MapQuant: massspec/MQ.rc.h Source File

00001 #ifndef _MS_RC_H_ 00002 #define _MS_RC_H_ 00003 00004 #include <stdio.h> 00005 #include <regex.h> 00006 #include <time.h> 00007 #include <float.h> 00008 #include "byte.h" 00009 00010 #include "util.h" 00011 #include "mqregex.h" 00012 #include "mqrange.h" 00013 #include "mqfilename.h" 00014 #include "paths.h" 00015 #include "mqstring.h" 00016 00017 #include "int_array.h" 00018 #include "float_array.h" 00019 #include "float_matrix.h" 00020 #include "arrayfind.h" 00021 #include "stat.h" 00022 00023 #include "mqaminoacid.h" 00024 00025 #include "rectangle.h" 00026 #include "insets4f.h" 00027 #include "restrictions.h" 00028 #include "peakrestrictions.h" 00029 00030 #include "openrawfile.h" 00031 #include "experiment.h" 00032 #include "experiment_rawio.h" 00033 00034 #include "archivescanheader.h" 00035 #include "archiveiterator.h" 00036 00037 #include "procscript.h" 00038 #include "session.h" 00039 00040 #include "options.h" 00041 00042 #include "peak2i.h" 00043 #include "peak2f.h" 00044 #include "point2f.h" 00045 #include "peak3f.h" 00046 #include "peak3iif.h" 00047 #include "baselinemark.h" 00048 00049 #include "mqtileid.h" 00050 #include "map_pos.h" 00051 00052 #include "map_tk.h" 00053 #include "map_io.h" 00054 00055 #include "param.h" 00056 #include "fpeak.h" 00057 #include "fitter.h" 00058 00059 #include "structelem.h" 00060 #include "peakfinder.h" 00061 #include "attributes.h" 00062 #include "image.h" 00063 #include "segment.h" 00064 #include "segment_extractor.h" 00065 00066 00067 #include "fpeakfile.h" 00068 #include "clustering.h" 00069 #include "peakgroup.h" 00070 #include "peakgroupfile.h" 00071 #include "isocluster.h" 00072 #include "isoclusterfile.h" 00073 #include "isoclusterrestr.h" 00074 00075 #include "fpeakfilter.h" 00076 #include "filter.h" 00077 #include "refiner.h" 00078 #include "deconvolve.h" 00079 #include "segment_handler.h" 00080 #include "tiling.h" 00081 00082 #include "variant.h" 00083 #include "property.h" 00084 #include "stdtables.h" 00085 00086 #include "ms_spectrum_tk.h" 00087 00088 #include "vertex_tree.h" 00089 #include "zset.h" 00090 00091 #include "heap.h" 00092 #include "queue.h" 00093 #include "errors.h" 00094 00095 #if defined (MFC) 00096 #include <conio.h> 00097 #define printf cprintf 00098 #define fprintf cfprintf 00099 #define CreateConsole() AllocConsole() 00100 int cfprintf(FILE* fp, const char* a, ...); 00101 #endif 00102 00103 extern time_t start, stop; 00104 00105 extern int screen_width; 00106 extern int screen_height; 00107 00108 extern char* PROGRAM_NAME; 00109 extern char* OPTIONS_NAME; 00110 extern char* PREFERENCES_FILENAME; 00111 00112 enum {MQ_FLOAT, MQ_INT, MQ_STRING}; 00113 00114 extern int NO_BINS_PER_MZ; 00115 extern int TILE_NUMBER_VERSION; 00116 00117 /* TEST BITS */ 00118 00119 extern Byte ALKYLATION_AGENT_SET ; 00120 00121 extern short EXPERIMENT_PARAMETERS_LOADED; 00122 00123 extern int NR_FUNC_EVAL; 00124 00125 /* PEAK FINDING PARAMETERS */ 00126 00127 extern int PEPTIDE_PEAK_ABU_THRESHOLD; 00128 extern const int MAX_NO_PEPTIDE_PEAKS; 00129 extern const int MAX_NO_CC; 00130 extern const int MAX_PIXELS_IN_CC; 00131 extern const float SEGMENTATION_ABUNDANCE_BIN_SIZE_FRACTION; 00132 extern float SEGMENTATION_BIN_SIZE; 00133 00134 /* PEPTIDE TOOLKIT PARAMETERS */ 00135 00136 extern char* MAPQUANT_PATHFILE; 00137 00138 extern char* PROC_METHOD_PATH; 00139 extern char* TABLES_PATH; 00140 00141 extern short ATOM_COMPOSITION_LOADED; 00142 00143 extern const char* PROTEIN_FOLDER; 00144 00145 extern const int MAX_PROT_NAME_LEN; /* The maximum number of letters for a protein name */ 00146 extern const int MAX_PEPSEQ_LEN; /* The maximum number of residues a peptide can have */ 00147 extern const int MAX_PEPLIB_FILENAME_LEN; /* The maximum number of letters a .pep file can have */ 00148 #define MAX_PROT_SEQ_LEN 5000 00149 00150 /* GLOBAL SAMPLING ARRAY PARAMETERS */ 00151 00152 extern const double RT_DECIMAL_SHIFT_FACTOR; 00153 extern const double MS_DECIMAL_SHIFT_FACTOR; 00154 00155 extern double RT_AVERAGE_SAMPLING_TIME; 00156 extern double MS_AVERAGE_SAMPLING_TIME; 00157 00158 extern const float THRESHOLD; 00159 extern int RANK_CUTOFF; 00160 extern int SCORE_CUTOFF; 00161 extern int NO_OF_CLUSTER_PEAKS; 00162 00163 /* Elements found in proteins */ 00164 extern const Element H; 00165 extern const Element C; 00166 extern const Element N; 00167 extern const Element O; 00168 extern const Element S; 00169 00170 extern const Element C12; 00171 extern const Element C13; 00172 extern const Element H1; 00173 extern const Element N14; 00174 extern const Element O16; 00175 extern const Element S32; 00176 00177 extern const float electron_mass; 00178 00179 #ifdef WIN32 00180 00181 void moveConsoleWindow(); 00182 00183 #endif 00184 00185 extern int* PARAM_sigfigs; 00186 extern void (*MAIN) (void); 00187 00188 Rectangle4i loadConsoleRectangle4i(); 00189 00190 extern char* value; 00191 00192 #define READ_PARAMETER(NAME) \ 00193 if (!strcmp(parameter_name, #NAME)) \ 00194 { \ 00195 int ntokens = 0; \ 00196 ntokens = sscanf(line, "%s %s", parameter_name, parameter_value); \ 00197 if(ntokens == 2) \ 00198 { \ 00199 if (PATH_BIT_STRING & NAME ## _SET) free(NAME); \ 00200 NAME = concat(1, parameter_value); \ 00201 PATH_BIT_STRING |= NAME ## _SET; \ 00202 } \ 00203 } \ 00204 00205 00206 #define FREE_PARAMETER(NAME) \ 00207 if (PATH_BIT_STRING & NAME ## _SET) \ 00208 { PATH_BIT_STRING &= (~(NAME ## _SET)); \ 00209 free(NAME); \ 00210 } 00211 00212 #define READ_INT_PROPERTY_ELSE_DEFAULT(NAME, default_value) \ 00213 if((value = loadLocalProperty(#NAME)) != NULL) \ 00214 { \ 00215 NAME = atoi(value); \ 00216 free(value); \ 00217 } \ 00218 else \ 00219 NAME = default_value; 00220 00221 #define GET_PARAMETER(NAME, value) \ 00222 if (!strcmp(parameter_name, NAME)) \ 00223 { \ 00224 sscanf(line, "%s %s", parameter_name, parameter_value); \ 00225 value = strrpl(parameter_value); \ 00226 found = 1; \ 00227 } 00228 00229 00230 #endif 00231 00232