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

eLastId = eEdgeColorID

mark_query_node =

,

linkoutType = 0);

vector<int>& mark_leaves,

vector<string>& seq_ids,

mv_build_name =

);

simpleTree =

);

mark_query_node =

);

IsSingleBlastName(

);

GetRootNodeID(

);

eLabelId:

;

eDistId :

;

eSeqIdId:

;

eTitleId:

;

eOrganismId :

;

eAccessionNbrId:

;

eBlastNameId :

;

eAlignIndexId :

;

eNodeColorId :

;

eLabelColorId :

;

eLabelBgColorId :

;

eLabelTagColorId:

;

eTreeSimplificationTagId :

;

eNodeInfoId :

;

eLeafCountId :

;

eCommonNameID :

;

eNodeSizeID :

;

eEdgeColorID :

;

:

;

& tree_name =

);

FullyExpand(

);

SimplifyTree(ETreeSimplifyMode method);

ExpandCollapseSubtree(

node_id);

RerootTree(

new_root_id);

ShowSubtree(

root_id);

CollapseToViewPort(

);

throw_if_null =

);

x_IsExpanded(

CBioTreeDynamic::CBioNode& node);

x_IsLeafEx(

CBioTreeDynamic::CBioNode& node);

x_Collapse(CBioTreeDynamic::CBioNode& node);

x_Expand(CBioTreeDynamic::CBioNode& node);

CBioTreeDynamic::CBioNode& node,

vector<string>& labels,

name_subtrees =

,

is_outer_node =

);

x_MarkNode(CBioTreeDynamic::CBioNode* node,

&

);

vector<int>& mark_leaves,

simpleTree =

,

linkoutType = 0);

x_GetSeqIDString(

& handle,

get_gi_first);

x_AddFeatureDesc(

,

& desc,

x_AddFeature(

,

&

,

CNodeSet::Tdata::iterator iter);

x_AddFeature(

,

&

,

* node);

CBioTreeDynamic::CBioNode*

(

) {

m_Node;}

((*node).GetId() == m_NodeId) {

: m_IsSingleBlastName(

)

=

.GetFeatureDict();

);

(m_CurrentBlastName.empty()) {

m_CurrentBlastName = node.GetFeature(

(m_CurrentBlastName != node.GetFeature(

m_IsSingleBlastName =

;

: m_HasQueryNode(

),

m_HasSeqFromType(

),

m_HasSeqFromVerifiedMat(

),

m_HasSeqReferenceDB(

),

m_HasSeqKmerBlast(

),

=

.GetFeatureDict();

);

(node.GetFeature(GetFeatureTag(eNodeInfoId))

m_HasQueryNode =

;

(node.GetFeature(GetFeatureTag(eNodeInfoId))

== kNodeInfoSeqFromType) {

m_HasSeqFromType =

;

(node.GetFeature(GetFeatureTag(eNodeInfoId))

== kNodeInfoSeqFromVerifiedMat) {

m_HasSeqFromVerifiedMat =

;

(node.GetFeature(GetFeatureTag(eNodeInfoId))

== kNodeInfoSeqReferenceDB) {

m_HasSeqReferenceDB =

;

(node.GetFeature(GetFeatureTag(eNodeInfoId))

== kNodeInfoSeqKmerBlast) {

m_HasSeqKmerBlast =

;

pair<CNode*, CSeq_id_Handle>&

)

.second.AsString() <

.second.AsString();

Things for representing and manipulating bio trees.

Computaion of distance-based phylognetic tree.

@ eTaxonomyError

Problem initializing CTax object.

@ eInvalidOptions

Invalid parameter values.

@ eInvalidInput

Invalid constructor arguments.

@ eNodeNotFound

Node with desired id not found.

@ eTraverseProblem

Problem in one of the tree visitor classes.

NCBI_EXCEPTION_DEFAULT(CPhyTreeFormatterException, CException)

Tree visitor, finds BioTreeDynamic node by id.

CBioTreeDynamic::CBioNode * GetNode(void)

Get pointer to found node.

CBioTreeDynamic::CBioNode * m_Node

CBioNodeFinder(TBioTreeNodeId id)

Constructor.

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

Check if node has desired id.

Tree visitor class, expands all nodes and corrects node colors.

Tree visitor for checking whether a subtree contains a query node.

bool HasSeqReferenceDB(void) const

int GetLeafCount(void) const

bool HasSeqFromVerifiedMat(void) const

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

Expamine node: check if query node.

bool HasSeqKmerBlast(void) const

bool HasSeqFromType(void) const

Check if an examined subtree has a sequence from type.

bool HasQueryNode(void) const

Check if an examined subtree has a query node.

bool m_HasSeqFromVerifiedMat

CQueryNodeChecker(CBioTreeDynamic &tree)

Constructor.

bool m_IsSingleBlastName

Is one blast name in the tree.

string m_CurrentBlastName

Last identified blast name.

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

Expamine node.

CSingleBlastNameExaminer(CBioTreeDynamic &tree)

Constructor.

bool IsSingleBlastName(void) const

Check if all sequences in examined tree have the same Blast Name.

Compare pairs (node, sequence id handle) by sequence id.

bool operator()(const pair< CNode *, CSeq_id_Handle > &a, const pair< CNode *, CSeq_id_Handle > &b)

Class for adding tree features, maniplating and printing tree in standard text formats.

ETreeSimplifyMode m_SimplifyMode

Current tree simplification mode.

static string GetFeatureTag(EFeatureID feat)

Get tree feature tag.

CPhyTreeFormatter(CPhyTreeFormatter &tree)

Forbiding copy constructor.

CBioTreeDynamic m_Dyntree

Stores tree data.

TBlastNameColorMap m_BlastNameColorMap

Blast Name to color map.

TBlastNameColorMap & SetBlastNameColorMap(void)

Set Blast Name to color map.

vector< CConstRef< CSeq_id > > GetTreeSeqIDs(void)

Get tree seqIds in the order of nodeIds.

static const char * kNodeInfoSeqFromType

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

vector< TBlastNameToColor > TBlastNameColorMap

EFeatureID

Feature IDs used in guide tree.

@ eLabelBgColorId

Color for backgroud of node label.

@ eNodeInfoId

Used for denoting query nodes.

@ eTitleId

Sequence title.

@ eTreeSimplificationTagId

Is subtree collapsed.

@ eLabelColorId

Node label color.

@ eNodeColorId

Node color.

@ eOrganismId

Taxonomic organism id (for sequence)

@ eBlastNameId

Sequence Blast Name.

@ eAccessionNbrId

Sequence accession.

@ eDistId

Edge length from parent to this node.

@ eAlignIndexId

Index of sequence in Seq_align.

ELabelType

Information shown as labels in the guide tree.

static const char * kNodeInfoSeqReferenceDB

map< string, int > m_SeqTypeMap

CPhyTreeFormatter & operator=(CPhyTreeFormatter &tree)

Forbiding assignment operator.

ETreeSimplifyMode

Tree simplification modes.

@ eFullyExpanded

Tree fully expanded.

@ eNone

No simplification mode.

const CBioTreeDynamic & GetTree(void) const

Get tree structure.

static const char * kNodeInfoQuery

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

ETreeSimplifyMode GetSimplifyMode(void) const

Get current tree simplification mode.

static const char * kNodeInfoSeqKmerBlast

ETreeFormat

Output formats.

pair< string, string > TBlastNameToColor

Type for BlastName to color map.

static const char * kNodeInfoSeqFromVerifiedMat

string m_MapViewerBuildName

vector< CConstRef< CSeq_id > > m_TreeSeqIDs

~CPhyTreeFormatter()

Destructor.

This file provides tree visitor classes and functions for node groupping and simplification of phylog...

std::ofstream out("events_result.xml")

main entry point for tests

#define NCBI_THROW(exception_class, err_code, message)

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

ELabelType

For compatibility with legacy code.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

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.

bool HasFeature(const string &feature_name) const

Check if feature is listed in the dictionary.

@ eTreeTraverseStop

Stop traversal (return form algorithm)

@ eTreeTraverse

Keep traversal.

#define NCBI_XALGOPHYTREE_EXPORT

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

const GenericPointer< typename T::ValueType > T2 value

Defines NCBI C++ exception handling.

Int4 delta(size_t dimension_, const Int4 *score_)

USING_SCOPE(align_format)

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