massspec/mqfilename.h

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#ifndef _MQFILENAME_H_
#define _MQFILENAME_H_

/* Copyright (c) Kyriacos Leptos and the President and Fellows of Harvard University
   Release Date: 2004-11-01
   Part of the MapQuant suite library "massspec.lib" 
*/

#define MAX_FILENAME_LENGTH             1000

typedef enum 
{
                MQFILE_TYPE_MAP, 
                MQFILE_TYPE_HEADER,
                MQFILE_TYPE_IPK, 
                MQFILE_TYPE_FPK, 
                MQFILE_TYPE_ATR, 
                MQFILE_TYPE_MS1, 
                MQFILE_TYPE_MS2, 
                MQFILE_TYPE_PGR, 
                MQFILE_TYPE_ISC,
                MQFILE_TYPE_DTA2FPEAK,
                MQFILE_TYPE_METRICS, 
                SESSION_PATH,
                SESSION_NAME
} MQFileType;


struct MQFilename
{
        unsigned mqformat: 2;

        char* szPath;
        char* szName;
        char* szSessionName;
        char* szTile;
} ;

typedef struct MQFilename MQFilename;

MQFilename MQFilename_tokenize(char* mqf);

// Extensions
#define         MAP_EXT                         "map"
#define     RAW_MAP_EXT                         "r.map"
#define     PRC_MAP_EXT                         "s.map"
#define         LBL_MAP_EXT                             "l.map"

#define                 MAP_HEADER_EXT          "header"
#define         RAW_MAP_HEADER_EXT              "r.header"
#define         PRC_MAP_HEADER_EXT              "s.header"
#define         LBL_MAP_HEADER_EXT              "l.header"


#define     PEAKS_EXT                           "peaks"
#define         FPEAKS_EXT                              "fpeaks"
#define         PEAK_GROUP_EXT                  "pgroups"
#define         ISC_EXT                                 "ic"

#define         MQFILE_EXT_DTA2FPEAK    "dta2fpeak"
#define         MQFILE_EXT_METRICS              "metrics"

#define         MS2_SPECTRUM_EXT                "MS2.spec"
#define         MS1_SPECTRUM_EXT                "MS1.spec"
#define         MASS_CHROM_EXT                  "mchrom"

#define         TABLES_EXT                               "table"
#define         PROC_METHOD_EXT              "mpm"
#define         PREFERENCES_EXT                  "pref"

#define         MQFILE_EXT_MSAR                  "msar"
#define         MQFILE_EXT_MS2AR                 "ms2ar"
#define         MQFILE_EXT_PARAM             "param"



char*           MQFileType_toString(int type);
int                     MQFileType_toIndex(char* string);
const char* MQFileType_getExtension(int type);

int             MQFilename_viewUsingPath(char* path, char* name);
int             MQFilename_view(char* filename);
int             MQFilename_fileExists(char* filename);
char*   MQFilename_getFileExtension(char* szFilename);
char*   MQFilename_removeFileExtension(char* szFilename); 
char*   MQFilename_assemble(char* path, char* name, MQFileType type, char* szModifier);
char*   MQFilename_getPath(char* fullfilename);
char*   MQFilename_getName(char* fullfilename);
int             MQFilename_createInexistentFile(char* name);

// Should go to MQFILE in the future

#define UNDERSCORE  "_"
#define COMMENT_CHAR '#'
#define HEADER_CHAR  '>'

#define MAX_LINE_LENGTH                 1000

extern char FILE_LINE[MAX_LINE_LENGTH];

#define FOR_EACH_LINE(fp) while(fgets(FILE_LINE, MAX_LINE_LENGTH, (fp)) != NULL)

int             MQFile_isLineComment(char* line);
int             MQFile_isLineHeader (char* line);
int             MQFile_countLines(FILE* fp);
int             MQFile_countNoEmptyNoCommentLines(FILE* fp);

int             countlines(FILE* fp);
int             checkln(char* line);
int             checkcommln(char* line);
int             checkheaderln(char* line);
void    chomp(char* string);
int             isLineEmpty(char* line);

#endif

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