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Public Types | Public Member Functions | Public Attributes | Protected Types | Protected Member Functions | Protected Attributes

CMain Class Reference

Collaboration diagram for CMain:
Collaboration graph
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List of all members.

Public Types

enum  EAligner { eAlignerExact, eAlignerNoGaps, eAlignerFast, eAlignerLcs }
enum  EAlignMode { eNever, eAlways, eFallback }

Public Member Functions

 CMain (int c, char **v)
 CMain (int c, char **v)
 CMain (int c, char **v)
 CMain (int c, char **v)
 CMain (int c, char **v)
int Run ()
int Run ()
int Run ()
int Run ()
int Run ()

Public Attributes

enum CMain::EAligner aligner

Protected Types

enum  ECommand {
  eNone, eBuild, eStat, eBuild,
  eStat, eDump, eList, eNone,
  ePrimerLookup, eSTSLookup
}
enum  ECommand {
  eNone, eBuild, eStat, eBuild,
  eStat, eDump, eList, eNone,
  ePrimerLookup, eSTSLookup
}
enum  ECommand {
  eNone, eBuild, eStat, eBuild,
  eStat, eDump, eList, eNone,
  ePrimerLookup, eSTSLookup
}
enum  EMode { eCmdline, eFile }
enum  EVersion { eVer1 = 1, eVer2 = 2 }

Protected Member Functions

int Build ()
int Build ()
int Dump ()
int Execute ()
int Execute ()
int Execute ()
int Execute ()
int Execute ()
int Help (FILE *=stdout)
int Help (FILE *=stdout)
int Help (FILE *=stdout)
int Help (FILE *=stdout)
int Help (FILE *=stdout)
int List ()
int ParseCmdline ()
int ParseCmdline ()
int ParseCmdline ()
int ParseCmdline ()
int ParseCmdline ()
void ParseVerbose (const char *opt)
int PrimerLookup ()
int Stat ()
int Stat ()
int STSLookup ()
int Version ()
int Version ()
int Version ()
int Version ()
int Version ()

Protected Attributes

int argc
char ** argv
int batchcnt
unsigned cachesize
enum CMain::ECommand command
const char * cvt
int defHi
int defLo
bool done
list< string > fafiles
string famap
string findex
bool fwd
int gaps
bool have_postprocess
int hi
int lo
IAlignm_AlignL
EAlignMode m_AlignMode
IAlignm_AlignR
bool m_blastdbs
int m_MaxGaps
int m_MaxMismatch
bool m_PrintAlignments
bool m_Quiet
int margin
int mism
enum CMain::EMode mode
string ofile
int ofmt
bool optimize
string outfile
CPcrMachine pcrMachine
int period
bool postprocess
bool presize
bool rev [2]
bool rev_lookup
bool skip_repetative
string stsfile
CStsFileHash stsFileHash
int verbose
enum CMain::EVersion version
int wdsize

Detailed Description

Definition at line 48 of file e-PCR_main.cpp.


The documentation for this class was generated from the following files:

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