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

,

,

,

),

;

;

* loc =

*

(it2->object.GetPointer());

( !loc )

;

(desc_iter) molInfo = &desc_iter->

();

genomic.push_back(*it2);

genomic.push_back(*it2);

genomic.push_back(*it2);

(!genomic.empty()) {

(genomic.begin(), genomic.end(), back_inserter(vec));

(na.begin(), na.end(), back_inserter(vec));

(vec.begin(), vec.end(), back_inserter(genomic));

(vec.begin(), vec.end(), back_inserter(cdna));

wxMessageBox(

(

),

(

), wxOK | wxICON_ERROR);

wxMessageBox(

(

),

(

), wxOK | wxICON_ERROR);

vector<CProjectService::TProjectId> projects;

(vec.begin(), vec.end(), back_inserter(

));

(vec.begin(), vec.end(), back_inserter(

));

(projects.empty())

: m_Params(params), m_Genomic(genomic), m_cDNA(cdna)

&

(it->object.GetObject());

vector<string> not_found_labels;

& seqloc_cdna =

&

(iter->object.GetObject());

& scope = *iter->scope;

(seqloc_genomic, scope),

( (*ii)->IsSet() ){

( hitref->GetQueryStrand() ==

){

hitref->FlipStrands();

hitrefs.push_back( hitref );

( hitrefs.size() ){

splign.

( &hitrefs );

sf.

( transcript_id, genomic_id );

( hitrefs.size() ){

splign.

( &hitrefs );

sf.

( transcript_id, genomic_id );

( !seqaln_set_neg->

() ){

seqaln_set->

().merge( seqaln_set_neg->

() );

( !seqaln_set->

().empty() ){

TAlign& seqannot_align = annot->

().SetAlign();

seqannot_align.push_back(*align);

+=

;

item->

().SetAnnot(*annot);

not_found_labels.push_back(

);

Declares the CBl2Seq (BLAST 2 Sequences) class.

vector< CRef< objects::CSeq_align_set > > TSeqAlignVector

Vector of Seq-align-sets.

@ eMegablast

Nucl-Nucl (traditional megablast)

Runs the BLAST algorithm between 2 sequences.

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

void AddProjectItem(objects::CProjectItem &item)

CDataLoadingAppTask - a task that executes CDataLoadingAppJob.

void DebugDumpText(ostream &out, const string &bundle, unsigned int depth) const

CProjectService - a service providing API for operations with Workspaces and Projects.

void GetObjProjects(TConstScopedObjects &objects, vector< TProjectId > &ids)

CProjectSelectOptions - describes how new Project Items shall be added to a workspace.

void Set_CreateNewProject(const string &folder=kEmptyStr)

void Set_AddToExistingProject(TProjectId &project_id, const string &folder=kEmptyStr)

void SetNameDesc(const string &name)

void SetCreateDate(const CTime &dt)

CRef< objects::CSeq_align_set > AsSeqAlignSet(const CSplign::TResults *results=0, int flags=eAF_SplicedSegWithParts) const

Format alignment as a seq-align-set.

void SetSeqIds(CConstRef< objects::CSeq_id > id1, CConstRef< objects::CSeq_id > id2)

@ eAF_SplicedSegWithParts

static Boolean s_BlastInterruptCallback(SBlastProgress *prog)

TConstScopedObjects m_cDNA

virtual void x_CreateProjectItems()

override this function in derived classes and populate m_Items.

CSplignJob(const CSplignParams &params, const TConstScopedObjects &genomic, const TConstScopedObjects &cdna)

CSplignJob.

static bool s_SplignInterruptCallback(CNWAligner::SProgressInfo *prog)

TConstScopedObjects m_Genomic

CSplign is the central library object for computing spliced cDNA-to-genomic alignments.

void SetPolyaDetection(bool on)

void Run(THitRefs *hitrefs)

void SetCompartmentPenalty(double penalty)

void SetMinSingletonIdentity(double idty)

CRef< objects::CScope > & SetScope(void)

void SetMaxIntron(size_t max_intron)

void SetMinExonIdentity(double idty)

void SetStrand(bool strand)

void PreserveScope(bool preserve=true)

Controls whether to clean the scope object's cache on a new sequence.

vector< THitRef > THitRefs

void SetMaxGenomicExtent(size_t mge)

CRef< TAligner > & SetAligner(void)

Access the spliced aligner core object.

void SetMinCompartmentIdentity(double idty)

static CRef< CSplicedAligner > s_CreateDefaultAligner(void)

void SetEndGapDetection(bool on)

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

static const char * str(char *buf, int n)

TInterruptFnPtr SetInterruptCallback(TInterruptFnPtr fnptr, void *user_data=NULL)

Set a function callback to be invoked by the CORE of BLAST to allow interrupting a BLAST search in pr...

virtual TSeqAlignVector Run()

Perform BLAST search Assuming N queries and M subjects, the structure of the returned vector is as fo...

#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.

CIRef< T > GetServiceByType()

retrieves a typed reference to a service, the name of C++ type is used as the name of the service.

bool Create(wxWindow *parent, wxWindowID id=ID_CSPLIGNPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxCLIP_CHILDREN|wxTAB_TRAVERSAL, bool visibale=true)

virtual void LoadSettings()

CSplignTool()

CSplignTool.

virtual string GetExtensionIdentifier() const

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

virtual void CleanUI()

override this function in a derived class and clean extra members

virtual CDataLoadingAppJob * x_CreateLoadingJob()

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

virtual void x_SelectCompatibleInputObjects()

virtual CAlgoToolManagerParamsPanel * x_GetParamsPanel()

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

virtual bool x_ValidateParams()

validates user input in Parameters panel, report errors if any

virtual IAppTask * QuickLaunch()

double GetCompPenalty() const

long GetMaxGenomicExtent() const

CSplignParams & GetData()

TConstScopedObjects GetCDNASeqs() const

bool GetPolyADetect() const

TObjects m_GenomicObjects

double GetMinExonIdentity() const

virtual wxPanel * GetMaxPanel()

Return the panel that occupies max size on display, to calculate dialog window size.

virtual IRegSettings * x_GetParamsAsRegSetting()

return a pointer to Parameters object as IRegSettings interface

bool GetEndGapDetect() const

virtual void SetRegistryPath(const string &path)

CAlgoToolManagerParamsPanel.

long GetMaxIntron() const

SConstScopedObject GetGenomicSeq() const

virtual void InitUI()

override this function in a derived class and initialize extra members

double GetMinCompIdentity() const

virtual bool x_CreateParamsPanelIfNeeded()

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

void SetData(const CSplignParams &data)

void SetObjects(map< string, TConstScopedObjects > *genomic, map< string, TConstScopedObjects > *na)

int GetCDNAStrand() const

virtual string GetExtensionLabel() const

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

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

string m_Descr

mutex to sync our internals

virtual bool IsCanceled() const override

vector< SConstScopedObject > TConstScopedObjects

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,...

void Reset(void)

Reset reference object.

TObjectType * Release(void)

Release a reference to the object and return a pointer to the object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

CTime CurrentTime(CTime::ETimeZone tz=CTime::eLocal, CTime::ETimeZonePrecision tzp=CTime::eTZPrecisionDefault)

static const char label[]

void SetLabel(const TLabel &value)

Assign a value to Label data member.

void SetItem(TItem &value)

Assign a value to Item data member.

Tdata & Set(void)

Assign a value to data member.

list< CRef< CSeq_align > > Tdata

const Tdata & Get(void) const

Get the member data.

bool IsWhole(void) const

Check if variant Whole is selected.

bool IsInt(void) const

Check if variant Int is selected.

void SetData(TData &value)

Assign a value to Data data member.

list< CRef< CSeq_align > > TAlign

TBiomol GetBiomol(void) const

Get the Biomol member data.

const TMolinfo & GetMolinfo(void) const

Get the variant data.

@ e_Molinfo

info on the molecule and techniques

Uint1 Boolean

bool replacment for C

#define TRUE

bool replacment for C indicating true.

#define FALSE

bool replacment for C indicating false.

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

#define SYMBOL_CSPLIGNPANEL_STYLE

Progress monitoring structure.

Structure to represent a single sequence to be fed to BLAST.

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