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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/msa__tool__job_8hpp_source.html below:

NCBI C++ ToolKit: include/gui/packages/pkg_alignment/msa_tool_job.hpp Source File

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1 #ifndef PKG_ALIGNMENT___CLI_TOOL_JOB__HPP 2 #define PKG_ALIGNMENT___CLI_TOOL_JOB__HPP 39 #include <wx/string.h> 73  virtual bool

BeforeRun();

74  virtual void

x_CreateProjectItems();

75  virtual void

x_AddTreeProjectItem(

const string

&title,

const string

&comment);

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

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

static SQLCHAR output[256]

TIdMap m_IdMap

to make the alignment as robust as possible, we assign every sequence a unique identifer independeont...

virtual TConstScopedObjects & x_GetObjects()=0

Returns the sequences that will be aligned.

map< string, TLocPair > TIdMap

pair< CConstRef< objects::CSeq_loc >, CRef< objects::CScope > > TLocPair

virtual wxString x_GetWorkingDirectory() const

Returns the directory where to execute the msa tool.

virtual wxString x_GetCommandLine(const wxString &input, const wxString &output, bool is_nucleotide)=0

Returns the command line, that will be used to execute the third-party tool.

map< objects::CSeq_id_Handle, bool > TSeqTypeMap

objects::CMappingRanges m_Ranges

vector< SConstScopedObject > TConstScopedObjects

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

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

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