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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/windowmasker__tool_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/packages/pkg_sequence/windowmasker_tool.cpp Source File

,

,

,

;

;

wxFileName fname(storage.

(), wxEmptyString);

wxDir dir(fname.GetPath());

(dir.IsOpened()) {

cont = dir.GetFirst(&dirName, wxEmptyString, wxDIR_DIRS);

cont = dir.GetNext(&dirName)

fname.AppendDir(dirName);

fname.GetPath();

( !wxFileName::FileExists(path) ) {

wxChar* sc_Files[] = {

(

),

(

),

(

wxChar** p = sc_Files; p && *p; ++p) {

wxString filepath = wxFileName(path, *p).GetFullPath();

(wxFileName::FileExists(filepath)) {

( !wxFileName::FileExists(path) ) {

(

) + path,

(

)

(!o.scope)

;

* seqLoc =

*

(o.object.GetPointerOrNull());

(!seqLoc)

;

( !wxFileName::FileExists(path) ) {

wxChar* sc_Files[] = {

(

),

(

),

(

wxChar** p = sc_Files; p && *p; ++p) {

wxString filepath = wxFileName(path, *p).GetFullPath();

(wxFileName::FileExists(filepath)) {

( !wxFileName::FileExists(path) ) {

vector<SMaskResult> mask_res;

wxString prog_name =

(

);

prog_name +=

(

);

wxFileName fname(agent_path, wxEmptyString);

fname.AppendDir(

(

));

fname.SetFullName(prog_name);

agent_path_utf8(fname.GetFullPath().ToUTF8());

args.push_back(

);

lstat_name(path.ToUTF8());

args.push_back(lstat_name);

args.push_back(

);

args.push_back(

);

args.push_back(

);

(vector<string>, arg, args){

agent_args += *arg +

;

(

<<

<< agent_path_utf8 <<

);

(

<<

<< agent_args <<

);

& loc =

&

(o.object.GetObject());

& scope =

&

(o.scope.GetObject());

name +=

;

fastm.

(handle, &loc);

<<

<<

(status) <<

<< exitcode

(res_loc->

()){

pair_loc->

(**int_iter);

pair_loc->

().SetId().Assign(*loc.

());

mask_res.push_back(rv);

res_loc->

().SetId().Assign(*loc.

());

mask_res.push_back(rv);

lstat_name(path.ToUTF8());

count_failures = 0;

& loc =

&

(o.object.GetObject());

& scope =

&

(o.scope.GetObject());

name +=

;

unique_ptr<CSeqMasker::TMaskList> mask_list( masker( vec ) );

tmp_loc.

().SetId().Assign( *loc.

() );

CSeqMasker::TMaskList::const_iterator it = mask_list->begin();

it != mask_list->end();

tmp_loc.

().SetFrom( it->first );

tmp_loc.

().SetTo( it->second );

mask_res.push_back( rv );

(output_type == 0 || output_type == 2) {

feat->

().SetImp().SetKey(

);

annot->

().SetFtable().push_back(feat);

item->

().SetAnnot(*annot);

(output_type == 1 || output_type == 2) {

big_mask_loc->

(**locitr);

item->

().SetId(idref);

User-defined methods of the data storage class.

CConn_PipeStream for command piping.

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

void AddProjectItem(objects::CProjectItem &item)

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

Main interface to window based masker functionality.

void SetNameDesc(const string &name)

void SetCreateDate(const CTime &dt)

namespace ncbi::objects::

static wxString GetStdPath(void)

the applicaton installation directory.

static CWinMaskerFileStorage & GetInstance()

access the application-wide singleton

CWindowMaskerJob(const CWindowMaskerParams &params)

TProcessHandle m_ProcHandle

virtual void RequestCancel()

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

CWindowMaskerParams m_Params

virtual void x_CreateProjectItems()

override this function in derived classes and populate m_Items.

void SetObjects(TConstScopedObjects *objects)

CWindowMaskerParams & GetData()

Data access.

void SetData(const CWindowMaskerParams &data)

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

Creation.

virtual void LoadSettings()

int GetOutputType() const

const TConstScopedObjects & GetObjects() const

bool GetStandalone() const

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

#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.

CPipe & GetPipe(void)

Return an underlying CPipe; it's valid for as long as the stream exists.

#define ERR_POST(message)

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

#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.

void Trace(CExceptionArgs_Base &args)

void Info(CExceptionArgs_Base &args)

static CRef< objects::CSeq_loc > RemapChildToParent(const objects::CSeq_loc &parent, const objects::CSeq_loc &child, objects::CScope *scope=NULL)

remap a location to a parent location.

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

string m_Descr

mutex to sync our internals

EDialogReturnValue NcbiMessageBoxW(const wxString &message, TDialogType type=eDialog_Ok, EDialogIcon icon=eIcon_Exclamation, const wxString &title=wxT("Error"), EDialogTextMode text_mode=eRaw)

virtual bool IsCanceled() const override

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 –.

void SetPacked_int(TPacked_int &v)

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.

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 ...

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

void Reset(void)

Reset reference object.

TProcessHandle GetProcessHandle(void) const

Get the process handle for the piped child.

EIO_Status CloseHandle(EChildIOHandle handle)

Close the specified child's pipe handle (even for CPipe opened with OpenSelf()).

EIO_Status Close(int *exitcode=0)

Close pipe.

@ fStdErr_Share

Keep stderr (share it with child)

bool Kill(unsigned long timeout=kDefaultKillTimeout)

Terminate process.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

@ eCurrent

Use current time. See also CCurrentTime.

const char * IO_StatusStr(EIO_Status status)

Get the text form of an enum status value.

#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.

void SetLocation(TLocation &value)

Assign a value to Location data member.

void SetData(TData &value)

Assign a value to Data data member.

E_Choice Which(void) const

Which variant is currently selected.

void SetData(TData &value)

Assign a value to Data data member.

vector< CRef< CSeq_loc > > mask_locs

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