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