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#ifndef _MS_MS_SPEC_H_
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#define _MS_MS_SPEC_H_
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#include "proteome/peptide_tk.h"
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#include "ms_ms_spectrum_header.h"
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#include "ms_ms_spectrum_header_array_search.h"
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struct MS_MS_Spectrum
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struct MS_MS_SpectrumHeader header;
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00013 Peptide* peptide;
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float threshold;
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00017 LPeak2f* peaks;
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int head;
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int tail;
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00021 } ;
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typedef struct MS_MS_Spectrum MS_MS_Spectrum;
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int saveMSMSSpectrum (
char* path_name, MS_MS_Spectrum* sp,
int pepNumber);
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void normalizeMSMSSpectrum (MS_MS_Spectrum* sp);
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void MS_MS_Spectrum_multiplyByFactor(MS_MS_Spectrum* sp,
float factor);
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void MSMSSpectrum_init (MS_MS_Spectrum* sp);
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void printMSMSSpectrum (MS_MS_Spectrum* sp);
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void MS_MS_Spectrum_create (MS_MS_Spectrum* sp,
int size);
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int MS_MS_Spectrum_load (MS_MS_Spectrum* sp,
Experiment expmnt,
int scanNumber);
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void MS_MS_Spectrum_destroy (MS_MS_Spectrum* sp);
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void createMSMSSpectrumFromPeptide(MS_MS_Spectrum* sp, Peptide* peptide);
00038 MS_MS_Spectrum MS_MS_Spectrum_merge(
Experiment expmnt,
int *pScanArray,
int nScans);
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void get_B_IONS(MS_MS_Spectrum* sp, Peptide* peptide);
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void get_A_IONS(MS_MS_Spectrum* sp, Peptide* peptide);
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void get_C_IONS(MS_MS_Spectrum* sp, Peptide* peptide);
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void get_B_MINUS_WATER_IONS(MS_MS_Spectrum* sp, Peptide* peptide);
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void get_Y_IONS(MS_MS_Spectrum* sp, Peptide* peptide);
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void get_Y_PLUS_TWO_IONS(MS_MS_Spectrum* sp, Peptide* peptide);
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void get_Y_MINUS_AMMONIA_IONS(MS_MS_Spectrum* sp, Peptide* peptide);
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void get_X_IONS(MS_MS_Spectrum* sp, Peptide* peptide);
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void get_Z_IONS(MS_MS_Spectrum* sp, Peptide* peptide);
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void get_PARENT_IONS(MS_MS_Spectrum* sp, Peptide* peptide);
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void MSMSSpectrum_sortByMoz(MS_MS_Spectrum* sp);
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float calcSumOfSquaresOfAbundances(MS_MS_Spectrum* sp);
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short insertPeakInMSMSSpectrumFromTail(MS_MS_Spectrum* sp, LPeak2f* p);
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short insertPeakInMSMSSpectrumFromHead(MS_MS_Spectrum* sp, LPeak2f* p);
00056 LPeak2f* popLPeak2fFromSpectrumFromHead(MS_MS_Spectrum* sp);
00057 LPeak2f* getLPeak2fOfMSMSSpectrumAtIndex(MS_MS_Spectrum* sp,
int index);
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#endif
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