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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/makeclusterdb_8cpp.html below:

NCBI C++ ToolKit: src/app/blastdb/makeclusterdb.cpp File Reference

Command line tool to create cluster databases. More...

#include <ncbi_pch.hpp>
#include <serial/objostrjson.hpp>
#include <algo/blast/api/version.hpp>
#include <algo/blast/blastinput/blast_input_aux.hpp>
#include <corelib/ncbiapp.hpp>
#include <serial/iterator.hpp>
#include <objmgr/util/create_defline.hpp>
#include <objmgr/util/sequence.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/general/User_object.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/blastdb/Blast_db_mask_info.hpp>
#include <objects/blastdb/Blast_mask_list.hpp>
#include <objtools/blast/seqdb_reader/seqdb.hpp>
#include <objtools/blast/seqdb_reader/seqdbcommon.hpp>
#include <objtools/blast/seqdb_writer/writedb.hpp>
#include <objtools/blast/seqdb_writer/writedb_error.hpp>
#include <util/format_guess.hpp>
#include <util/util_exception.hpp>
#include <objtools/blast/seqdb_writer/build_db.hpp>
#include <algo/blast/blastinput/blast_input.hpp>
#include "../blast/blast_app_util.hpp"
#include "masked_range_set.hpp"
#include <iostream>
#include <sstream>
#include <fstream>

Include dependency graph for makeclusterdb.cpp:

Go to the source code of this file.

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Classes class CClusterSeq class CCluster class CClusterDBSource class CMakeClusterDBApp The main application class. More...
Functions USING_SCOPE (blast) USING_SCOPE (objects) bool SortClusterSeqs (CRef< CClusterSeq > &a, CRef< CClusterSeq > &b) bool SortCluster (CRef< CCluster > &a, CRef< CCluster > &b) static const string kInput ("in") Command line flag to represent the input. More...
static const string kInputSeparators (" ") Defines token separators when multiple inputs are present. More...
static const string kOutput ("out") Command line flag to represent the output. More...
static string Uint8ToString_DataSize (Uint8 v, unsigned minprec=10) Converts a Uint8 into a string which contains a data size (converse to NStr::StringToUInt8_DataSize) More...
int main (int argc, const char *argv[]) Variables USING_NCBI_SCOPE Detailed Description

Command line tool to create cluster databases.

Definition in file makeclusterdb.cpp.

Function Documentation ◆ kInput() static const string kInput ( "in" ) static

Command line flag to represent the input.

Referenced by CMakeClusterDBApp::Init(), and CMakeClusterDBApp::x_BuildDatabase().

◆ kInputSeparators() static const string kInputSeparators ( " " ) static

Defines token separators when multiple inputs are present.

◆ kOutput() static const string kOutput ( "out" ) static

Command line flag to represent the output.

Referenced by CMakeClusterDBApp::Init(), and CMakeClusterDBApp::x_BuildDatabase().

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

Definition at line 619 of file makeclusterdb.cpp.

References CNcbiApplicationAPI::AppMain().

◆ SortCluster() bool SortCluster ( CRef< CCluster > & a, CRef< CCluster > & b )

Definition at line 121 of file makeclusterdb.cpp.

References a, and b.

Referenced by CMakeClusterDBApp::x_ProcessInputData().

◆ SortClusterSeqs() bool SortClusterSeqs ( CRef< CClusterSeq > & a, CRef< CClusterSeq > & b )

Definition at line 116 of file makeclusterdb.cpp.

References a, and b.

Referenced by CMakeClusterDBApp::x_ProcessInputFile().

◆ Uint8ToString_DataSize() static string Uint8ToString_DataSize ( Uint8 v, unsigned minprec = 10 ) static

Converts a Uint8 into a string which contains a data size (converse to NStr::StringToUInt8_DataSize)

Parameters: v value to convert [in] minprec minimum precision [in]

Definition at line 437 of file makeclusterdb.cpp.

References i, and NStr::UInt8ToString().

Referenced by CMakeClusterDBApp::x_BuildDatabase().

◆ USING_SCOPE() [1/2] USING_SCOPE ( blast ) ◆ USING_SCOPE() [2/2] USING_SCOPE ( objects ) Variable Documentation ◆ USING_NCBI_SCOPE USING_NCBI_SCOPE

Definition at line 68 of file makeclusterdb.cpp.

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