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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cuSeqTreeAPI_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/structure/cd_utils/cuSeqTreeAPI.cpp Source File

45

: m_ma(), m_cd(0), m_family(0), m_seqTree(0), m_taxTree(0), m_taxClient(0),

46

m_useMembership(

true

), m_taxLevel(BySuperkingdom), m_treeOptions(), m_triedTreeMaking(

false

),

47

m_loadOnly(loadExistingTreeOnly)

49

vector<CDFamily*> families;

51  if

(families.size() != 1 )

53  for

(

int i

= 0 ;

i

<families.size();

i

++)

57

m_ma.setAlignment(*families[0]);

58

m_family = families[0];

62

: m_ma(), m_cd(cd), m_family(0), m_seqTree(0), m_taxTree(0), m_taxClient(0),

63

m_useMembership(

true

), m_taxLevel(BySuperkingdom), m_treeOptions(), m_triedTreeMaking(

false

),

69

: m_ma(), m_cd(0), m_family(&cdfam), m_seqTree(0), m_taxTree(0), m_taxClient(0),

70

m_useMembership(

true

), m_taxLevel(BySuperkingdom), m_treeOptions(

option

), m_triedTreeMaking(

false

),

140

<<

" because it does not have a consistent block alognment."

);

160  bool

loaded =

false

;

202

nodeParent.

isLeaf

=

false

;

203

nodeParent.

x

= cursor->x;

204

nodeParent.

y

= cursor->y;

206  while

(sib != cursor.

end

())

209

nodeChild.

x

= sib->x;

210

nodeChild.

y

= sib->y;

211

nodeTurn.

isLeaf

=

false

;

212

nodeTurn.

x

= nodeParent.

x

;

213

nodeTurn.

y

= nodeChild.

y

;

216

nodeChild.

isLeaf

=

true

;

217

nodeChild.

name

= sib->name;

222

nodeChild.

isLeaf

=

false

;

224

e1.first = nodeParent;

225

e1.second = nodeTurn;

227

e2.second = nodeChild;

279  string

rankName =

"superkingdom"

;

317  bool

validated =

false

;

342

tmpTree = &tmpTreeObj;

CCdCore * GetScopedLeafCD(int row) const

CCdCore * getFirstCD() const

string GetAccession(int &Version) const

CCdCore * getRootCD() const

static int createFamilies(vector< CCdCore * > &cds, vector< CDFamily * > &families)

void subfamily(CDFamilyIterator cit, CDFamily *&subfam, bool childrenOnly=false)

static bool DistMethodUsesScoringMatrix(EDistMethod method)

string GetDistMethodName()

bool isBlockAligned() const

bool setAlignment(const CDFamily &family)

CConstRef< CSeq_id > seqId

void annotateTreeByTaxonomy(TaxonomyLevel tax)

void annotateLeafNode(const SeqItem &nodeData, SeqTreeNode &node)

bool loadExistingTree(CCdCore *cd, TreeOptions *treeOptions, SeqTree *seqTree)

SeqTreeAPI(vector< CCdCore * > &cds, bool loadExistingTreeOnly=true)

bool loadAndValidateExistingTree()

void getEdgesFromSubTree(const SeqTree::iterator &cursor, vector< SeqTreeEdge > &edges)

TreeOptions m_treeOptions

string layoutSeqTree(int maxX, int maxY, vector< SeqTreeEdge > &edges)

int getAllEdges(vector< SeqTreeEdge > &edges)

void annotateTreeByMembership()

static bool convertToSeqTree(CSequence_tree &asnSeqTree, SeqTree &seqTree, SeqLocToSeqItemMap &liMap)

static bool convertToTreeOption(const CRef< CAlgorithm_type > &alg, TreeOptions &treeOption)

static bool resolveRowId(const AlignmentCollection &ac, SeqLocToSeqItemMap &liMap)

static bool refillAsnMembership(const AlignmentCollection &ac, SeqLocToSeqItemMap &liMap)

void calculateNodePositions(SeqTree &treeData, int maxX, int maxY)

bool isSequenceCompositionSame(AlignmentCollection &aligns)

void fixRowName(AlignmentCollection &aligns, SeqNameMode mode)

virtual string GetSuperKingdom(TTaxId taxid)

virtual TTaxId GetTaxIDForSeqId(CConstRef< CSeq_id > sid)

TaxTreeIterator getParentAtRank(int row, string rankName)

static SeqTree * makeTree(AlignmentCollection *alignData, const TreeOptions &treeOptions)

sibling_iterator end() const

unsigned int number_of_children() const

sibling_iterator begin() const

pre_order_iterator begin() const

string GetScoringMatrixName(EScoreMatrixType type)

pair< SeqTreeNode, SeqTreeNode > SeqTreeEdge

string GetTreeAlgorithmName(ETreeMethod algorithm)

SStrictId_Tax::TId TTaxId

Taxon id type.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

const TAlgorithm & GetAlgorithm(void) const

Get the Algorithm member data.

void SetSeqtree(TSeqtree &value)

Assign a value to Seqtree data member.

bool IsSetSeqtree(void) const

Check if a value has been assigned to Seqtree data member.

const TSeqtree & GetSeqtree(void) const

Get the Seqtree member data.

@ eTree_scope_immediateChildrenOnly

ETreeMethod clusteringMethod

CAlgorithm_type::ETree_scope scope

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