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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/pairwise__aln__app_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/alnmgr/demo/pairwise_aln_app.cpp Source File

59 using namespace ncbi

;

79  virtual void Init

(

void

);

80  virtual int Run

(

void

);

82  void

LoadInputAlns(

void

);

85

m_AlnContainer.insert(*aln);

102

arg_desc->AddDefaultKey

103

(

"in"

,

"InputFileName"

,

104  "Name of file to read from (standard input by default)"

,

107

arg_desc->AddDefaultKey

108

(

"b"

,

"bin_obj_type"

,

109  "This forces the input file to be read in binary ASN.1 mode\n" 110  "and specifies the type of the top-level ASN.1 object.\n"

,

113

arg_desc->AddDefaultKey

115  "Query (anchor) row (zero-based)"

,

118

arg_desc->AddDefaultKey

119

(

"s"

,

"SubjectRow"

,

120  "Subject row (zero-based)"

,

124  string

prog_description =

"Alignment build application.\n"

;

125

arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),

126

prog_description,

false

);

128

SetupArgDescriptions(arg_desc.release());

135  string

sname = args[

"in"

].AsString();

138  string

asn_type = args[

"b"

].AsString();

139  bool

binary = !asn_type.empty();

140

unique_ptr<CObjectIStream>

in 168

m_QueryRow =

GetArgs

()[

"q"

].AsInteger();

169

m_SubjectRow =

GetArgs

()[

"s"

].AsInteger();

264 int main

(

int

argc,

const char

* argv[])

static CRef< CScope > m_Scope

Helper class for reading seq-align objects from a CObjectIStream.

void Read(CObjectIStream *obj_in_stream, TCallback callback, const string &top_level_asn_object=kEmptyStr)

Read all seq-align objects from the stream.

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

CAlnContainer m_AlnContainer

CRef< CObjectManager > m_ObjMgr

CScope & GetScope(void) const

bool InsertAln(const CSeq_align *aln)

void Validate(bool full_test=false) const

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

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eInteger

Convertible into an integer number (int or Int8)

@ eDS_Default

Try standard log file (app.name + ".log") in /log/, use stderr on failure.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

void Run(void)

Enter the main loop.

void CONNECT_Init(const IRWRegistry *reg=0, CRWLock *lock=0, TConnectInitFlags flag=eConnectInit_OwnNothing, FSSLSetup ssl=0)

Init [X]CONNECT library with the specified "reg" and "lock" (ownership for either or both can be deta...

Magic spell ;-) needed for some weird compilers... very empiric.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

#define GetArgs

Avoid preprocessor name clash with the NCBI C Toolkit.

Defines command line argument related classes.

Defines unified interface to application:

std::istream & in(std::istream &in_, double &x_)

int main(int argc, const char *argv[])

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