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

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/phytree__format_8cpp_source.html below:

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

vector<int> mark_leaves;

(mark_query_node) {

mark_leaves.push_back(0);

label_type, mark_leaves,

vector<int>& mark_leaves,

label_type, mark_leaves,

vector<string>& seq_ids,

mv_build_name)

vector<int> mark_leaves;

label_type, mark_leaves,

mark_query_node)

vector<int> mark_leaves;

(mark_query_node) {

mark_leaves.push_back(0);

vector<int> mark_leaves;

mark_leaves.push_back(0);

lbl_type, mark_leaves,

vector<string> labels;

& tree_name)

vector<string> labels;

<<

<< labels.size() <<

<<

(vector<string>, it, labels) {

<<

<< tree_name <<

<<

(!groupper.

().empty()) {

(!groupper.

().empty()) {

);

CBioTreeDynamic::CBioNode* node =

(node_id);

(!

.GetError().empty()) {

= it->first;

(; it !=

.End(); ++it) {

+=

+ it->first;

(

.GetNumLabels() == 1) {

(

.FoundQueryNode()) {

(

.FoundSeqFromType()) {

(

.FoundSeqFromVerifiedMat()) {

(

.FoundSeqReferenceDB()) {

(

.FoundSeqKmerBlast()) {

leafCount =

.GetLeafCount();

(leafCount != 0) {

CBioTreeDynamic::CBioNode* parent

= (CBioTreeDynamic::CBioNode*)node->GetParent();

parent->GetValue().features.SetFeature(fid,

node->GetValue().features.GetFeatureValue(fid));

node = parent->DetachNode(node);

node->AddNode(parent);

CBioTreeDynamic::CBioNode* node =

(new_root_id);

(node &&

(*node) && node->GetParent()) {

node = (CBioTreeDynamic::CBioNode*)node->GetParent();

(!node->GetParent()) {

vector<CBioTreeDynamic::CBioNode*> children;

CBioTreeDynamic::CBioNode::TParent::TNodeList_I it

= old_root->SubNodeBegin();

(; it != old_root->SubNodeEnd();it++) {

children.push_back((CBioTreeDynamic::CBioNode*)*it);

old_root->DetachNode(*ch);

CBioTreeDynamic::CBioNode* new_old_root

=

CBioTreeDynamic::CBioNode(*old_root);

(vector<CBioTreeDynamic::CBioNode*>, ch, children) {

new_old_root->AddNode(*ch);

CBioTreeDynamic::CBioNode* parent

= (CBioTreeDynamic::CBioNode*)node->GetParent();

node = parent->DetachNode(node);

node->AddNode(parent);

CBioTreeDynamic::CBioNode* node =

(root_id);

collapsed =

;

CBioTreeDynamic::CBioNode::TParent* parent = node->GetParent();

parent->DetachNode(node);

(!finder.

() && throw_if_null) {

it != groupper.

(); ++it) {

(leafCount != 0) {

(nodeMap.

() <= 2) {

leafCount = it->second.size();

(nodeMap.

() == 1) {

nodeColor = it->second[0].nodeColor;

(nodeMap.

() == 2) {

(leafCount > it->second.size()) {

title +=

+ it->first;

title = it->first +

+ title;

leafCount += it->second.size();

title =

;

(

it = nodeMap.

(); it != nodeMap.

(); ++it) {

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

leafCount += vecInf.size();

it != groupper.

(); ++it) {

(leafInfoMap && !(*leafInfoMap).

()) {

,nodeColor;

(!nodeColor.empty()) {

&

)

CBioTreeDynamic::CBioNode& node,

vector<string>& labels,

(!node.IsLeaf()) {

(CBioTreeDynamic::CBioNode::TNodeList_CI it = node.SubNodeBegin(); it != node.SubNodeEnd(); ++it) {

(it != node.SubNodeBegin())

name_subtrees,

);

(!is_outer_node) {

(node.IsLeaf() || !

.empty()) {

(

=0;

<

.length();

++)

(node.IsLeaf() || name_subtrees) {

labels.push_back(

);

((*node)->CanGetFeatures()) {

blastName =

,accNbr;

(*node)->SetFeatures().Set()) {

((*node_feature)->GetFeatureid() ==

) {

label_feature_node = *node_feature;

blastName = (*node_feature)->GetValue();

accNbr = (*node_feature)->GetValue();

((*node_feature)->GetFeatureid() == featureSelectedID) {

selected_feature_node = *node_feature;

= selected_feature_node->GetValue();

label_feature_node->ResetValue();

label_feature_node->SetValue() =

;

get_best_id =

;

(seq_id_handle.

()) {

get_best_id =

;

(*seq_id).GetLabel(&id_string);

blast_tax_name)

= {

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

};

(;

< blast_name_color_map.size();

++) {

pair<string, string>& map_item = blast_name_color_map[

];

(map_item.first == blast_tax_name) {

= map_item.second;

blast_name_color_map.push_back(make_pair(blast_tax_name,

));

vector<int>& mark_leaves,

success = tax.

();

);

sequence::CDeflineGenerator defgen;

num_rows = (

)seqids.size();

vector<string> labels(num_rows);

vector<string> organisms(num_rows);

vector<string> accession_nbrs(num_rows);

vector<string> titles(num_rows);

vector<string> blast_names(num_rows);

vector<string> tax_node_colors(num_rows);

vector<CBioseq_Handle> bio_seq_handles(num_rows);

vector<string> common_names(num_rows);

(

=0;

< num_rows;

++) {

common_names[

] = (common_names[

].empty()) ? organisms[

] : common_names[

];

(!success || blast_names[

].

()) {

titles[

] = defgen.GenerateDefline(bio_seq_handles[

]);

& dtg =

->GetGeneral();

(accession_nbrs[

].

()) {

accession_nbrs[

] =

->GetSeqIdString(

);

(label_type) {

labels[

] = organisms[

];

labels[

] = titles[

];

labels[

] = blast_names[

];

labels[

] = accession_nbrs[

];

labels[

] = accession_nbrs[

] +

+ blast_names[

] +

;

labels[

] = organisms[

] +

+ accession_nbrs[

] +

;

labels[

] = common_names[

];

(labels[

].

()) {

(*best_id).GetLabel(&labels[

]);

((*node)->CanGetFeatures()) {

(*node)->SetFeatures().Set()) {

((*node_feature)->GetFeatureid() ==

) {

label_id = (*node_feature)->GetValue();

seq_number;

(!

((

) label_id[0])) {

* ptr = label_id.c_str();

(*node_feature)->GetValue());

((

)seq_number >= num_rows) {

(*node_feature)->SetValue(labels[seq_number]);

(!organisms[seq_number].

()) {

(!titles[seq_number].

()) {

(!accession_nbrs[seq_number].

()) {

(!blast_names[seq_number].

()) {

(!common_names[seq_number].

()) {

(seqTypeMap.

()) {

tax_node_colors[seq_number], node);

(!seqTypeMap.

()) {

(!mark_leaves.empty()

&& binary_search(mark_leaves.begin(),

mark_leaves.end(), seq_number)) {

(linkoutDB) {

seqLinkout = linkoutDB->

(*seqids[seq_number],

);

(!seqTypeMap.

()) {

(simpleTree) {

(simpleTree) {

((

)num_rows != num_leaves) {

);

( iter != seqTypeMap.

() ){

seqType = iter->second;

vector<string>& ids,

vector< pair< CNode*, CSeq_id_Handle> > nodes;

((*node)->CanGetFeatures()) {

(*node)->SetFeatures().Set()) {

((*node_feature)->GetFeatureid() ==

pair<CNode*, CSeq_id_Handle> p;

p.first = node->GetNonNullPointer();

(vector<string>, sid, ids) {

pair<CNode*, CSeq_id_Handle> p(

, idhandle);

vector< pair<CNode*, CSeq_id_Handle> >::iterator node;

(node = nodes.begin();node != nodes.end();++node) {

feat_descr->SetId(

);

feat_descr->SetName(desc);

btc.

().Set().push_back(feat_descr);

CNodeSet::Tdata::iterator iter)

node_feature->SetFeatureid(

);

node_feature->SetValue(

);

(*iter)->SetFeatures().Set().push_back(node_feature);

node_feature->SetFeatureid(

);

node_feature->SetValue(

);

node->

().Set().push_back(node_feature);

Things for representing and manipulating bio trees.

static const char * bgColor

static string GetGnlID(const objects::CDbtag &dtg)

Return ID for GNL label.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

Computaion of distance-based phylognetic tree.

CRef< CBioTreeContainer > GetSerialTree(void) const

Get serial tree.

const vector< CRef< CSeq_id > > & GetSeqIds(void) const

Get seq-ids of sequences used in tree construction.

CRef< CScope > GetScope(void)

Get scope.

Tree visitor, finds BioTreeDynamic node by id.

CBioTreeDynamic::CBioNode * GetNode(void)

Get pointer to found node.

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

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

Expand subtree.

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

bool HasSeqReferenceDB(void) const

int GetLeafCount(void) const

bool HasSeqFromVerifiedMat(void) const

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 IsSingleBlastName(void) const

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

ETreeSimplifyMode m_SimplifyMode

Current tree simplification mode.

void x_InitTreeFeatures(CBioTreeContainer &btc, const vector< CRef< CSeq_id > > &seqids, CScope &scope, ELabelType label_type, const vector< int > &mark_leaves, TBlastNameColorMap &bcolormap, map< string, int > &seqTypeMap, bool simpleTree=false, ILinkoutDB *linkoutDB=NULL, int linkoutType=0)

Create and initialize tree features.

static void x_AddFeature(int id, const string &value, CNodeSet::Tdata::iterator iter)

Add feature to tree node.

void x_MarkNode(CBioTreeDynamic::CBioNode *node, const string &color)

Mark node.

void RerootTree(int new_root_id)

Reroot tree.

void x_Init(void)

Init class attributes to default values.

static string GetFeatureTag(EFeatureID feat)

Get tree feature tag.

int GetRootNodeID(void)

Get tree root node id.

CBioTreeDynamic m_Dyntree

Stores tree data.

string x_GetSeqIDString(CBioseq_Handle &handle, bool get_gi_first)

static void x_Expand(CBioTreeDynamic::CBioNode &node)

Expand node (show subtree)

bool WriteTreeAs(CNcbiOstream &out, ETreeFormat format)

Write tree structure to stream in selected format.

void FullyExpand(void)

Fully expand tree.

CPhyTreeFormatter(CPhyTreeCalc &guide_tree_calc, ELabelType lbl_type=eSeqId, bool mark_query_node=true, ILinkoutDB *linkoutDB=NULL, int linkoutType=0)

Constructor.

TBlastNameColorMap m_BlastNameColorMap

Blast Name to color map.

CBioTreeDynamic::CBioNode * GetNonNullNode(TBioTreeNodeId id)

Get pointer to the node with given id and throw exception if node not found.

bool ExpandCollapseSubtree(int node_id)

Expand or collapse subtree rooted in given node.

static const char * kNodeInfoSeqFromType

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

vector< TBlastNameToColor > TBlastNameColorMap

@ 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.

static void x_Collapse(CBioTreeDynamic::CBioNode &node)

Collapse node (do not show subtree)

CBioTreeDynamic::CBioNode * x_GetBioNode(TBioTreeNodeId id, bool throw_if_null=true)

Find pointer to a BioTreeDynamic node with given numerical id.

void x_AddFeaturesForInnerNodes(CPhyTreeNodeAnalyzer &groupper)

bool PrintNewickTree(CNcbiOstream &ostr)

Write tree in Newick format to stream.

ELabelType

Information shown as labels in the guide tree.

bool WriteTree(CNcbiOstream &out)

Write tree structure to stream.

static const char * kNodeInfoSeqReferenceDB

map< string, int > m_SeqTypeMap

bool IsSingleBlastName(void)

Check whether tree is composed of sequences with the same Blast Name.

void x_CollapseSubtrees(CPhyTreeNodeGroupper &groupper)

Collapse given subtrees.

void CollapseToViewPort(void)

CBioTreeDynamic::CBioNode * GetNode(TBioTreeNodeId id)

Get pointer to the node with given id.

static int x_FindSeqType(map< string, int > &seqTypeMap, string idString)

ETreeSimplifyMode

Tree simplification modes.

@ eFullyExpanded

Tree fully expanded.

@ eNone

No simplification mode.

@ eCollapseToViewPort

collapse to viewport

@ eByBlastName

Subtrees that contain sequences with the the same Blast Name are collapsed.

void x_PrintNewickTree(CNcbiOstream &ostr, const CBioTreeDynamic::CBioNode &node, vector< string > &labels, bool name_subtrees=true, bool is_outer_node=true)

Generates tree in Newick format, recursive.

void x_InitTreeLabels(CBioTreeContainer &btc, ELabelType lbl_type)

Init tree leaf labels with selected labels type.

void x_MarkLeavesBySeqId(CBioTreeContainer &btc, vector< string > &ids, CScope &scope)

Mark leave nodes corresponding to sequences with given sequence ids.

bool ShowSubtree(int root_id)

Show subtree.

static const char * kNodeInfoQuery

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

static bool x_IsLeafEx(const CBioTreeDynamic::CBioNode &node)

Check if node is a leaf or collapsed.

CRef< CBioTreeContainer > GetSerialTree(void)

Get serialized tree.

static void x_AddFeatureDesc(int id, const string &desc, CBioTreeContainer &btc)

Add feature descriptor to tree.

static const char * kNodeInfoSeqKmerBlast

static bool x_IsExpanded(const CBioTreeDynamic::CBioNode &node)

Check if node is expanded (subtree shown)

ETreeFormat

Output formats.

static const char * kNodeInfoSeqFromVerifiedMat

string m_MapViewerBuildName

vector< CConstRef< CSeq_id > > m_TreeSeqIDs

void SimplifyTree(ETreeSimplifyMode method)

Group nodes according to user-selected scheme and collapse subtrees composed of nodes that belong to ...

bool PrintNexusTree(CNcbiOstream &ostr, const string &tree_name="Blast_guide_tree")

Write tree in Nexus format to stream.

Tree visitor, finds all labels and node colors for leafes.

TLabelColorMap::iterator TLabelColorMap_I

CLabeledNodes::iterator CLabeledNodes_I

CLabeledNodes_I Begin(void)

const string & GetError(void) const

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

CLabeledNodes::iterator CLabeledNodes_I

CLabeledNodes_I Begin(void)

const string & GetError(void) const

bool GetBlastName(TTaxId tax_id, string &blast_name_out)

virtual int GetLinkout(TGi gi, const string &mv_build_name)=0

Retrieve the Linkout for a given GI.

container_type::iterator iterator

const_iterator begin() const

const_iterator end() const

const_iterator find(const key_type &key) const

static const Colors colors

API (CDeflineGenerator) for computing sequences' titles ("definitions").

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

main entry point for tests

#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.

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 MSerial_AsnText

I/O stream manipulators –.

CConstRef< CSeq_id > GetSeqId(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

@ fParse_Default

By default in ParseIDs and IsValid, allow raw parsable non-numeric accessions and plausible local acc...

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

const COrg_ref & GetOrg_ref(const CBioseq_Handle &handle)

Return the org-ref associated with a given sequence.

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

@ eGetId_ForceGi

return only a gi-based seq-id

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

bool IsSameBioseq(const CSeq_id_Handle &id1, const CSeq_id_Handle &id2, EGetBioseqFlag get_flag)

Check if two seq-ids are resolved to the same Bioseq.

@ eGetBioseq_All

Search bioseq, load if not loaded yet.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

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

Convert int to string.

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.

unsigned int TBioTreeFeatureId

Feature Id.

TBioTreeNode * GetTreeNodeNonConst()

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

Convert Dynamic tree to ASN.1 BioTree container.

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

Convert ASN.1 BioTree container to dynamic tree.

const TBioTreeNode * GetTreeNode() const

void SetTreeNode(TBioTreeNode *node)

Assign new top level tree node.

@ eTreeTraverse

Keep traversal.

static const char label[]

void SetNodes(TNodes &value)

Assign a value to Nodes data member.

void SetFdict(TFdict &value)

Assign a value to Fdict data member.

void SetFeatures(TFeatures &value)

Assign a value to Features data member.

list< CRef< CNodeFeature > > Tdata

list< CRef< CNode > > Tdata

const TTaxname & GetTaxname(void) const

Get the Taxname member data.

const TCommon & GetCommon(void) const

Get the Common member data.

E_Choice Which(void) const

Which variant is currently selected.

@ e_General

for other databases

unsigned int

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

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

constexpr bool empty(list< Ts... >) noexcept

const GenericPointer< typename T::ValueType > T2 value

Static variables safety - create on demand, destroy on application termination.

NCBI C++ auxiliary debug macros.

Int4 delta(size_t dimension_, const Int4 *score_)

static const char * s_kQueryNodeColor

static const char * s_kSeqKmerBlastNodeBgColor

static const char * s_kSubtreeDisplayed

static CSafeStatic< map< int, string > > seqTypeToBGColor

static const char * s_kNodeSize

static void s_InitFeatures(CPhyTreeNodeAnalyzer::TLeafNodeInfoMap nodeMap, string &title, int &leafCount, string &nodeColor)

static const char * s_kSeqReferenceDBNodeBgColor

static const char * s_kSeqFromVerifiedMatNodeBgColor

static const char * s_kUnknown

static CSafeStatic< map< int, string > > linkotTypeToBGColor

static const char * s_kSeqOfTypeNodeBgColor

#define MAX_NODES_TO_COLOR

static const char * s_kBranchColor

static const char * s_kQueryNodeBgColor

static const char * s_kSeqQueryNodeBgColor

void s_RerootUpstream(CBioTreeDynamic::CBioNode *node, TBioTreeFeatureId fid)

static string s_GetBlastNameColor(CPhyTreeFormatter::TBlastNameColorMap &blast_name_color_map, string blast_tax_name)

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