mqexperiment.h

#ifndef _MQEXPERIMENT_H_
#define _MQEXPERIMENT_H_

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

#ifdef WITH_MQXML
    #include "mqxml/mqXMLAPI.h"
#endif

#define MQEXPERIMENT_MZ_RULER_ID_WITH_MOST_SCANS 255

extern MQByte MQEXPERIMENT_MZ_RULER_ID;

extern MQByte MQEXPERIMENT_RT_RULER_MODE;
extern MQByte MQEXPERIMENT_MZ_RULER_MODE;

extern int      NO_BINS_PER_MZ;

enum {ABS_TO_REL, REL_TO_ABS};
enum {D1, D2};

// These bits use the last eight bits
#define SCAN_MS1 0x00000001
#define SCAN_MS2 0x00000002
#define SCAN_MS3 0x00000004
#define SCAN_MS4 0x00000008

// These bits use the nest eight bits
#define SCAN_PROFILE  0x00000100
#define SCAN_CENTROID 0x00000200

// These bits use the nest eight bits
#define SCAN_FULL 0x00010000
#define SCAN_ZOOM 0x00020000

#define SCAN_ALL      0xFFFFFFFF

enum {MQ_REL, MQ_ABS};

struct MQExperiment
{
    unsigned    rtsize_loaded:  1;
    unsigned    rtloaded:       1;

    unsigned    msloaded:       1;
    unsigned    mssize_loaded:  1;

    unsigned    ms2loaded:      1;

    // ******** Directories *********

    char*       szName;
    char*       szFileName;
    FILE*       pFile;

    char*       szProcExpDir;


    char*       szProcMapsDir;
    char*       szProcResultsDir;

    // ******** Size & Sampling Info *******
    Rectangle4i rect;

    // ********* Ruler Info *****************

    // RT Ruler

    MQScanHeader*   scanheaders;
    int             SIZE_GLOBAL_RT_SAMPLING_ARRAY;
    float*          GLOBAL_RT_SAMPLING_ARRAY;

    // MZ Ruler
    MQMZRuler*      rulers;
    int             nrulers;
    int             SIZE_GLOBAL_MS_SAMPLING_ARRAY;
    float*          GLOBAL_MS_SAMPLING_ARRAY;

    // ******** ChromatographyInfo **********

    char* szInstrumentInfo;
    char* szInstrumentName;
    float dInjectionVolume;
    char* szInjectionVolumeUnits;

    // FileFormatSpecific

    int             nFileFormat;

    OpenRawFile     orFile;

#ifdef WITH_MQXML
    mqXMLTopology   mqXMLTop;
#endif
};

typedef struct MQExperiment MQExperiment;

void    MQExperiment_destroy(MQExperiment* exp);

int MQExperiment_isScanFull  (MQExperiment* expmnt, int scanno);
int MQExperiment_isScanZoom  (MQExperiment* expmnt, int scanno);
int MQExperiment_isScanMS        (MQExperiment* expmnt, int scanno);
int MQExperiment_isScanMS2   (MQExperiment* expmnt, int scanno);
int MQExperiment_isScanCentroid(MQExperiment* expmnt, int scanno);
int MQExperiment_isScanProfile (MQExperiment* expmnt, int scanno);
int MQExperiment_isScanProfileUncompressed(MQExperiment* expmnt, int scanno);
int MQExperiment_isScanProfileCompressed(MQExperiment* expmnt, int scanno);
int MQExperiment_hasScanMZRulerID(MQExperiment* expmnt, int scanno, MQByte mzrulerID);

void    MQExperiment_setStrings(MQExperiment* expmnt, char* szExpName);
int     MQExperiment_verifyInstrumentMethod(MQExperiment* MQExperiment);

// CREATING DIRECTORIES

void    MQExperiment_createProcFolder           (MQExperiment* expmnt);
void    MQExperiment_createProcMapsFolder       (MQExperiment* expmnt);
void    MQExperiment_createProcResultsFolder    (MQExperiment* expmnt);

char* MQExperiment_createCmpFolder(MQExperiment* expmnt_1, MQExperiment* expmnt_2);

// RT SAMPLING ARRAY
float   MQExperiment_getRTFromScan(MQExperiment* expmnt, int scanNumber);
int     MQExperiment_getScanFromRT(MQExperiment* expmnt, float RT);
float   MQExperiment_calcMeanRTSamplingTime(MQExperiment* expmnt);

// MS SAMPLING ARRAY

void    MQExperiment_setGlobalMZSamplingArray(MQExperiment* expmnt, MQByte rulerID);
void    MQExperiment_createGlobalMSSamplingArray(MQExperiment* exp, float binSize,
                                                float moz_start, float moz_stop);

int     MQExperiment_getSizeGlobalMSSamplingArray(MQExperiment* exp, float binSize, float moz_start, float moz_stop);

void    MQExperiment_saveGlobalMSSamplingArray(MQExperiment* expmnt);
float*  MQExperiment_getRTSamplingArray     (MQExperiment* expmnt);
float*  MQExperiment_copyRTSamplingArray        (MQExperiment* expmnt, int scan_start, int scan_stop, int* size);
int*    MQExperiment_copySCSamplingArray        (MQExperiment* expmnt, int scan_start, int scan_stop, int* size);

float   MQExperiment_getMOZFromMassBin      (MQExperiment* expmnt, int binNumber);
int     MQExperiment_getMassBinFromMOZ      (MQExperiment* expmnt, float MOZ);
MQByte  MQExperiment_getMZRulerID(MQExperiment* expmnt, int scanNumber);

// MISCELLANEOUS

Insets4f MQExperiment_getRealInsets(MQExperiment* expmnt, Insets4i* samplingInsets);
void     MQExperiment_getRangeOfIndependentScan(MQExperiment* MQExperiment, double* mass_start, double* mass_stop);
int      MQExperiment_getParentMSScan(MQExperiment* expmnt, int nScanNumber);
int      MQExperiment_isCentroidOnly(MQExperiment* expmnt);
int      MQExperiment_countScans(MQExperiment* expmnt, int type_bits);
int      MQExperiment_countScansWithinLimits(MQExperiment* expmnt, int scan_start, int scan_stop, int type);
int      MQExperiment_getMapTileIndex(MQExperiment* expmnt, int x, int y);

// ************* PRINTING FUNCTIONS ********************

void        MQExperiment_fprintMS2ScansAsTabDelimitedTable(FILE* fp, MQExperiment* expmnt);
void        MQExperiment_fprintMZRuler(FILE* fp, MQExperiment* expmnt);
MQPoint2f*  MQExperiment_convertPoint2fArrayFromCentroidToProfileWithLimits(MQExperiment* expmnt, MQPoint2f* dpCentroid, int csize, int bin_start, int bin_stop);
float*      MQExperiment_resampleIntensityVectorToMZRuler(MQExperiment* expmnt, int scanNumber, float* pUncopressedIntensity, int nSize, MQByte mzrulerID, int* count_inconsistancies);


#endif

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