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

(

.empty()) {

& scope = *p.second;

* loc =

*

(iter->object.GetPointer());

* scope = iter->scope;

ostr <<

<<

<< loc_id << endl;

ostr <<

<< endl;

m_ToolName(tool_name)

= wxFileName::CreateTempFileName(

(

));

= wxFileName::CreateTempFileName(

(

));

(

));

ors =

, ands =

;

ors = ors || iter->second;

ands = ands && iter->second;

+

(

),

(

), wxOK | wxICON_ERROR

(working_dir.IsEmpty()) {

.cwd = working_dir;

(

);

+=

;

::wxKill(

, wxSIGKILL);

ncbi::CProcess

(

(

), ncbi::CProcess::ePid);

(!

.IsAlive()) {

(

== 0 ||

== wxInvalidSize) {

align.

(&*iter);

(

<<

);

align = mapper.

( *align );

annot->

().SetAlign().push_back(align);

align_title(

+

);

align_title += title;

comment =

;

comment +=

;

item->

().SetAnnot(*annot);

item->

().push_back(descr);

err_msg =

+ e.

();

(std::exception& e) {

err_msg =

+

(e.

());

(!err_msg.empty())

kLabelId = 0;

kSeqIdId = 2;

feat_descr->SetId(kSeqIdId);

feat_descr->SetName(

);

btc->

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

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

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

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

id_node_feature->SetFeatureid(kSeqIdId);

id_node_feature->SetValue((*node_feature)->GetValue());

(*node)->SetFeatures().Set().push_back(id_node_feature);

<<

<<

);

(

std::exception& e) {

<<

<<

);

tree_title =

+ title;

item->

().SetOther().Set(*btc);

item->

().push_back(descr);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

std::invoke_result< _Fty, ICanceled & >::type GUI_AsyncExec(_Fty &&_Fnarg, const wxString &msg=wxT("Accessing network..."))

void AddProjectItem(objects::CProjectItem &item)

CRef< objects::CScope > m_Scope

Base class for reading FASTA sequences.

Storage for multiple mapping ranges.

void SetNameDesc(const string &name)

void SetCreateDate(const CTime &dt)

Simple implementation of ILineReader for i(o)streams.

definition of a Culling tree

Template class for iteration on objects of class C.

Interface for testing cancellation request in a long lasting operation.

container_type::iterator iterator

const_iterator end() const

const_iterator find(const key_type &key) const

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

Conversion from TPhyTreeNode to CBioTreeContainer.

Operators to edit gaps in sequences.

#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.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Error(CExceptionArgs_Base &args)

#define NCBI_THROW(exception_class, err_code, message)

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

const string & GetMsg(void) const

Get message string.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

void Info(CExceptionArgs_Base &args)

TIdMap m_IdMap

to make the alignment as robust as possible, we assign every sequence a unique identifer independeont...

virtual TConstScopedObjects & x_GetObjects()=0

Returns the sequences that will be aligned.

pair< CConstRef< objects::CSeq_loc >, CRef< objects::CScope > > TLocPair

virtual wxString x_GetWorkingDirectory() const

Returns the directory where to execute the msa tool.

virtual void x_CreateProjectItems()

override this function in derived classes and populate m_Items.

virtual wxString x_GetCommandLine(const wxString &input, const wxString &output, bool is_nucleotide)=0

Returns the command line, that will be used to execute the third-party tool.

virtual bool BeforeRun()

Function will be called on the main thread before execution of Run Should not do any lengthy work ret...

objects::CMappingRanges m_Ranges

virtual void x_AddTreeProjectItem(const string &title, const string &comment)

CMSAToolJob(const wxString &tool_name)

CMSAToolJob.

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

virtual bool IsCanceled() const override

vector< SConstScopedObject > TConstScopedObjects

CRef< CSeq_entry > ReadAlignedSet(int reference_row, ILineErrorListener *pMessageListener=nullptr)

Read as many sequences as are available, and interpret them as an alignment, with hyphens marking rel...

@ fParseGaps

Make a delta sequence if gaps found.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

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,...

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

TSeqPos GetStart(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the start of the location.

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

void SetSeqTypeById(const CSeq_id_Handle &idh, ESeqType seqtype) const

Methods for setting sequence types.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void AddConversion(CRef< CMappingRange > cvt)

Add new mapping range to the proper place.

bool IsNucleotide(void) const

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

#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.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

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

Convert size_t to string.

@ eCurrent

Use current time. See also CCurrentTime.

Fun TreeDepthFirstTraverse(TTreeNode &tree_node, Fun func)

Depth-first tree traversal algorithm.

ETreeTraverseCode

Tree traverse code returned by the traverse predicate function.

const TValue & GetValue(void) const

Return node's value.

@ 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.

list< CRef< CNodeFeature > > Tdata

void SetTreetype(const TTreetype &value)

Assign a value to Treetype data member.

list< CRef< CNode > > Tdata

TDescr & SetDescr(void)

Assign a value to Descr data member.

void SetLabel(const TLabel &value)

Assign a value to Label data member.

void SetItem(TItem &value)

Assign a value to Item data member.

void SetData(TData &value)

Assign a value to Data data member.

TComment & SetComment(void)

Select the variant.

const struct ncbi::grid::netcache::search::fields::SIZE size

Defines a portable execute class.

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

TPhyTreeNode * ReadNewickTree(CNcbiIstream &is)

Newick format input.

ETreeTraverseCode operator()(TPhyTreeNode &node, int level)

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