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

,

,

),

;

;

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

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

* loc =

*

(it2->object.GetPointer());

( !loc )

;

protein.push_back(*it2);

(bsh.

()) {

(!protein.empty()) {

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

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

: m_Params(params), m_Protein(protein), m_NA(na)

kCutoff = 9;

& na_loc =

&

(it->object.GetObject());

orig_genomic_loc.

().SetId(*seqid);

orig_genomic_loc.

().SetFrom(0);

vector<CRef<CSeq_align>> align_result;

(

() || comparts.empty())

;

(

&& it : comparts) {

align_result.push_back(align);

kMaxCompartCount = 25;

pair<SKey, CRef<CSeq_annot>> TItem;

deque<TItem> TAlignInfo;

operator() (

TItem& item1,

TItem& item2)

(item1.first.protein < item2.first.protein) {

(item2.first.protein < item1.first.protein) {

(item1.first.bit_score > item2.first.bit_score);

SKey operator() (

& compartment)

found_protein =

;

found_score =

;

(desc.

()) {

found_protein =

;

* kBitScore =

;

(!found_protein) {

(comparts.size() > kMaxCompartCount) {

opts_hndl->SetEvalueThreshold(0.001);

opts_hndl->SetMatrixName(

);

opts_hndl->SetSegFiltering(

);

opts_hndl->SetMaskAtHash(

);

opts_hndl->SetWordThreshold(12);

opts_hndl->GetOptions().DebugDumpText(

,

, 5);

opts_hndl->Validate();

vector<CRef<CSeq_align>> align_list;

align_list.push_back(align);

(

<<

);

(align_list.empty()) {

hit_refs.push_back(hitref);

prosplign::CCompartOptions compart_opts;

<SKey(

&)> extractor = SExtractor();

TAlignInfo alignment_info;

SKey

= extractor(**compart_it);

alignment_info.emplace_back(

, *compart_it);

<

(

TItem&,

TItem&)> sorter = SKey_Less();

(alignment_info.begin(), alignment_info.end(), sorter);

(

index = 0; index < alignment_info.size() && index < kMaxCompartCount; ++index) {

sorted_comparts.emplace_back(alignment_info[index].second);

comparts.swap(sorted_comparts);

(desc.

()) {

(!new_genomic_loc) {

(

exception& e) {

(align_result.empty())

;

(

&& align_it : align_result) {

(align_it->GetSegs().IsSpliced() &&

align_it->GetSegs().GetSpliced().IsSetExons() &&

!align_it->GetSegs().GetSpliced().GetExons().empty()) {

seqannot_align.push_back(align_it);

(seqannot_align.empty())

;

+=

;

item->

().SetAnnot(*annot);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

Declares the CBl2Seq (BLAST 2 Sequences) class.

Interface for converting blast-related command line arguments into blast options.

Definitions used throughout BLAST.

vector< CRef< objects::CSeq_align_set > > TSeqAlignVector

Vector of Seq-align-sets.

EProgram

This enumeration is to evolve into a task/program specific list that specifies sets of default parame...

@ eTblastn

Protein-Translated nucl.

Runs the BLAST algorithm between 2 sequences.

Defines BLAST error codes (user errors included)

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

void AddProjectItem(objects::CProjectItem &item)

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

blast::TSeqAlignVector x_SetupAndRuntBlastn(const CSeq_loc &protein_loc, const CSeq_loc &genomic_loc)

prosplign::TCompartments x_GetCompartments(const CSeq_loc &protein_loc, const CSeq_loc &genomic_loc)

virtual void x_CreateProjectItems()

override this function in derived classes and populate m_Items.

CProSplignJob(const CProSplignParams &params, const TConstScopedObjects &protein, const TConstScopedObjects &nucleotide)

CProSplignJob.

static Boolean s_BlastInterrupt(SBlastProgress *prog)

static callback for BLAST interruption this must match the API in CBl2Seq and BLAST

CRef< CSeq_align > x_RunProSplign(const CSeq_id &protein_id, const CSeq_loc &genomic_loc)

void x_CreateOneProjectItem(const vector< CRef< CSeq_align >> &align_result, const CSeq_loc &protein_loc, const CSeq_loc &genomic_loc)

CRef< CSeq_align > x_ProcessCompartment(CRef< CSeq_annot > compartment)

CProSplignParams m_Params

static bool s_ProSplignInterruptCallback(void *user_data)

void x_FilterCompartments(prosplign::TCompartments &comparts)

TConstScopedObjects m_Protein

prosplign::TCompartments x_GenerateCompartments(const blast::TSeqAlignVector &blast_results)

const CProSplignParams & GetData() const

virtual void LoadSettings()

void SetObjects(map< string, TConstScopedObjects > *protein, map< string, TConstScopedObjects > *nucleotide)

SConstScopedObject GetProteinSeq() const

void SetData(const CProSplignParams &data)

virtual void SetRegistryPath(const string &path)

CAlgoToolManagerParamsPanel.

TConstScopedObjects GetNucleotideSeqs() const

CRef< CProSplignScoring > GetScoringParams() const

CRef< CProSplignOutputOptions > GetOutputOptions() const

spliced protein to genomic alignment

void AssignGeneticCode(objects::CScope &scope, const objects::CSeq_id &gid, int gcode)

void SetInterruptCallback(TInterruptFnPtr prg_callback, void *data)

CRef< objects::CSeq_align > FindAlignment(objects::CScope &scope, const objects::CSeq_id &protein, const objects::CSeq_loc &genomic, CProSplignOutputOptions output_options=CProSplignOutputOptions())

Aligns protein to a region on genomic sequence.

void SetNameDesc(const string &name)

void SetCreateDate(const CTime &dt)

vector< THitRef > THitRefs

Handle to the protein-translated nucleotide options to the BLAST algorithm.

const CUser_field & GetField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Access a named field in this user object.

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

TCompartments SelectCompartmentsHits(const THitRefs &hitrefs, CCompartOptions compart_options, const vector< pair< THit::TCoord, THit::TCoord > > *gaps=NULL)

Composition of first two functions.

list< CRef< CSeq_annot > > TCompartments

@ eNoCompositionBasedStats

Don't use composition based statistics.

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.

#define ERR_POST(message)

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

#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)

virtual void x_SelectCompatibleInputObjects()

virtual string GetExtensionLabel() const

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

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 string GetExtensionIdentifier() const

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

TObjects m_ProteinObjects

virtual bool x_ValidateParams()

validates user input in Parameters panel, report errors if any

CProSplignPanel * m_Panel

virtual void InitUI()

override this function in a derived class and initialize extra members

CProSplignTool()

CProSplignTool.

CProSplignParams m_Params

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

virtual CAlgoToolManagerParamsPanel * x_GetParamsPanel()

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

virtual void CleanUI()

override this function in a derived class and clean extra members

virtual bool x_CreateParamsPanelIfNeeded()

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

virtual CDataLoadingAppJob * x_CreateLoadingJob()

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

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

string m_Descr

mutex to sync our internals

virtual bool IsCanceled() const override

virtual void x_SetStatusText(const string &text)

vector< SConstScopedObject > TConstScopedObjects

C & SerialAssign(C &dest, const C &src, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

#define MSerial_AsnText

I/O stream manipulators –.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Optimized implementation of CSerialObject::Assign, which is not so efficient.

CConstRef< CSeq_id > GetSeqId(void) const

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.

void SetStrand(ENa_strand strand)

Set the strand for all of the location's ranges.

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.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

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

void SetLabel(const TLabel &value)

Assign a value to Label data member.

void SetItem(TItem &value)

Assign a value to Item data member.

const TData & GetData(void) const

Get the Data member data.

const TStr & GetStr(void) const

Get the variant data.

TReal GetReal(void) const

Get the variant data.

bool IsReal(void) const

Check if variant Real is selected.

const TType & GetType(void) const

Get the Type member data.

bool IsSetData(void) const

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

bool IsStd(void) const

Check if variant Std is selected.

list< CRef< CSeq_align > > Tdata

const TSegs & GetSegs(void) const

Get the Segs 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.

const Tdata & Get(void) const

Get the member data.

list< CRef< CSeq_align > > TAlign

const TUser & GetUser(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

const TDesc & GetDesc(void) const

Get the Desc member data.

const TRegion & GetRegion(void) const

Get the variant data.

const TIds & GetIds(void) const

Get the Ids member data.

const TAlign & GetAlign(void) const

Get the variant data.

list< CRef< CAnnotdesc > > Tdata

@ e_Align

definition of the SeqAligns

@ e_Region

all contents cover this region

@ e_User

user defined object

constexpr auto sort(_Init &&init)

const struct ncbi::grid::netcache::search::fields::KEY key

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_CPROSPLIGNPANEL_STYLE

Progress monitoring structure.

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

Main argument class for TBLASTN application.

Declares the CTBlastnOptionsHandle class.

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