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

75

distanceToRoot(rhs.distanceToRoot),x(rhs.x), y(rhs.y), rowID(rhs.rowID),

76

selections(rhs.selections), selected(rhs.selected),

77

collapsed(rhs.collapsed),interesting(rhs.interesting), membership(rhs.membership), seqId(rhs.seqId) {}

85 int

_Pos = nameDist.find(

'_'

);

91 rowID

= atoi(nameDist.substr(0, _Pos).c_str());

92

tail = nameDist.substr(_Pos + 1);

96 int

colonPos = tail.find(

':'

);

100 name

= tail.substr(0,colonPos);

103 distance

= atof(tail.substr(colonPos+1).c_str());

155

m_longestName(), m_leafNodes(), m_collapsedNodes()

167

os <<

" ID: "

.id <<

" RowID: "

.rowID

168

" Distance ="

.distance << std::endl;

173 bool

isEqual =

false

;

223

cursor->distanceToRoot =

parent

(cursor)->distanceToRoot + cursor->distance;

225

cursor->id = numLeaf;

226 if

(cursor->distanceToRoot > maxDist)

227

maxDist = cursor->distanceToRoot;

236 if

( cursor ==

begin

())

237

cursor->distanceToRoot = 0;

239

cursor->distanceToRoot =

parent

(cursor)->distanceToRoot + cursor->distance;

240 if

(cursor->collapsed)

242 if

(cursor->distanceToRoot > maxDist)

243

maxDist = cursor->distanceToRoot;

249 while

(sib != cursor.

end

())

251 prepare

(numLeaf, maxDist,sib);

263

colNode->id = numLeaf;

297 if

(start->distanceToRoot > dist)

299

nodes.push_back(start);

303 while

(sib != start.

end

())

314

it->collapsed =

false

;

335 if

(treeId > masterRowTreeId)

338

positions.push_back(treeId);

389

rankList.push_back(node->rowID);

394 while

(sib != node.

end

())

405 if

(sib == node.

end

())

409

selections.push_back(node->rowID);

413 while

(sib != node.

end

())

423 if

(sib == node.

end

())

425

selections.push_back(node->rowID);

428 while

(sib != node.

end

())

439

node->selected = select;

442 if

(sib == node.

end

())

445

node->select(cd, select);

447

node->select(select);

448 if

(node->getAllSelectedInstances() > 0)

449

node->selected =

true

;

451

node->selected =

false

;

454 while

(sib != node.

end

())

469 if

(selection.

find

(

row

) != selection.

end

())

482 if

(

leaf

->id ==

id

)

491

vector<int> rowsForOne;

492 for

(

unsigned int i

= 0;

< gis.size();

++)

497 for

(

unsigned int

k = 0; k < rowsForOne.size(); k++)

498

rows.

insert

(rowsForOne[k]);

508 int

num = rows.size();

509 for

(

int i

= 0;

< num;

++)

515

leafNode = mapIt->second;

516

leafNode->taxid = taxid;

527

mapIt->second->taxid = -1;

535 for

(; cursor !=

end

(); ++cursor)

537 if

((cursor.

number_of_children

() == 0) && (cursor->rowID >= 0) && (cursor->rowID < num))

542

cursor->name.erase();

552

cursor->name = species;

555

cursor->name = gi +

"["

+ species +

"]"

;

558

cursor->name = gi + loc;

561

cursor->name = gi + loc +

"["

+ species +

"]"

;

574 for

(; cursor !=

end

(); ++cursor)

578

cursor->selected =

false

;

587 for

(; cursor !=

end

(); ++cursor)

592

vector<RowSource> rss;

594 for

(

unsigned int i

= 0;

< rss.size();

++)

606 for

(; cursor !=

end

(); ++cursor)

610

cursor->selections.clear();

611

vector<RowSource> rss;

613 for

(

unsigned int i

= 0;

< rss.size();

++)

624 for

(; cursor !=

end

(); ++cursor)

628

vector<RowSource> rss;

630 for

(

unsigned int i

= 0;

< rss.size();

++)

632 if

((cursor->selections).find(rss[

].cd) == cursor->selections.

end

())

650 unsigned int

com1Size = com1.

size

();

651 if

(com1Size != com2.

size

())

653 for

(

unsigned int i

= 0;

< com1Size;

++)

655 if

(com1[

].compare(com2[

]))

665 for

(cursor =

begin

(); cursor !=

end

(); ++cursor)

671

seqComposition[cursor->rowID] = cursor->name;

683 for

(

int i

= 0;

< num; ++

)

693 while

(cit != rowColorMap->

end

())

699

leafNode = mapIt->second;

701

leafNode->membership = cit->second;

bool Get_GI_or_PDB_String_FromAlignment(int row, std::string &result) const

bool GetSpeciesForRow(int row, string &species) const

CCdCore * GetScopedLeafCD(int row) const

const RowSourceTable & GetRowSourceTable() const

int GetRowsWithSeqID(const CRef< CSeq_id > &SeqID, vector< int > &rows) const

int GetLowerBound(int row) const

int GetUpperBound(int row) const

string GetAccession(int &Version) const

int findEntries(int row, vector< RowSource > &src, bool scopedOnly=false) const

void select(bool on=true)

bool operator==(const SeqItem &rhs) const

int getAllSelectedInstances()

void setMembershipColor(const RowMembershipColor *rowColorMap)

void getDistantNodes(double dist, vector< SeqTreeIterator > &nodes)

void selectByRowID(const set< int > &receivedSelection, bool select=true, CCdCore *cd=0)

bool isSequenceCompositionSame(AlignmentCollection &aligns)

void addSelectionFields(AlignmentCollection &aligns)

void getSequenceRowid(const iterator &node, vector< int > &selections)

void selectByTax(const vector< int > &rows, long taxid)

void getDiversityRankUnderNode(SeqTreeIterator node, list< int > &rankList)

IteQueue m_collapsedNodes

bool compareSequenceCompositions(IntToStringMap &com1, IntToStringMap &com2)

std::string getLongestName()

void getDiversityRankToRow(int colRow, list< int > &rankList)

void fixRowNumber(AlignmentCollection &aligns)

double getMaxDistanceToRoot()

void getOrdersInTree(vector< int > &positions)

void getSelectedSequenceRowid(const iterator &node, vector< int > &selections)

void clearInternalNodeSelection()

void selectByGI(const AlignmentCollection &aligns, const vector< CRef< CSeq_id > > &gis)

SeqTreeIterator getLeafById(int id)

void fixRowName(AlignmentCollection &aligns, SeqNameMode mode)

void getSequenceComposition(IntToStringMap &seqComposition)

void prepareCollapsedNodes(int &numLeaf)

void updateSeqCounts(const AlignmentCollection &aligns)

void selectNode(const iterator &node, bool select=true, CCdCore *cd=0)

std::string m_longestName

container_type::const_iterator const_iterator

container_type::iterator iterator

const_iterator begin() const

const_iterator end() const

iterator_bool insert(const value_type &val)

container_type::value_type value_type

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

sibling_iterator end() const

unsigned int number_of_children() const

sibling_iterator begin() const

sibling_iterator previous_sibling(const iterator_base &) const

sibling_iterator next_sibling(const iterator_base &) const

pre_order_iterator begin() const

pre_order_iterator end() const

Include a standard set of the NCBI C++ Toolkit most basic headers.

ostream & operator<<(ostream &os, const SeqItem &si)

SeqTreeBase::iterator SeqTreeIterator

static const char si[8][64]

static void DLIST_NAME() init(DLIST_LIST_TYPE *list)

#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.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

#define row(bind, expected)

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