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#ifndef _MS_RC_H_
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#define _MS_RC_H_
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#include <stdio.h>
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#include <regex.h>
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#include <time.h>
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#include <float.h>
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#include "byte.h"
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#include "util.h"
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#include "mqregex.h"
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#include "mqrange.h"
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#include "mqfilename.h"
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#include "paths.h"
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#include "mqstring.h"
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#include "int_array.h"
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#include "float_array.h"
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#include "float_matrix.h"
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#include "arrayfind.h"
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#include "stat.h"
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#include "mqaminoacid.h"
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#include "rectangle.h"
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#include "insets4f.h"
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#include "restrictions.h"
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#include "peakrestrictions.h"
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#include "openrawfile.h"
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#include "experiment.h"
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#include "experiment_rawio.h"
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#include "archivescanheader.h"
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#include "archiveiterator.h"
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#include "procscript.h"
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#include "session.h"
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#include "options.h"
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#include "peak2i.h"
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#include "peak2f.h"
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#include "point2f.h"
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#include "peak3f.h"
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#include "peak3iif.h"
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#include "baselinemark.h"
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#include "mqtileid.h"
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#include "map_pos.h"
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#include "map_tk.h"
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#include "map_io.h"
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#include "param.h"
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#include "fpeak.h"
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#include "fitter.h"
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#include "structelem.h"
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#include "peakfinder.h"
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#include "attributes.h"
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#include "image.h"
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#include "segment.h"
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#include "segment_extractor.h"
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#include "fpeakfile.h"
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#include "clustering.h"
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#include "peakgroup.h"
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#include "peakgroupfile.h"
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#include "isocluster.h"
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#include "isoclusterfile.h"
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#include "isoclusterrestr.h"
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#include "fpeakfilter.h"
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#include "filter.h"
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#include "refiner.h"
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#include "deconvolve.h"
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#include "segment_handler.h"
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#include "tiling.h"
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#include "variant.h"
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#include "property.h"
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#include "stdtables.h"
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#include "ms_spectrum_tk.h"
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#include "vertex_tree.h"
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#include "zset.h"
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#include "heap.h"
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#include "queue.h"
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#include "errors.h"
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#if defined (MFC)
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#include <conio.h>
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#define printf cprintf
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#define fprintf cfprintf
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#define CreateConsole() AllocConsole()
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int cfprintf(FILE* fp,
const char* a, ...);
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#endif
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extern time_t start, stop;
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extern int screen_width;
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extern int screen_height;
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extern char* PROGRAM_NAME;
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extern char* OPTIONS_NAME;
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extern char* PREFERENCES_FILENAME;
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enum {MQ_FLOAT, MQ_INT, MQ_STRING};
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extern int NO_BINS_PER_MZ;
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extern int TILE_NUMBER_VERSION;
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extern Byte ALKYLATION_AGENT_SET ;
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extern short EXPERIMENT_PARAMETERS_LOADED;
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extern int NR_FUNC_EVAL;
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extern int PEPTIDE_PEAK_ABU_THRESHOLD;
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extern const int MAX_NO_PEPTIDE_PEAKS;
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extern const int MAX_NO_CC;
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extern const int MAX_PIXELS_IN_CC;
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extern const float SEGMENTATION_ABUNDANCE_BIN_SIZE_FRACTION;
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extern float SEGMENTATION_BIN_SIZE;
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extern char* MAPQUANT_PATHFILE;
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extern char* PROC_METHOD_PATH;
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extern char* TABLES_PATH;
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extern short ATOM_COMPOSITION_LOADED;
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extern const char* PROTEIN_FOLDER;
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extern const int MAX_PROT_NAME_LEN;
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extern const int MAX_PEPSEQ_LEN;
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extern const int MAX_PEPLIB_FILENAME_LEN;
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#define MAX_PROT_SEQ_LEN 5000
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extern const double RT_DECIMAL_SHIFT_FACTOR;
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extern const double MS_DECIMAL_SHIFT_FACTOR;
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extern double RT_AVERAGE_SAMPLING_TIME;
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extern double MS_AVERAGE_SAMPLING_TIME;
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extern const float THRESHOLD;
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extern int RANK_CUTOFF;
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extern int SCORE_CUTOFF;
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extern int NO_OF_CLUSTER_PEAKS;
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extern const Element H;
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extern const Element C;
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extern const Element N;
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extern const Element O;
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extern const Element S;
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extern const Element C12;
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extern const Element C13;
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extern const Element H1;
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extern const Element N14;
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extern const Element O16;
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extern const Element S32;
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extern const float electron_mass;
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#ifdef WIN32
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void moveConsoleWindow();
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#endif
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extern int* PARAM_sigfigs;
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extern void (*MAIN) (
void);
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Rectangle4i loadConsoleRectangle4i();
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extern char* value;
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#define READ_PARAMETER(NAME) \
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if (!strcmp(parameter_name, #NAME)) \
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{ \
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int ntokens = 0; \
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ntokens = sscanf(line, "%s %s", parameter_name, parameter_value); \
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if(ntokens == 2) \
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{ \
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if (PATH_BIT_STRING & NAME ## _SET) free(NAME); \
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NAME = concat(1, parameter_value); \
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PATH_BIT_STRING |= NAME ## _SET; \
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} \
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} \
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#define FREE_PARAMETER(NAME) \
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if (PATH_BIT_STRING & NAME ## _SET) \
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{ PATH_BIT_STRING &= (~(NAME ## _SET)); \
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free(NAME); \
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}
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#define READ_INT_PROPERTY_ELSE_DEFAULT(NAME, default_value) \
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if((value = loadLocalProperty(#NAME)) != NULL) \
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{ \
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NAME = atoi(value); \
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free(value); \
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} \
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else \
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NAME = default_value;
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#define GET_PARAMETER(NAME, value) \
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if (!strcmp(parameter_name, NAME)) \
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{ \
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sscanf(line, "%s %s", parameter_name, parameter_value); \
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value = strrpl(parameter_value); \
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found = 1; \
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}
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#endif
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