MapQuant: mqparser/mqscriptfunc.h Source File

00001 #ifndef _MQSCRIPT_FUNC_H_ 00002 #define _MQSCRIPT_FUNC_H_ 00003 00029 double length(VariantArray array); 00030 00038 double verbose(void); 00039 00040 00050 double Number_Save(double number, char* filename); 00051 00055 // ******************************************************* 00056 // ***************** mqsriptfunc_map.c ******************* 00057 // ******************************************************* 00058 00077 Map2D Map_Load(char* mqf_map); // long 00078 00079 00080 00085 Map2D lmap(char* mqf_map); // short 00086 00087 00097 double Map_Save(Map2D map, char* mqf_map); // long 00098 00104 double smap(Map2D map, char* mqf_map); // short 00105 00115 double Map_Remove(char* mqf_map); // long 00116 00122 double rmmap(char* mqf_map); // short 00123 00143 double Map_GetArea(Map2D map); 00144 00155 double Map_GetMedian(Map2D map, double mode); 00156 00168 double Map_GetAvgAbsDevFromValue(Map2D map, double value, double mode); 00169 00181 double Map_GetMedianAbsDevFromValue(Map2D map, double value, double mode); 00182 00193 double Map_GetMean(Map2D map, double mode); 00194 00205 double Map_GetSD(Map2D map, double mean, double mode); 00206 00217 VariantArray /* A */ Map_GetSegmentArray(Map2D map); 00218 00233 VariantArray /* A */ Map_GetSegmentArrayContainingPeaks(Map2D map, VariantArray peaks, double dMZTolerance, double nScanTolerance); 00234 00265 Map2D Map_ApplyFilter(Map2D map, char* filter, double dim); // long 00266 00272 Map2D filtermap(Map2D map, char* filter, double dim); // short 00273 00293 Map2D Map_Segment(Map2D map, double bin_size); // long 00294 00300 Map2D segmap(Map2D map, double bin_size); // short 00301 00302 00314 Map2D Map_ApplyOpening(Map2D map, char* structel); // long 00315 00321 Map2D openmap(Map2D map, char* structel); // short 00322 00334 Map2D Map_ApplyClosing(Map2D map, char* structel); // long 00335 00341 Map2D closemap(Map2D map, char* structel); // short 00342 00343 00352 Map2D Map_ApplyLinearInterpolation(Map2D map); // long 00353 00354 00359 Map2D linintermap(Map2D map); // short 00360 00361 00362 00372 Map2D Map_RemoveStreaks4(Map2D map); 00373 00378 Map2D rstreaks4(Map2D map); // short 00379 00392 VariantArray /* P */ Map_FindPeaks(Map2D source, char* structel, double abuthr); // long 00393 00399 VariantArray /* P */ findpk(Map2D source, char* structel, double abuthr); // short 00400 00401 00416 Map2D Map_Extract(Map2D source, Map2D stencil, Segment segment); 00417 00418 00423 Map2D extractmap(Map2D source, Map2D stencil, Segment segment); 00424 00428 // ******************************************************* 00429 // **************** mqsriptfunc_fpeaks.c ***************** 00430 // ******************************************************* 00431 00449 VariantArray /* P */ PeakArray_Load(char* mqf_pk); 00450 00456 VariantArray /* P */ lpk(char* mqf_pk); 00457 00466 double PeakArray_Print(VariantArray array); 00467 00468 00478 double PeakArray_Save(VariantArray array, char* mqf_pk); 00479 00480 00496 double PeakArray_SaveWithMapValue(VariantArray array, Map2D map, char* mqf_pk); 00497 00498 00515 double PeakArray_SavePhysQuantWithMapValue(VariantArray array, Map2D map, char* mqf_pk); 00516 00534 double PeakArray_SaveWithBaseline(VariantArray array, Map2D map, char* mqf_pk); 00535 00556 VariantArray /* K */ FPeakArray_Load(char* mqf_fpk); // long version 00557 00562 VariantArray /* K */ lfpk(char* name); // short version 00563 00564 00565 00573 double FPeakArray_Print(VariantArray array); 00574 00575 00576 00577 00590 VariantArray /* K */ FPeakArray_GetPeaksNotInPeakGroup(VariantArray pFPeaksAll, PeakGroup peakgroup); 00591 00592 00593 00603 VariantArray /* P */ FPeakArray_GetPeakArray(VariantArray array); 00604 00605 00614 Map2D FPeakArray_CreateMapFrom(VariantArray array, Map2D template_map); 00615 00616 00617 //double setfpeakfile(char* file 00618 00623 // ******************************************************* 00624 // ************** mqsriptfunc_segfpeak.c ***************** 00625 // ******************************************************* 00626 00664 Segment Segment_FindAndFitPeaks(Segment segment, Map2D map, char* structel, double abuthr, char* curve); 00665 00678 Map2D Segment_GetMap (Segment segment, Map2D source, Map2D mask); 00679 00688 double Segment_Save (Segment segment, char* mqf_fpk); 00689 00696 double Segment_Print (Segment segment); 00697 00704 VariantArray /* K */ Segment_GetFPeaks(Segment segment); 00705 00706 00715 VariantArray /* A */ SegmentArray_Load(char* mqf_fpk); 00716 00717 00729 double FPeakFile_WriteHeader(char* szFilename, Map2D source, char* curve, double nsegments); 00730 00731 00745 double FPeakFile_CalcStatAndSave(char* mqf_fpk); 00746 00750 // ******************************************************* 00751 // ************** mqsriptfunc_peakgroup.c **************** 00752 // ******************************************************* 00753 00769 VariantArray /* G */ PeakGroupArray_Load(char* mqf_pgr); // long 00770 00771 00772 00777 VariantArray /* G */ lpg(char* mqf_pgr); // short 00778 00779 00787 double PeakGroup_Print(PeakGroup peakgroup); 00788 00800 double PeakGroup_Save (PeakGroup peakgroup, char* filename, double type); 00801 00808 VariantArray /* K */ PeakGroup_GetFPeaks(PeakGroup peakgroup); // long 00809 00814 VariantArray /* K */ getfpk(PeakGroup peakgroup); // short 00815 00824 PeakGroup PeakGroup_Create(VariantArray array); // long 00825 00830 PeakGroup mkpg(VariantArray array); // short 00831 00838 VariantArray /* K */ PeakGroupArray_GetFPeaks(VariantArray pg_array); // long 00839 00840 00845 VariantArray /* K */ vgetfpk(VariantArray pg_array); // short 00846 00847 00862 Map2D getpgmap(PeakGroup peakgroup, Map2D source, Map2D stencil); // short 00863 00864 00880 VariantArray /* K */ getpgmappeaks(PeakGroup peakgroup, char* mqf_fpk); // short 00881 00882 00894 double PeakGroupFile_WriteHeader(char* mqf_fpk, char* type, char* curve, double npg, double npeaks); 00895 00896 00897 00898 //Map2D PeakGroup_CreateMapFrom(PeakGroup pg, Map2D map 00899 00903 // ******************************************************* 00904 // *************** mqsriptfunc_cluster.c ***************** 00905 // ******************************************************* 00906 00934 double FPeakFile_ClusterAndSave(char* mqf_fpk_in, char* mgf_pgr_out, double scan_thr, double mz_thr, double abund_thr, double nLinkageType); 00935 00936 00950 double PeakGroupFile_ClusterAndSave(char* mgf_pgr_in, char* mgf_pgr_out, double scan_thr, double mz_thr, double abund_thr, double nLinkageType); 00951 00952 00956 // ******************************************************* 00957 // *************** mqsriptfunc_seghand.c ***************** 00958 // ******************************************************* 00959 00976 SegmentHandler SegmentHandler_Init(char* peakgroupfilename); 00977 00986 SegmentHandler SegmentHandler_Set(SegmentHandler seghand, PeakGroup peakgroup); 00987 00996 Map2D SegmentHandler_GetMap(SegmentHandler seghand, PeakGroup peakgroup); 00997 01006 VariantArray /* K */ SegmentHandler_GetMapPeaks(SegmentHandler seghand, PeakGroup peakgroup); 01007 01011 // ******************************************************* 01012 // ************** mqsriptfunc_refdcv.c **************** 01013 // ******************************************************* 01014 01031 //PeakGroup PeakGroup_Refine (PeakGroup peakgroup, Map2D PGMap, VariantArray pPGMapFPeaks, char* struct_elem, double abu_thr, double noisefactor, double numberofsd, char* curve 01032 //PeakGroup PeakGroup_Refine5 (PeakGroup peakgroup, Map2D PGMap, VariantArray pPGMapFPeaks, char* struct_elem, double abu_thr, char* curve 01033 //PeakGroup PeakGroup_Refine6 (PeakGroup peakgroup, Map2D PGMap, VariantArray pPGMapFPeaks, char* struct_elem, double abu_thr, char* curve 01034 //PeakGroup PeakGroup_Refine6_1(PeakGroup peakgroup, Map2D PGMap, VariantArray pPGMapFPeaks, char* struct_elem, double abu_thr, char* curve 01035 //PeakGroup PeakGroup_Refine6_2(PeakGroup peakgroup, Map2D PGMap, VariantArray pPGMapFPeaks, char* struct_elem, double abu_thr, char* curve 01036 //PeakGroup PeakGroup_Refine6_3(PeakGroup peakgroup, Map2D PGMap, VariantArray pPGMapFPeaks, char* struct_elem, double abu_thr, char* curve 01037 //PeakGroup PeakGroup_Refine6_4(PeakGroup peakgroup, Map2D PGMap, VariantArray pPGMapFPeaks, char* struct_elem, double abu_thr, char* curve 01038 01052 PeakGroup PeakGroup_Refine7 (PeakGroup peakgroup, Map2D PGMap, VariantArray pPGOutFPeaks, char* struct_elem, double abu_thr, char* curve, double scan_window, double mz_overlap_thr); 01053 01058 PeakGroup refine7(PeakGroup peakgroup, Map2D PGMap, VariantArray pPGOutFPeaks, char* struct_elem, double abu_thr, char* curve, double scan_window, double mz_overlap_thr); 01059 01060 01070 PeakGroup PeakGroup_Deconv3 (PeakGroup peakgroup, Map2D PGMap, VariantArray pPGOutFPeaks, char* curve); 01071 01076 PeakGroup deconv3(PeakGroup peakgroup, Map2D PGMap, VariantArray pPGOutFPeaks, char* curve); 01077 01078 01079 01088 PeakGroup PeakGroup_Deconv4 (PeakGroup peakgroup); // without fitting 01089 01094 PeakGroup deconv4(PeakGroup peakgroup); 01095 01096 01097 01098 //PeakGroup PeakGroup_Deconv2 (PeakGroup peakgroup, Map2D PGMap, VariantArray pPGOutFPeaks, char* curve 01099 //PeakGroup PeakGroup_Deconv3_1(PeakGroup peakgroup, Map2D PGMap, VariantArray pPGOutFPeaks, char* curve 01100 //PeakGroup PeakGroup_Deconv5 (PeakGroup peakgroup, Map2D PGMap, VariantArray pPGOutFPeaks, char* curve 01101 01102 01103 01107 // ******************************************************* 01108 // ************** mqsriptfunc_fitter.c ******************* 01109 // ******************************************************* 01110 01127 double fixmz(void); 01128 01137 double fixz(void); 01138 01147 double fixc(void); 01148 01157 double fixsmz(void); 01158 01167 double setsmz(double index, double value); 01168 01177 double clrfitter(void); 01178 01187 double commonsmz(void); 01188 01197 VariantArray /* K */ fit(double init_sigma_rt, double init_sigma_mz); 01198 01207 VariantArray /* K */ fitsmz(double init_sigma_rt, double smz_begin, double smz_end, double delta_sigma_mz); 01208 01217 VariantArray /* K */ fitpep(double charge, double carbons); 01218 01227 double sfpk(VariantArray array, char* mqf); 01228 01229 //double fitMapShown(double scan, double bin, double charge 01230 //VariantArray /* K */ fitPeptidesInMapShown(char* sequence1, double scan1, double mz1, double smz1, double charge1, char* sequence2, double scan2, double mz2, double smz2, double charge2 01231 //VariantArray /* K */ auxFitPeptideInMapShown(char* sequence, double scan, double guess_mz, double charge, char* curve 01232 01236 // ******************************************************* 01237 // **************** mqsriptfunc_graph.c ****************** 01238 // ******************************************************* 01239 01240 // Plotting 01241 01260 double plotmap(Map2D map); 01261 01272 double overlaymap(Map2D map); 01273 01274 01284 double plotpk(VariantArray array); 01285 01286 01296 double plotpg(VariantArray array); 01297 01309 double plotseqsum(char* filename, char* which); 01310 01321 double movepk(double handle, double dx); 01322 01333 double plotmqsqmap(char* filename); 01334 01344 double plotms2(char* ms2_exp_name); 01345 01358 double coversegments(VariantArray peak_array, double mz_threshold, double scan_theshold); 01359 01367 double coversegmentsonedge(void); 01368 01369 01378 double showlabels(void); 01379 01388 double axes(void); 01389 01397 double grid(void); 01398 01412 double zoomin(double x1, double x2, double y1, double y2); 01413 01414 01415 01425 double setgraylevel(char* level); 01426 01427 01437 double goscan(double scan); 01438 01439 01447 double show(double handle, char* field); 01448 01449 01457 double hide(double handle); 01458 01465 double clear(double handle); 01466 01470 // ******************************************************* 01471 // ******************************************************* 01472 // ******************************************************* 01473 01474 // ******************************************************* 01475 // ***************** mqsriptfunc_aux.c ******************* 01476 // ******************************************************* 01477 01487 Map2D extractseam(Map2D smap1, Map2D smap2, Map2D lmap1, Map2D lmap2); 01488 double tilefpeakfile(char* mqf_fpk, char* mqf_pgf); 01489 char* print(char* string); 01490 char* int2str(double number, double width); 01491 double setfilter(char* filter); 01492 double createMS2table(char* expmntname); 01493 double printZoomBoundaries(void); 01494 01495 double auxExtractMapShown(char* filename); 01496 double auxExtractMap(Map2D map, double x1, double x2, double y1, double y2, char* filename); 01497 01498 double PrintFPeaksArrayInfo(VariantArray fpeaks, double parameter); 01499 01500 // ******************************************************* 01501 // ***************** mqsriptfunc_seq.c ******************* 01502 // ******************************************************* 01503 01504 // ******************************************************* 01505 // ***************** mqsriptfunc_quant.c ***************** 01506 // ******************************************************* 01507 01508 double PeakArray_SaveDTAPositionsWithSequence(char* szSequestSummaryName, char* szSExperimentName, char* szQExperimentName, char* szOutputfile); 01509 VariantArray /* K */ PeakArray_GetDTAPositions(char* szSequestSummaryName, char* szSExperimentName, char* szQExperimentName); 01510 double MS2GuidedQuantitation(Map2D map, double bin_width); 01511 01512 01513 //double createDTAFiles(Map2D map, double bin_width 01514 //double LinkFPeaksToSPeaks[VariantArray fpeaks, VariantArray speaks, char* szQExpmntName, double mz_half_window, double scan_half_window); 01515 01516 01517 //Segment Segment_RefinePeaks(Segment segment, Map2D sg_map, char* structel, double abuthr, char* curve 01518 01519 //Map2D GetAlignmentMap(char* expmntQ, char* expmntS 01520 01521 01522 //double plotPeptidesOnTIC(char* filename, double tichandle 01523 //double plotPeptides(char* filename 01524 //double plotMFRP(char* filename 01525 01526 //double plotRectsAroundPeaks(double handle, double half_width 01527 01531 #endif 01532 01533 01534 01535