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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/bio__tree_8cpp_source.html below:

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

45

: m_FeatureList(flist.m_FeatureList)

57  const string

&

value

)

114

: m_Dict(btr.m_Dict),

115

m_Name2Id(btr.m_Name2Id),

116

m_IdCounter(btr.m_IdCounter)

174  const string

& feature_name)

176  if

(

m_Dict

.count(

id

)) {

177  if

(

m_Dict

[

id

] == feature_name) {

186  "Duplicate feature name: "

+ feature_name);

190

pair<TBioTreeFeatureId, string>(

id

, feature_name));

192

pair<string, TBioTreeFeatureId>(feature_name,

id

));

199  if

(!

m_Dict

.count(

id

)) {

232  if

(!node.IsLeaf()) {

234

CBioTreeDynamic::TBioTreeNode::TNodeList_CI it = node.SubNodeBegin();

235  for

(; it != node.SubNodeEnd(); ++it) {

236  if

(it != node.SubNodeBegin()) {

240  const

CBioTreeDynamic::TBioTreeNode::TParent* p = *it;

253  if

(

tree

.GetFeatureDict().HasFeature(

"label"

)) {

254  label

= node.GetValue().features

255

.GetFeatureValue(

tree

.GetFeatureDict().GetId(

"label"

));

258  if

(!

label

.empty()) {

263  if

(

tree

.GetFeatureDict().HasFeature(

"dist"

)) {

264

dist_string = node.GetValue().features

265

.GetFeatureValue(

tree

.GetFeatureDict().GetId(

"dist"

));

267  if

(!dist_string.empty()) {

268

os <<

':'

<< dist_string;

289

os <<

"#nexus\n\nbegin trees;\ntree "

<< tree_name <<

" = "

;

291

os <<

"\nend;"

<< endl;

300  if

(

label

.find_first_of(

"()[]':;,_"

) == string::npos) {

302  string

unquoted =

label

;

303  for

(

size_t i

= 0;

i

<

label

.size(); ++

i

) {

304  if

(unquoted[

i

] ==

' '

) {

305

unquoted[

i

] =

'_'

;

310  if

(

label

.find_first_of(

"'"

) == string::npos) {

311  return '\''

+

label

+

'\''

;

314

rv.reserve(

label

.size() + 2);

316  for

(

unsigned int i

= 0;

i

<

label

.size(); ++

i

) {

317

rv.append(1,

label

[

i

]);

318  if

(

label

[

i

] ==

'\''

) {

320

rv.append(1,

label

[

i

]);

static string s_EncodeLabel(const string &label)

Things for representing and manipulating bio trees.

Features storage for the bio tree node.

Interface to obtain custom labels for nodes.

container_type::const_iterator const_iterator

const_iterator end() const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#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.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

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.

string GetName(TBioTreeFeatureId id) const

Return the featue name given the id, or "" if not found.

TFeatureDict m_Dict

id -> feature name map

void PrintNode(CNcbiOstream &os, const CBioTreeDynamic &tree, const CBioTreeDynamic::TBioTreeNode &node, const IBioTreeDynamicLabelFormatter *label_fmt)

Newick but without the terminal ';'.

void WriteNewickTree(CNcbiOstream &os, const CBioTreeDynamic &tree, const IBioTreeDynamicLabelFormatter *label_fmt)

Newick format output.

void Clear()

Clear the dictionary.

CBioTreeFeatureDictionary & operator=(const CBioTreeFeatureDictionary &btr)

unsigned int TBioTreeFeatureId

Feature Id.

TFeatureNameIdx m_Name2Id

id -> feature name map

void SetFeature(TBioTreeFeatureId id, const string &value)

Set feature value, feature if exists replaced, if not added.

virtual string GetLabelForNode(const CBioTreeDynamic::TBioTreeNode &node) const =0

TFeatureList m_FeatureList

TBioTreeFeatureId GetId(const string &feature_name) const

If feature is already registered returns its id by name.

CBioTreeFeatureList & operator=(const CBioTreeFeatureList &flist)

TBioTreeFeatureId Register(const string &feature_name)

Register new feature, return its id.

const string & GetFeatureValue(TBioTreeFeatureId id) const

Get feature value by id.

CBioNode TBioTreeNode

Biotree node (forms the tree hierarchy)

void Unregister(TBioTreeFeatureId id)

unsigned int m_IdCounter

Feature id counter.

bool HasFeature(const string &feature_name) const

Check if feature is listed in the dictionary.

CBioTreeFeatureDictionary()

void WriteNexusTree(CNcbiOstream &os, const CBioTreeDynamic &tree, const string &tree_name, const IBioTreeDynamicLabelFormatter *label_fmt)

Nexus format output (Newick with some stuff around it).

vector< CBioTreeFeaturePair > TFeatureList

void RemoveFeature(TBioTreeFeatureId id)

Remove feature from the list.

CNcbiOstream & operator<<(CNcbiOstream &os, const CBioTreeDynamic &tree)

Newick format output.

static const char label[]

const GenericPointer< typename T::ValueType > T2 value

Tree node feature pair (id to string)

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