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

vec.reserve(locs.size());

loc.

= it->scope;

(mask_lc_regions || mask_rep_feats) {

(mask_lc_regions) {

( ; feat_iter; ++feat_iter) {

==

) {

( ; feat_iter; ++feat_iter) {

vector<string> arg_vec;

unique_ptr<CAutoEnvironmentVariable> p_wm_path;

( !wm_dir.empty() ){

prog_name = arg_vec.front();

prog_name +=

;

arg_vec.erase( arg_vec.begin() );

vector< CRef<CSeq_annot> > res_annots;

queries_fname = subjects_fname +

;

output_fname = subjects_fname +

;

subjects_fname +=

;

(!s_locs.empty()) {

fasta_sub_ostr.

(handle);

fasta_sub_ostr.

(handle, loc);

seq_types[local_sihd] = seqType;

seq_types[base_sihd] = seqType;

fasta_que_ostr.

( handle );

fasta_que_ostr.

( handle, loc );

seq_types[local_sihd] = seqType;

seq_types[base_sihd] = seqType;

wxFileName fname( agent_path, wxEmptyString );

fname.AppendDir(

(

));

fname.SetFullName(

( prog_name ) );

agent_path = fname.GetFullPath();

arg_vec.push_back(

+

(

) );

arg_vec.push_back(

);

arg_vec.push_back(

+

);

(localDB.find(

) != string::npos)

arg_vec.push_back(

+ localDB +

);

arg_vec.push_back(localDB);

arg_vec.push_back(subjects_fname);

arg_vec.push_back( queries_fname );

arg_vec.push_back( output_fname );

( vector<string>, argit, arg_vec ){

agent_args += *argit +

;

(

<<

<< agent_path.ToUTF8() <<

);

(

<<

<< agent_args <<

);

** arg_vec_ptr =

*[arg_vec.size() +2];

arg_vec_ptr[xi] =

;

( xi < arg_vec.size() ){

* arg_ptr = arg_vec[xi].c_str();

arg_vec_ptr[++xi] = arg_ptr;

arg_vec_ptr[++xi] =

;

[] arg_vec_ptr;

( !result_istr.eof() ){

res_annots.push_back( next_annot );

exitres[] = {

<<

<< prog_name <<

<<

<< exitcode

<< (exitcode <

(exitres)/

(

) ? exitres[exitcode] :

)

(

<< prog_name <<

<< ex.

() );

list< CRef<CSeq_align> > aligns;

(

&

: seq_types)

(; id_iter; ++id_iter) {

(seq_types.find(h) == seq_types.end())

list< CRef<CSeq_align> > raw_aligns = next_annot->

().

();

aligns.push_back( align );

( !aligns.empty() ){

list< CRef<CSeq_align_set> > align_sets;

al_set->

() = aligns;

align_sets.push_back( al_set );

annot->

().SetAlign() = (*as_itr)->Set();

item->

().SetAnnot( *annot );

(

<<

<< dumpname <<

);

(

<< prog_name <<

<< ex.

() );

subject_entry( subjects_fname );

blaster( query_vec, subject_vec, *blast_opts );

(

<<

<< dumpname <<

);

list< CRef< CSeq_align > >& align_list = annot->SetData().SetAlign();

sas->Set().insert(sas->Set().end(), disc.begin(), disc.end());

align_list.insert(align_list.end(), sas->Get().begin(), sas->Get().end());

align_list.push_back(align);

( !align_list.empty() ){

list< CRef<CSeq_align_set> > align_sets;

al_set->Set() = align_list;

align_sets.push_back( al_set );

annot->SetData().SetAlign() = (*as_itr)->Set();

+=

;

item->SetItem().SetAnnot( *annot );

item->SetLabel(

);

annot->SetTitleDesc(

);

annot->SetNameDesc(

);

(

<<

<< dumpname <<

);

Declares the CBl2Seq (BLAST 2 Sequences) class.

vector< CRef< objects::CSeq_align_set > > TSeqAlignVector

Vector of Seq-align-sets.

CAutoEnvironmentVariable –.

CBLASTParams - save user-specified parameters and preferences.

Runs the BLAST algorithm between 2 sequences.

void AddProjectItem(objects::CProjectItem &item)

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

The result type for Spawn methods.

FASTA-format output; see also ReadFasta in <objtools/readers/fasta.hpp>

Storage for multiple mapping ranges.

Extended exit information for waited process.

void SetNameDesc(const string &name)

void SetCreateDate(const CTime &dt)

void SetTitleDesc(const string &title)

static wxString GetStdPath(void)

the applicaton installation directory.

Template class for iteration on objects of class C (non-medifiable version)

Constant declarations for command line arguments for BLAST programs.

const string kArgOutput

Output file name.

const string kArgQuery

Query sequence(s)

const string kArgDb

BLAST database name.

const string kArgSubject

Subject input file to search.

static const char si[8][64]

void FindCompartments(const list< CRef< CSeq_align > > &aligns, list< CRef< CSeq_align_set > > &align_sets, TCompartOptions options=fCompart_Defaults, float diff_len_filter=3.0f)

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...

const CBlastOptions & GetOptions() const

Return the object which this object is a handle for.

string EProgramToTaskName(EProgram p)

Convert a EProgram enumeration value to a task name (as those used in the BLAST command line binaries...

string WindowMaskerPathGet()

Retrieves the path to the windowmasker data files.

int WindowMaskerPathInit(const string &window_masker_path)

Initialize the path to the windowmasker data files.

#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)

const string & GetMsg(void) const

Get message string.

void Warning(CExceptionArgs_Base &args)

void Info(CExceptionArgs_Base &args)

TProcessHandle GetProcessHandle(void)

Get process handle/pid.

static CResult SpawnV(EMode mode, const char *cmdname, const char *const *argv=NULL)

Spawn a new process with variable number of command-line arguments.

@ eNoWait

Continues to execute calling process concurrently with new process (asynchronous spawn).

virtual bool Remove(TRemoveFlags flags=eRecursive) const

Remove a directory entry.

static string GetTmpName(ETmpFileCreationMode mode=eTmpFileGetName)

Get temporary file name.

static CRef< objects::CLoaderDescriptor > CreateLoader(const string &db, bool nucleotide)

static objects::SAnnotSelector GetAnnotSelector(TAnnotFlags flags=0)

request an annotation selector for a given type

CBLASTSeqToolJob(const CBLASTParams &params)

bool GetLocalDBLoader() const

TConstScopedObjects & GetSeqLocs()

const string & GetWmDir() const

TProcessHandle m_ProcHandle

TConstScopedObjects & GetSubjSeqLocs()

CRef< blast::CBlastOptionsHandle > ToArgVecBlastOptions(vector< string > &arg_vec, bool local=true) const

string GetLocalNucDB() const

SProgParams & GetCurrParams()

returns params for the current program

int m_WM_TaxId

winmask tax id

bool IsCompartmentsRequested() const

bool m_MaskLowercase

mask Lowercase features

static Boolean s_BlastInterrupt(SBlastProgress *prog)

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

blast::EProgram & GetCurrProgram()

returns the current program for the currently selected input type

string GetLocalProtDB() const

virtual void RequestCancel()

RequestCancel() is called to notify the Job that it shall exit Run() function ASAP.

bool m_MaskRepeats

mask Repeat features

virtual void x_CreateProjectItems()

override this function in derived classes and populate m_Items.

bool IsSubjNucInput() const

ESubjectType GetSubjectType() const

bool IsStandaloneRequested() const

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)

virtual void RequestCancel() override

RequestCancel() is called to notify the Job that it shall exit Run() function ASAP.

vector< SConstScopedObject > TConstScopedObjects

#define MSerial_AsnText

I/O stream manipulators –.

@ eSerial_AsnText

ASN.1 text.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

void Add(const CSeq_loc &other)

Simple adding of seq-locs.

const CSeq_id * GetId(void) const

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

void ResetStrand(void)

Reset the strand on this location.

static CObjectOStream * Open(ESerialDataFormat format, CNcbiOstream &outStream, bool deleteOutStream)

Create serial object writer and attach it to an output stream.

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

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

ENa_strand GetStrand(const CSeq_loc &loc, CScope *scope=0)

Returns eNa_strand_unknown if multiple Bioseqs in loc Returns eNa_strand_other if multiple strands in...

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.

virtual void Write(const CSeq_entry_Handle &handle, const CSeq_loc *location=0)

Unspecified locations designate complete sequences; non-empty custom titles override the usual title ...

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

const CSeqFeatData & GetData(void) const

const CSeq_loc & GetLocation(void) const

SAnnotSelector & SetFeatSubtype(TFeatSubtype subtype)

Set feature subtype (also set annotation and feat type)

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

const unsigned long kInfiniteTimeoutMs

Infinite timeout in milliseconds.

bool Kill(unsigned long timeout=kDefaultKillTimeout)

Terminate process.

int Wait(unsigned long timeout=kInfiniteTimeoutMs, CExitInfo *info=0) const

Wait until process terminates.

int GetExitCode(void) const

Get process exit code.

#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::ifstream CNcbiIfstream

Portable alias for ifstream.

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

Convert int to string.

@ eCurrent

Use current time. See also CCurrentTime.

virtual const char * GetErrCodeString(void) const override

Get error code interpreted as text.

static const char label[]

#define INVALID_HANDLE_VALUE

A value for an invalid file handle.

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.

bool IsDisc(void) const

Check if variant Disc is selected.

list< CRef< CSeq_align > > Tdata

const TDisc & GetDisc(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

const TRegion & GetRegion(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

bool IsWhole(void) const

Check if variant Whole is selected.

@ e_not_set

No variant selected.

void SetData(TData &value)

Assign a value to Data data member.

const TAlign & GetAlign(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

Uint1 Boolean

bool replacment for C

#define TRUE

bool replacment for C indicating true.

#define FALSE

bool replacment for C indicating false.

Defines a portable execute class.

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

describes parameters for a BLAST program

Progress monitoring structure.

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

CConstRef< objects::CSeq_loc > seqloc

Seq-loc describing the sequence to use as query/subject to BLAST The types of Seq-loc currently suppo...

CRef< objects::CScope > scope

Scope where the sequence referenced can be found by the toolkit's object manager.

CRef< objects::CSeq_loc > mask

Seq-loc describing regions to mask in the seqloc field Acceptable types of Seq-loc are Seq-interval a...

Interface to retrieve list of available windowmasker filtering.

wxString ToWxString(const string &s)

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