MapQuant: sequence/sequest_summary

00001 #ifndef _SEQUEST_SUMMARY_FILE_H_ 00002 #define _SEQUEST_SUMMARY_FILE_H_ 00003 00004 extern char* SEQUEST_SUMMARY_FILE_HEADER; 00005 00006 struct SequestSummaryFile 00007 { 00008 SequestSummaryEntry* pEntries; 00009 int nEntries; 00010 int MZ_DIMENSION_UNIT; 00011 int LC_DIMENSION_UNIT; 00012 int LC_DIMENSION_MERGE; 00013 }; 00014 00015 typedef struct SequestSummaryFile SequestSummaryFile; 00016 00017 void SequestSummaryFile_alloc(SequestSummaryFile* file, int nSize); 00018 00019 int SequestSummaryFile_aLoad(SequestSummaryFile* file, char* fullname); 00020 int SequestSummaryFile_eLoad(SequestSummaryFile* file, char* folder, char* filename); 00021 00022 int SequestSummaryFile_aLoadUsingExpmntFilter(SequestSummaryFile* ssf, char* fullname, char* szExperimentNameFilter); 00023 int SequestSummaryFile_eLoadUsingExpmntFilter(SequestSummaryFile* ssf, char* folder, char* filename, char* szExperimentNameFilter); 00024 00025 int SequestSummaryFile_aLoadUsingPeptideFilter(SequestSummaryFile* hsf, char* fullname, char* szPeptideNameFilter); 00026 int SequestSummaryFile_eLoadUsingPeptideFilter(SequestSummaryFile* hsf, char* folder, char* filename, char* szPeptideNameFilter); 00027 00028 int SequestSummaryFile_aLoadUsingXCorrFilter(SequestSummaryFile* hsf, char* fullname, SequestXCorrFilter* filter); 00029 int SequestSummaryFile_eLoadUsingXCorrFilter(SequestSummaryFile* hsf, char* folder, char* filename, SequestXCorrFilter* filter); 00030 00031 int SequestSummaryFile_aLoadUsingMultiFilters(SequestSummaryFile* hsf, char* fullname, Insets4f* borders, SequestXCorrFilter* filter); 00032 00033 Point2i* SequestSummaryFile_getPoint2iArray(SequestSummaryFile* ssf, Experiment* q_expmnt); 00034 00035 // Get of valid 00036 Point2i* SequestSummaryFile_getPoint2iArrayOfValid(SequestSummaryFile* ssf, Experiment* q_expmnt, int *npeaks); 00037 Peak2f* SequestSummaryFile_getRealPeak2fArrayOfValid(SequestSummaryFile* ssf, int *npeaks); 00038 Peak2f* SequestSummaryFile_getMS2EventCoordinatesOfValid(SequestSummaryFile* ssf, int *npeaks, int x_axis_units); 00039 Peak2f* SequestSummaryFile_getRealPeak2fArrayOfValidUniqueChargeVariants(SequestSummaryFile* ssf, int *npeaks, char* type); 00040 00041 MQString* SequestSummaryFile_getPeptideSequenceArray(SequestSummaryFile* ssf); 00042 MQString* SequestSummaryFile_getXCorrArray(SequestSummaryFile* ssf); 00043 MQString* SequestSummaryFile_getChargeArray(SequestSummaryFile* ssf); 00044 00045 void SequestSummaryFile_sortByScanBoundsAndXCorr(SequestSummaryFile *file); 00046 void SequestSummaryFile_sortBySequenceAndCharge(SequestSummaryFile *file); 00047 00048 void Peak2i_translateScan(Peak2i* peak, Experiment* s_expmnt, Experiment* q_expmnt); 00049 00050 // ******************* PRINT FUNCTIONS ****************** 00051 00052 void SequestSummaryFile_fprint(FILE* fp, SequestSummaryFile* ssf); 00053 void SequestSummaryFile_fprintWithMS2ToFPeak2iArrayUsingAligner( FILE* fp, 00054 SequestSummaryFile* ssf, 00055 MS2ToFPeak2i* ms2toms1, 00056 float scale, int displacement); 00057 00058 void SequestSummaryFile_fprintWithMS2ToFPeak2iArrayUsingCommonRTSampling(FILE* fp, 00059 SequestSummaryFile* ssf, 00060 MS2ToFPeak2i* ms2toms1, 00061 Experiment* q_expmnt); 00062 00063 00064 void SequestSummaryFile_fprintTabDelimitedWithFPeak2iArrayUsingCommonRTSampling(FILE* fp, SequestSummaryFile* ssf, MS2ToFPeak2i* ms2toms1, Experiment* q_expmnt); 00065 void SequestSummaryFile_fprintTabDelimitedWithFPeak2iArray(FILE* fp, SequestSummaryFile* ssf, Peak2f* speaks, MS2ToFPeak2i* ms2toms1); 00066 00067 void SequestSummaryFile_applyMZFilter (SequestSummaryFile *file, Insets4f* borders); 00068 void SequestSummaryFile_applyXCorrFilter(SequestSummaryFile *file, SequestXCorrFilter* seqfilter); 00069 00070 00071 #endif 00072

sequence/sequest_summary_file.h