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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/tree__builder__tool_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/packages/pkg_alignment/tree_builder_tool.cpp Source File

74 static const string sc_Kimura

(

"Kimura (protein)"

);

77 static const string sc_FastMe

(

"Fast Minimum Evolution"

);

78 static const string sc_Nj

(

"Neighbor Joining"

);

80 static const string sc_SeqId

(

"Sequence ID"

);

81 static const string sc_TaxName

(

"Taxonomic Name (if available)"

);

82 static const string sc_SeqTitle

(

"Sequence Title (if available)"

);

89  "Build Phylogenetic Tree from Alignment"

,

90  "Build Phylogenetic Tree from Alignment"

,

91  "https://www.ncbi.nlm.nih.gov/tools/gbench/tutorial28/"

,

99  return "tree_building_tool"

;

105  return "Phylogenetic Tree Builder Tool"

;

195

feat_descr->SetId(

id

);

196

feat_descr->SetName(name);

197

btc.

SetFdict

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

203

node_feature->SetFeatureid(

id

);

204

node_feature->SetValue(

value

);

205

node.

SetFeatures

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

212

vector<string> labels;

213

vector<string> organisms;

214

vector<string> titles;

215

vector<string> taxids;

247  BuildAln

(anchored_aln_vec, anchored_aln, aln_user_options);

249  if

(anchored_aln.

GetDim

() == 1) {

254  BuildAln

(anchored_aln_vec, anchored_aln, aln_user_options);

256

sparse_aln_ref =

new CSparseAln

(anchored_aln, *scope);

267

labels.resize(num_rows);

268

organisms.resize(num_rows);

269

titles.resize(num_rows);

270

taxids.resize(num_rows);

272  for

(

int i

= 0;

i

< num_rows; ++

i

) {

281  catch

(std::exception&) {

291  if

(seq_id && seq_id->

IsGi

())

292

gi = seq_id->

GetGi

();

296  ERR_POST

(

"CTreeBuilder: No tax_id for gi|"

<< gi);

303  bool

is_species =

false

;

304  bool

is_uncultured =

false

;

306

org_ref = taxon.

GetOrgRef

(tax_id, is_species,

307

is_uncultured, blast_name);

309  catch

(std::exception&) {

313

organisms[

i

] = org_ref->GetTaxname();

316

labels[

i

] = organisms[

i

];

322

titles[

i

] = sequence::CDeflineGenerator().GenerateDefline(bsh);

324

labels[

i

] = titles[

i

];

328  if

(labels[

i

].

empty

()) {

343  throw

runtime_error(

"The sequence divergence matrix contained " 344  "invalid or infinite values.\n" 345  "This can happen when some pairs of sequences " 346  "share no non-gap positions\n" 347  "in the alignment, leading to fractional " 348  "sequence identities of 0/0."

);

353  throw

runtime_error(

"The calculated distance matrix contained " 354  "invalid or infinite values.\nThis can happen " 355  "with the Kimura method when some " 356  "pairs of sequences are less than about 14.6% " 362  throw

runtime_error(

"The calculated distance matrix contained " 363  "invalid or infinite values.\nThis can happen " 364  "with the Jukes-Cantor method when some " 365  "pairs of sequences are less than 25% " 371  throw

runtime_error(

"The calculated distance matrix contained " 372  "invalid or infinite values."

);

375  throw

runtime_error(

string

(

"Invalid distance calculation type: "

)

382

vector<string> numerical_labels(dmat.

GetCols

());

383  for

(

size_t i

= 0;

i

< numerical_labels.size(); ++

i

) {

387

unique_ptr<TPhyTreeNode>

tree

;

390

}

else if

(sCons ==

sc_Nj

) {

393  throw

runtime_error(

string

(

"Invalid tree reconstruction algorithm: "

)

402  const int

kLabelId = 0;

403  const int

kSeqIdId = 2;

404  const int

kOrganismId = 3;

405  const int

kTitleId = 4;

407  const int

kHostId = 6;

408  const int

kCountryId = 7;

409  const int

kIsolationSourceId = 8;

410  const int

kCollectionDateId = 9;

420  if

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

424  if

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

430

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

438  if

(!organisms[seq_number].

empty

()) {

439  s_AddFeature

(**node, kOrganismId, organisms[seq_number]);

445  if

(!titles[seq_number].

empty

()) {

451  if

(biosource->IsSetOrgname()) {

452  const COrgName

& on = biosource->GetOrgname();

454  for

(

const auto

& orgmod : on.

GetMod

()) {

456  if

(created_descr.

insert

(kHostId).second)

465  if

(biosource->IsSetSubtype()) {

466  for

(

const auto

& subsrc : biosource->GetSubtype()) {

467  if

(subsrc->IsSetSubtype()) {

468  switch

(subsrc->GetSubtype()) {

470  if

(created_descr.

insert

(kCountryId).second)

475  if

(created_descr.

insert

(kIsolationSourceId).second)

477  s_AddFeature

(**node, kIsolationSourceId, subsrc->GetName());

480  if

(created_descr.

insert

(kCollectionDateId).second)

482  s_AddFeature

(**node, kCollectionDateId, subsrc->GetName());

507

dm->FromMatrix(dmat);

508

dm->SetLabels() = labels;

522  result

.Resize(nseqs, nseqs);

523

vector<string> seq(nseqs);

525  for

(

int i

= 0;

i

< nseqs; ++

i

) {

529  for

(

int i

= 0;

i

< nseqs; ++

i

) {

531  for

(

int

j =

i

+ 1; j < nseqs; ++j) {

User-defined methods of the data storage class.

void BuildAln(TAnchoredAlnVec &in_alns, CAnchoredAln &out_aln, const CAlnUserOptions &options, TAlnSeqIdIRef pseudo_seqid=TAlnSeqIdIRef())

Build anchored alignment from a set of alignmnets.

void CreateAnchoredAlnVec(_TAlnStats &aln_stats, TAnchoredAlnVec &out_vec, const CAlnUserOptions &options)

Create anchored alignment from each seq-align in the stats.

const_iterator insert(const CSeq_align &seq_align)

Insert new CSeq_align into the list.

size_type size(void) const

Container mapping seq-aligns to vectors of participating seq-ids.

void push_back(const CSeq_align &aln)

Adding an alignment.

TDim GetNumRows(void) const

Helper class which collects seq-align statistics: seq-ids participating in alignments and rows,...

Options for different alignment manager operations.

@ ePreserveRows

Preserve all rows as they were in the input (e.g.

const CBioseq_Handle & GetBioseqHandle(TNumrow row) const

void SetEndChar(TResidue gap_char)

void SetGapChar(TResidue gap_char)

Query-anchored alignment can be 2 or multi-dimentional.

TDim GetDim(void) const

How many rows.

CDataLoadingAppJob - a base class for Jobs loading data into projects.

void AddProjectItem(objects::CProjectItem &item)

static bool AllFinite(const TMatrix &mat)

Check a matrix for NaNs and Infs.

static TTree * NjTree(const TMatrix &dist_mat, const vector< string > &labels=vector< string >())

Compute a tree by neighbor joining; as per Hillis et al.

static double Divergence(const string &seq1, const string &seq2)

Calculate pairwise fractions of non-identity.

static void PoissonDist(const TMatrix &frac_diff, TMatrix &result)

Simple distance calculation for protein sequences: d = -ln(1 - p).

static TTree * FastMeTree(const TMatrix &dist_mat, const vector< string > &labels=vector< string >(), EFastMePar btype=eOls, EFastMePar wtype=eOls, EFastMePar ntype=eBalanced)

Compute a tree using the fast minimum evolution algorithm.

static void KimuraDist(const TMatrix &frac_diff, TMatrix &result)

Kimura's distance for protein sequences: d = -ln(1 - p - 0.2p^2).

static void JukesCantorDist(const TMatrix &frac_diff, TMatrix &result)

Jukes-Cantor distance calculation for DNA sequences: d = -3/4 ln(1 - (4/3)p).

size_t GetCols() const

get the number of columns in this matrix

void SetObject(CSerialObject &object)

wrapper for setting the object pointed to by this item

TRng GetAlnRange(void) const

Get whole alignment range.

TNumrow GetNumRows(void) const

Synonym of the above.

void SetGapChar(TResidue gap_char)

Gap character modifier.

string & GetAlnSeqString(TNumrow row, string &buffer, const TSignedRange &rq_aln_rng, bool force_translation=false) const

Fetch alignment sequence data.

const objects::CBioseq_Handle & GetBioseqHandle(TNumrow row) const

Get bioseq handle for the row.

const string & GetLastError() const

bool GetTaxId4GI(TGi gi, TTaxId &tax_id_out)

CConstRef< COrg_ref > GetOrgRef(TTaxId tax_id, bool &is_species, bool &is_uncultured, string &blast_name, bool *is_specified=NULL)

static void x_Divergence(CSparseAln &spaln, CDistMethods::TMatrix &result)

virtual void x_CreateProjectItems()

override this function in derived classes and populate m_Items.

CTreeBuilderJob(const CTreeBuilderParams &params)

CTreeBuilderJob.

CTreeBuilderParams m_Params

IRegSettings An interface for objects that save / restore settings using CGuiRegistry.

iterator_bool insert(const value_type &val)

CRef< objects::CBioTreeContainer > MakeBioTreeContainer(const TPhyTreeNode *tree)

Conversion from TPhyTreeNode to CBioTreeContainer.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define ERR_POST(message)

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

wxString GetLeafLabels() const

virtual CAlgoToolManagerParamsPanel * x_GetParamsPanel()

returns a pointer to the parameters panel, override in derived classes

virtual void x_SelectCompatibleInputObjects()

select only Seq-ids

virtual void LoadSettings()

virtual IRegSettings * x_GetParamsAsRegSetting()

return a pointer to Parameters object as IRegSettings interface

CTreeBuilderPanel * m_Panel

CTreeBuilderParams m_Params

wxString GetConstructMethod() const

virtual CDataLoadingAppJob * x_CreateLoadingJob()

factory method for creating the job that executes the tool algorithm override in derived classes

virtual void CleanUI()

override this function in a derived class and clean extra members

TConstScopedObjects m_SeqIds

void SetData(const CTreeBuilderParams &data)

CTreeBuilderParams & GetData()

bool Create(wxWindow *parent, wxWindowID id=ID_CTreeBuilderPanel, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL)

virtual void InitUI()

override this function in a derived class and initialize extra members

const SConstScopedObject & GetObject() const

virtual string GetExtensionIdentifier() const

returns the unique human-readable identifier for the extension the id should use lowercase letters se...

CTreeBuilderTool()

CTreeBuilderTool.

virtual bool x_CreateParamsPanelIfNeeded()

returns / creates Parameters panel, override in derived classes see cpp file for example

virtual string GetExtensionLabel() const

returns a displayable label for this extension ( please capitalize the key words - "My Extension" )

virtual bool x_ValidateParams()

validates user input in Parameters panel, report errors if any

void SetObjects(TConstScopedObjects *objects)

wxString GetDistanceMethod() const

static void GetLabel(const CObject &obj, string *label, ELabelType type=eDefault)

CRef< objects::CScope > scope

string m_Descr

mutex to sync our internals

static void SetLabelByData(objects::CProjectItem &item, objects::CScope *scope=NULL)

CConstRef< CObject > object

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

CConstRef< CSeq_id > GetSeqId(void) const

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 CBioSource * GetBioSource(const CBioseq &bioseq)

Retrieve the BioSource object for a given bioseq handle.

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

CConstRef< CSeq_id > GetNonLocalIdOrNull(void) const

Find a non-local ID if present, consulting assembly details if all IDs for the overall sequence are l...

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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

Convert size_t to string.

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

Convert int to string.

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

Convert string to unsigned int.

@ eSubtype_collection_date

DD-MMM-YYYY format.

@ eSubtype_isolation_source

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

void SetTreetype(const TTreetype &value)

Assign a value to Treetype data member.

list< CRef< CNode > > Tdata

const TMod & GetMod(void) const

Get the Mod member data.

bool CanGetMod(void) const

Check if it is safe to call GetMod method.

@ eSubtype_nat_host

natural host of this specimen

const TDenseg & GetDenseg(void) const

Get the variant data.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool IsDenseg(void) const

Check if variant Denseg is selected.

TGi GetGi(void) const

Get the variant data.

bool IsGi(void) const

Check if variant Gi is selected.

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

const GenericPointer< typename T::ValueType > T2 value

vector< CRef< CAnchoredAln > > TAnchoredAlnVec

Collection of anchored alignments.

string ToStdString(const wxString &s)

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