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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/label__rna_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/packages/pkg_sequence_edit/label_rna.cpp Source File

41 #include <wx/filename.h> 42 #include <wx/sstream.h> 43 #include <wx/txtstrm.h> 44 #include <wx/msgdlg.h> 74 if

((*it)->IsGenbank() && (*it)->GetGenbank().IsSetAccession())

76

accession = (*it)->GetGenbank().GetAccession();

78 if

((*it)->IsGeneral() && (*it)->GetGeneral().IsSetDb() && (*it)->GetGeneral().GetDb() ==

"TMSMART"

&& (*it)->GetGeneral().IsSetTag())

80 if

((*it)->GetGeneral().GetTag().IsStr())

81

tmsmart = (*it)->GetGeneral().GetTag().GetStr();

82 else if

((*it)->GetGeneral().GetTag().IsId())

86 if

(!accession.empty())

96 string

acc = GetGenBankId(*bi);

107 if

(!tse)

return false

;

109

wxString tmpIn = wxFileName::CreateTempFileName(

wxT

(

"in"

));

112

PrepareInputFile(tse,ostr);

114

wxString tmpOut = wxFileName::CreateTempFileName(

wxT

(

"out"

));

117

wxString script =

(

"\\\\snowman\\win-coremake\\App\\Ncbi\\smart\\bin\\cmd_sequin_fetch_FindITS.bat"

);

119

wxString script =

(

"/netopt/genbank/subtool/bin/cmd_sequin_fetch_FindITS"

);

122

wxString cmdline = script+

(

" -i "

)+tmpIn+

(

" -o "

) + tmpOut;

123 if

(!wxFileName::FileExists(script))

125

wxMessageBox(

(

"Path to FindITS executable does not exist"

wxT

(

"Error"

), wxOK | wxICON_ERROR,

NULL

);

130 long

pid = ::wxExecute(cmdline, wxEXEC_SYNC | wxEXEC_HIDE_CONSOLE);

134

wxMessageBox(

(

"Bad return code from FindITS executable"

wxT

(

"Error"

), wxOK | wxICON_ERROR,

NULL

);

144

edit::CFindITSParser parser(tmpOut.mb_str(), tse);

149

AddNewMrnaCommand(composite, parser.GetBSH(), new_mrna, parser.GetNegative());

150 string msg

(parser.GetMsg());

153

}

while

( !parser.AtEOF() );

156 if

error

.IsEmpty())

159

report->SetTitle(

wxT

(

"Label RNA Error"

));

166

wxMessageBox(

(

"Unable to read Label RNA|ITS results"

wxT

(

"Error"

), wxOK | wxICON_ERROR,

NULL

);

172

::wxRemoveFile(tmpIn);

177

::wxRemoveFile(tmpOut);

void AddCommand(IEditCommand &command)

void SetText(const wxString &text)

void PrepareInputFile(CSeq_entry_Handle tse, CNcbiOfstream &ostr)

bool apply(objects::CSeq_entry_Handle tse, ICommandProccessor *cmdProcessor, string title, wxWindow *parent)

void AddNewMrnaCommand(CRef< CCmdComposite > composite, CBioseq_Handle bsh, CRef< CSeq_feat > new_mrna, bool negative)

string GetGenBankId(CBioseq_Handle bsh)

Undo/Redo interface for editing operations.

virtual void Execute(IEditCommand *command, wxWindow *window=0)=0

iterator_bool insert(const value_type &val)

Include a standard set of the NCBI C++ Toolkit most basic headers.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

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

Convert int to string.

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

const TId & GetId(void) const

Get the Id member data.

list< CRef< CSeq_id > > TId

@ eMol_na

just a nucleic acid

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

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

CRef< CCmdComposite > GetReverseComplimentSequenceCommand(objects::CBioseq_Handle bsh)

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