBioTreeDynamic::CBioNode &x_node)

map< string, vector< TLeafNodeInfo > > TLeafNodeInfoMap

ETreeTraverseCode operator()(CBioTreeDynamic::CBioNode &node, int delta)

bool x_IsRoot(CBioTreeDynamic::CBioNode *node) const

ETreeTraverseCode x_OnStepRight(CBioTreeDynamic::CBioNode &x_node)

stack< pair< string, string > > m_LabelStack

stack< TBioTreeNodeId > m_ParentIdStack

string m_ColorFeatureName

CBioTreeDynamic::CBioNode * m_Root

void Init(const string &feature_name, const string &feature_color, CBioTreeDynamic &tree)

CLabeledNodes m_LabeledNodes

CPhyTreeNodeGroupper(const string &feature_name, const string &feature_color, CBioTreeDynamic &tree, CNcbiOfstream *ostr=NULL)

ETreeTraverseCode x_OnStepLeft(CBioTreeDynamic::CBioNode &x_node)

string m_LabelFeatureName

ETreeTraverseCode x_OnStepDown(CBioTreeDynamic::CBioNode &x_node)

const_iterator begin() const

const_iterator end() const

iterator_bool insert(const value_type &val)

container_type::value_type value_type

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

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

Convert int to string.

ETreeTraverseCode

Tree traverse code returned by the traverse predicate function.

bool HasFeature(const string &feature_name) const

Check if feature is listed in the dictionary.

@ eTreeTraverseStop

Stop traversal (return form algorithm)

@ eTreeTraverse

Keep traversal.

static const char label[]

Int4 delta(size_t dimension_, const Int4 *score_)

static const string s_kDifferentGroups

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