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//\Ignore{
#ifndef MATCHTASK_H
#define MATCHTASK_H
#include "maxfiles.h"
#include "markinfo.h"
#include "mparms.h"
#include "markinfo.h"
#include "vplugin-interface.h"
#include "vmotif-data.h"
#include "cpridx-data.h"
#include "chaincall.h"
#include "mcldef.h"
#include "vmcldef.h"
#include "fqfinfo.h"
#include "outinfo.h"
#include "pathmax.h"
#ifdef VMATCHDB
#include "vmdbparms.h"
#endif
//}
/*
This file contains some definitions for types used when analyzing the
user given parameters specifying the matching task.
*/
#define TASKONLINE UintConst(1) // match is performed online
#define TASKCOMPLETEMATCH (UintConst(1) << 1) // require complete matches
#define TASKMUM (UintConst(1) << 2) // require maximal unique matches
#define TASKMUMCANDIDATE (UintConst(1) << 3) // require mum candidates
#define TASKSUPER (UintConst(1) << 4) // require maximal unique matches
#define TASKTANDEM (UintConst(1) << 5) // require maximal unique matches
#define TASKPREINFO (UintConst(1) << 6) // require to only compute number of exact matches
#define ISTASKONLINE\
((matchcallinfo->matchtask & TASKONLINE) ? True: False)
#define DOMATCHBUFFERING(MCINFO)\
(BOOL) (((MCINFO)->chaincallinfo.defined ||\
(MCINFO)->matchclustercallinfo.defined))
/*
The following type aggregates information parsed from the
argument vector, as provided when calling the vmatch-program.
*/
typedef struct
{
Uint numberofqueryfiles,// number of query files
matchtask; // a combination of the bits TASKONLINE .. TASKPREFINFO
BOOL ownpostprocessing; // vmatch does own postprocessing
Maskmatch maskmatch;
Nomatch nomatch;
char progname[PATH_MAX+1], // program name
indexormatchfile[PATH_MAX+1], // name of index or match file
*mfargs, // args for the matchfile
*queryfiles[MAXNUMBEROFFILES]; // table of query files
BOOL withindexfile; // last argument is indexname
FQFsubstringinfo fqfsubstringinfo; // for the first file containing
// only one sequence
Matchparam matchparam; // user specified match parameters
Outinfo outinfo; // information determining the output
Clusterparms clusterparms; // parameters required for clustering
Showverbose showverbose; // function to show status info
Markinfo markinfo; // for marking matches
Sequenceclusterinfo seqclinfo; // sequence clustering
Chaincallinfo chaincallinfo;
Matchclustercallinfo matchclustercallinfo;
Vpluginbundle vmotifbundle,
cpridxpatsearchbundle;
Vmotifdata vmotifdata;
Cpridxpatsearchdata cpridxpatsearchdata;
//\Ignore{
#ifdef VMATCHDB
Databaseparms databaseparms;
#endif
//}
} Matchcallinfo; // \Typedef{Matchcallinfo}
//\Ignore{
#endif
//}
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