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A7DA2006113FECD400BF472F /* bootstrap.h */, + A7DA2009113FECD400BF472F /* bstick.cpp */, + A7DA200A113FECD400BF472F /* bstick.h */, + A7DA200F113FECD400BF472F /* chao1.cpp */, + A7DA2010113FECD400BF472F /* chao1.h */, + A7DA2033113FECD400BF472F /* coverage.cpp */, + A7DA2034113FECD400BF472F /* coverage.h */, + A7DA203D113FECD400BF472F /* dist.h */, + A7DA2044113FECD400BF472F /* eachgapdist.h */, + A7DA2045113FECD400BF472F /* eachgapignore.h */, + A7DA2046113FECD400BF472F /* efron.cpp */, + A7DA2047113FECD400BF472F /* efron.h */, + A7DA204E113FECD400BF472F /* filters.h */, + A7DA2058113FECD400BF472F /* geom.cpp */, + A7DA2059113FECD400BF472F /* geom.h */, + A7DA206C113FECD400BF472F /* goodscoverage.cpp */, + A7DA206D113FECD400BF472F /* goodscoverage.h */, + A7DA2080113FECD400BF472F /* ignoregaps.h */, + A7DA2083113FECD400BF472F /* jackknife.cpp */, + A7DA2084113FECD400BF472F /* jackknife.h */, + A7DA2093113FECD400BF472F /* logsd.cpp */, + A7DA2094113FECD400BF472F /* logsd.h */, + A7DA20AE113FECD400BF472F /* npshannon.cpp */, + A7DA20AF113FECD400BF472F /* npshannon.h */, + A7DA20B0113FECD400BF472F /* nseqs.h */, + A7DA20B2113FECD400BF472F /* onegapdist.h */, + A7DA20B3113FECD400BF472F /* onegapignore.h */, + A7DA20BE113FECD400BF472F /* parsimony.cpp */, + A7DA20BF113FECD400BF472F /* parsimony.h */, + A7DA20CE113FECD400BF472F /* qstat.cpp */, + A7DA20CF113FECD400BF472F /* qstat.h */, + A7DA2104113FECD400BF472F /* shannon.cpp */, + A7DA2105113FECD400BF472F /* shannon.h */, + A7DA2106113FECD400BF472F /* sharedace.cpp */, + A7DA2107113FECD400BF472F /* sharedace.h */, + A7DA2108113FECD400BF472F /* sharedanderberg.h */, + A7DA2109113FECD400BF472F /* sharedanderbergs.cpp */, + A7DA210A113FECD400BF472F /* sharedanderbergs.h */, + A7DA210B113FECD400BF472F /* sharedbraycurtis.cpp */, + A7DA210C113FECD400BF472F /* sharedbraycurtis.h */, + A7DA210D113FECD400BF472F /* sharedchao1.cpp */, + A7DA210E113FECD400BF472F /* sharedchao1.h */, + A7DA2111113FECD400BF472F /* sharedjabund.cpp */, + A7DA2112113FECD400BF472F /* sharedjabund.h */, + A7DA2113113FECD400BF472F /* sharedjackknife.cpp */, + A7DA2114113FECD400BF472F /* sharedjackknife.h */, + A7DA2115113FECD400BF472F /* sharedjclass.cpp */, + A7DA2116113FECD400BF472F /* sharedjclass.h */, + A7DA2117113FECD400BF472F /* sharedjest.cpp */, + A7DA2118113FECD400BF472F /* sharedjest.h */, + A7DA2119113FECD400BF472F /* sharedkstest.cpp */, + A7DA211A113FECD400BF472F /* sharedkstest.h */, + A7DA211B113FECD400BF472F /* sharedkulczynski.cpp */, + A7DA211C113FECD400BF472F /* sharedkulczynski.h */, + A7DA211D113FECD400BF472F /* sharedkulczynskicody.cpp */, + A7DA211E113FECD400BF472F /* sharedkulczynskicody.h */, + A7DA211F113FECD400BF472F /* sharedlennon.cpp */, + A7DA2120113FECD400BF472F /* sharedlennon.h */, + A7DA2123113FECD400BF472F /* sharedmarczewski.cpp */, + A7DA2124113FECD400BF472F /* sharedmarczewski.h */, + A7DA2125113FECD400BF472F /* sharedmorisitahorn.cpp */, + A7DA2126113FECD400BF472F /* sharedmorisitahorn.h */, + A7DA2127113FECD400BF472F /* sharednseqs.h */, + A7DA2128113FECD400BF472F /* sharedochiai.cpp */, + A7DA2129113FECD400BF472F /* sharedochiai.h */, + A7DA2130113FECD400BF472F /* sharedsobs.cpp */, + A7DA2131113FECD400BF472F /* sharedsobs.h */, + A7DA2132113FECD400BF472F /* sharedsobscollectsummary.cpp */, + A7DA2133113FECD400BF472F /* sharedsobscollectsummary.h */, + A7DA2134113FECD400BF472F /* sharedsorabund.cpp */, + A7DA2135113FECD400BF472F /* sharedsorabund.h */, + A7DA2136113FECD400BF472F /* sharedsorclass.cpp */, + A7DA2137113FECD400BF472F /* sharedsorclass.h */, + A7DA2138113FECD400BF472F /* sharedsorest.cpp */, + A7DA2139113FECD400BF472F /* sharedsorest.h */, + A7DA213A113FECD400BF472F /* sharedthetan.cpp */, + A7DA213B113FECD400BF472F /* sharedthetan.h */, + A7DA213C113FECD400BF472F /* sharedthetayc.cpp */, + A7DA213D113FECD400BF472F /* sharedthetayc.h */, + A7DA2140113FECD400BF472F /* shen.cpp */, + A7DA2141113FECD400BF472F /* shen.h */, + A7DA2142113FECD400BF472F /* simpson.cpp */, + A7DA2143113FECD400BF472F /* simpson.h */, + A7DA2149113FECD400BF472F /* sobs.h */, + A7DA214A113FECD400BF472F /* solow.cpp */, + A7DA214B113FECD400BF472F /* solow.h */, + A7DA2160113FECD400BF472F /* treecalculator.h */, + A7DA216D113FECD400BF472F /* unweighted.cpp */, + A7DA216E113FECD400BF472F /* unweighted.h */, + A7DA216F113FECD400BF472F /* uvest.cpp */, + A7DA2170113FECD400BF472F /* uvest.h */, + A7DA2179113FECD400BF472F /* weighted.cpp */, + A7DA217A113FECD400BF472F /* weighted.h */, + A7DA217B113FECD400BF472F /* whittaker.cpp */, + A7DA217C113FECD400BF472F /* whittaker.h */, ); name = calculators; sourceTree = ""; }; - 37D928A90F2133E5001D4494 /* commands */ = { + A7CB593E11402F110010EB83 /* commands */ = { isa = PBXGroup; children = ( - 37D927CD0F21331F001D4494 /* command.hpp */, - 378DC5CD0FBDE1C8003B8607 /* aligncommand.h */, - 378DC5CE0FBDE1C8003B8607 /* aligncommand.cpp */, - 37C1D9710F86506E0059E3F0 /* binsequencecommand.h */, - 37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */, - 21DDC0190F97A8FE0060691C /* bootstrapsharedcommand.h */, - 21DDC01A0F97A8FE0060691C /* bootstrapsharedcommand.cpp */, - 37D927C40F21331F001D4494 /* clustercommand.h */, - 37D927C30F21331F001D4494 /* clustercommand.cpp */, - 37D927C80F21331F001D4494 /* collectcommand.h */, - 37D927C70F21331F001D4494 /* collectcommand.cpp */, - 37D927CC0F21331F001D4494 /* collectsharedcommand.h */, - 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */, - 377326640FAF16E0007ABB8B /* consensuscommand.h */, - 377326630FAF16E0007ABB8B /* consensuscommand.cpp */, - 379D3D4F0FF90E090068C1C0 /* chimeraseqscommand.h */, - 379D3D500FF90E090068C1C0 /* chimeraseqscommand.cpp */, - A7861476109F5FA00010AAAF /* classifyseqscommand.h */, - A7861477109F5FA00010AAAF /* classifyseqscommand.cpp */, - 37B28F660F27590100808A62 /* deconvolutecommand.h */, - 37B28F670F27590100808A62 /* deconvolutecommand.cpp */, - 37C753CC0FB3415200DBD02E /* distancecommand.h */, - 37C753CD0FB3415200DBD02E /* distancecommand.cpp */, - 378C1AEF0FB0644D004D63F5 /* filterseqscommand.h */, - 378C1AEE0FB0644D004D63F5 /* filterseqscommand.cpp */, - A70B53A50F4CD7AD0064797E /* getgroupcommand.h */, - A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */, - A70B53A70F4CD7AD0064797E /* getlabelcommand.h */, - A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */, - A73329CD1083B3B3003B10C5 /* getlistcountcommand.h */, - A73329CE1083B3B3003B10C5 /* getlistcountcommand.cpp */, - 370B88050F8A4EE4005AB382 /* getoturepcommand.h */, - 370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */, - 3749273D0FD5956B0031C06B /* getrabundcommand.h */, - 3749273E0FD5956B0031C06B /* getrabundcommand.cpp */, - 3749271B0FD58C840031C06B /* getsabundcommand.h */, - 3749271C0FD58C840031C06B /* getsabundcommand.cpp */, - 37B73CA41004D89A008C4B41 /* getseqscommand.h */, - 37B73CA51004D89A008C4B41 /* getseqscommand.cpp */, - A7E4A781106913F900688F62 /* getsharedotucommand.h */, - A7E4A782106913F900688F62 /* getsharedotucommand.cpp */, - A729ACCE10848E6100139801 /* hclustercommand.h */, - A729ACCF10848E6100139801 /* hclustercommand.cpp */, - 375873F10F7D64800040F377 /* heatmapcommand.h */, - 375873F00F7D64800040F377 /* heatmapcommand.cpp */, - 378598640FDD497000EF9D03 /* heatmapsimcommand.h */, - 378598650FDD497000EF9D03 /* heatmapsimcommand.cpp */, - 37D927E40F21331F001D4494 /* helpcommand.h */, - 37D927E30F21331F001D4494 /* helpcommand.cpp */, - 375873F40F7D648F0040F377 /* libshuffcommand.h */, - 375873F30F7D648F0040F377 /* libshuffcommand.cpp */, - 37B73C741004BEFD008C4B41 /* listseqscommand.h */, - 37B73C751004BEFD008C4B41 /* listseqscommand.cpp */, - 21E859D60FC4632E005E1A48 /* matrixoutputcommand.h */, - 21E859D70FC4632E005E1A48 /* matrixoutputcommand.cpp */, - 7E5A17AD0FE57292003C6A03 /* mergefilecommand.h */, - 7E5A17AE0FE57292003C6A03 /* mergefilecommand.cpp */, - A7E0AAB410D2886D00CF407B /* mgclustercommand.h */, - A7E0AAB510D2886D00CF407B /* mgclustercommand.cpp */, - 375873F70F7D649C0040F377 /* nocommands.h */, - 375873F60F7D649C0040F377 /* nocommands.cpp */, - A704E8A11106045D00870157 /* otuhierarchycommand.h */, - A704E8A21106045D00870157 /* otuhierarchycommand.cpp */, - A71CB8A111354B9F00848EF7 /* parselistscommand.h */, - A71CB8A211354B9F00848EF7 /* parselistscommand.cpp */, - 3792946E0F2E191800B9034A /* parsimonycommand.h */, - 3792946F0F2E191800B9034A /* parsimonycommand.cpp */, - A7D176CD10F2558500159497 /* pcacommand.h */, - A7D176CE10F2558500159497 /* pcacommand.cpp */, - A773808E10B6EFD1002A6A61 /* phylotypecommand.h */, - A773808F10B6EFD1002A6A61 /* phylotypecommand.cpp */, - A7027F2610DFF86D00BF45FE /* preclustercommand.h */, - A7027F2710DFF86D00BF45FE /* preclustercommand.cpp */, - 37D927FE0F21331F001D4494 /* quitcommand.h */, - 37D927FD0F21331F001D4494 /* quitcommand.cpp */, - 37D928080F21331F001D4494 /* rarefactcommand.h */, - 37D928070F21331F001D4494 /* rarefactcommand.cpp */, - 37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */, - 37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */, - 372E12940F263D5A0095CF7E /* readdistcommand.h */, - 372E12950F263D5A0095CF7E /* readdistcommand.cpp */, - 372E126E0F26365B0095CF7E /* readotucommand.h */, - 372E126F0F26365B0095CF7E /* readotucommand.cpp */, - 37E5F4900F2A3DA800F8D827 /* readtreecommand.h */, - 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */, - 37B73CBE1004EB38008C4B41 /* removeseqscommand.h */, - 37B73CBF1004EB38008C4B41 /* removeseqscommand.cpp */, - 7E09C5120FDA79C5002ECAE5 /* reversecommand.h */, - 7E09C5130FDA79C5002ECAE5 /* reversecommand.cpp */, - A70DECD71063D8B40057C03C /* secondarystructurecommand.h */, - A70DECD81063D8B40057C03C /* secondarystructurecommand.cpp */, - 371B30B30FD7EE67000414CA /* screenseqscommand.h */, - 371B30B20FD7EE67000414CA /* screenseqscommand.cpp */, - 3799A94F0FD6A58C00E33EDE /* seqsummarycommand.h */, - 3799A94E0FD6A58C00E33EDE /* seqsummarycommand.cpp */, - A70B00C6110885EB002F453A /* setdircommand.h */, - A70B00C7110885EB002F453A /* setdircommand.cpp */, - 37D928270F21331F001D4494 /* sharedcommand.h */, - 37D928260F21331F001D4494 /* sharedcommand.cpp */, - 37D928470F21331F001D4494 /* summarycommand.h */, - 37D928460F21331F001D4494 /* summarycommand.cpp */, - 37D9284B0F21331F001D4494 /* summarysharedcommand.h */, - 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */, - 37B73CCD1004F5E0008C4B41 /* systemcommand.h */, - 37B73CCE1004F5E0008C4B41 /* systemcommand.cpp */, - 211C38370F961E1F00FEE541 /* treegroupscommand.h */, - 211C38360F961E1F00FEE541 /* treegroupscommand.cpp */, - 7E09C5340FDA7F65002ECAE5 /* trimseqscommand.h */, - 7E09C5350FDA7F65002ECAE5 /* trimseqscommand.cpp */, - 3746109B0F40657600460C57 /* unifracunweightedcommand.h */, - 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */, - 374610760F40645300460C57 /* unifracweightedcommand.h */, - 374610770F40645300460C57 /* unifracweightedcommand.cpp */, - 37519A9F0F810D0200FED5E8 /* venncommand.h */, - 37519AA00F810D0200FED5E8 /* venncommand.cpp */, + A7DA202B113FECD400BF472F /* command.hpp */, + A7DA1FEF113FECD400BF472F /* aligncommand.h */, + A7DA1FEE113FECD400BF472F /* aligncommand.cpp */, + A7DA1FFD113FECD400BF472F /* binsequencecommand.cpp */, + A7DA1FFE113FECD400BF472F /* binsequencecommand.h */, + A7DA2007113FECD400BF472F /* bootstrapsharedcommand.cpp */, + A7DA2008113FECD400BF472F /* bootstrapsharedcommand.h */, + A7DA2017113FECD400BF472F /* chimeraseqscommand.cpp */, + A7DA2018113FECD400BF472F /* chimeraseqscommand.h */, + A7DA201D113FECD400BF472F /* classifyseqscommand.cpp */, + A7DA201E113FECD400BF472F /* classifyseqscommand.h */, + A7DA2021113FECD400BF472F /* clustercommand.cpp */, + A7DA2022113FECD400BF472F /* clustercommand.h */, + A7DA2025113FECD400BF472F /* collectcommand.cpp */, + A7DA2026113FECD400BF472F /* collectcommand.h */, + A7DA2029113FECD400BF472F /* collectsharedcommand.cpp */, + A7DA202A113FECD400BF472F /* collectsharedcommand.h */, + A7DA2031113FECD400BF472F /* consensuscommand.cpp */, + A7DA2032113FECD400BF472F /* consensuscommand.h */, + A7DA203A113FECD400BF472F /* deconvolutecommand.cpp */, + A7DA203B113FECD400BF472F /* deconvolutecommand.h */, + A7DA203E113FECD400BF472F /* distancecommand.cpp */, + A7DA203F113FECD400BF472F /* distancecommand.h */, + A7DA204F113FECD400BF472F /* filterseqscommand.cpp */, + A7DA2050113FECD400BF472F /* filterseqscommand.h */, + A7DA205A113FECD400BF472F /* getgroupcommand.cpp */, + A7DA205B113FECD400BF472F /* getgroupcommand.h */, + A7DA205C113FECD400BF472F /* getlabelcommand.cpp */, + A7DA205D113FECD400BF472F /* getlabelcommand.h */, + A7DA205E113FECD400BF472F /* getlistcountcommand.cpp */, + A7DA205F113FECD400BF472F /* getlistcountcommand.h */, + A7DA2060113FECD400BF472F /* getoturepcommand.cpp */, + A7DA2061113FECD400BF472F /* getoturepcommand.h */, + A7DA2062113FECD400BF472F /* getrabundcommand.cpp */, + A7DA2063113FECD400BF472F /* getrabundcommand.h */, + A7DA2064113FECD400BF472F /* getsabundcommand.cpp */, + A7DA2065113FECD400BF472F /* getsabundcommand.h */, + A7DA2066113FECD400BF472F /* getseqscommand.cpp */, + A7DA2067113FECD400BF472F /* getseqscommand.h */, + A7DA2068113FECD400BF472F /* getsharedotucommand.cpp */, + A7DA2069113FECD400BF472F /* getsharedotucommand.h */, + A7DA2074113FECD400BF472F /* hclustercommand.cpp */, + A7DA2075113FECD400BF472F /* hclustercommand.h */, + A7DA2078113FECD400BF472F /* heatmapcommand.cpp */, + A7DA2079113FECD400BF472F /* heatmapcommand.h */, + A7DA207C113FECD400BF472F /* heatmapsimcommand.cpp */, + A7DA207D113FECD400BF472F /* heatmapsimcommand.h */, + A7DA207E113FECD400BF472F /* helpcommand.cpp */, + A7DA207F113FECD400BF472F /* helpcommand.h */, + A7DA208D113FECD400BF472F /* libshuffcommand.cpp */, + A7DA208E113FECD400BF472F /* libshuffcommand.h */, + A7DA208F113FECD400BF472F /* listseqscommand.cpp */, + A7DA2090113FECD400BF472F /* listseqscommand.h */, + A7DA2098113FECD400BF472F /* matrixoutputcommand.cpp */, + A7DA2099113FECD400BF472F /* matrixoutputcommand.h */, + A7DA209A113FECD400BF472F /* mergefilecommand.cpp */, + A7DA209B113FECD400BF472F /* mergefilecommand.h */, + A7DA209C113FECD400BF472F /* mgclustercommand.cpp */, + A7DA209D113FECD400BF472F /* mgclustercommand.h */, + A7DA20AC113FECD400BF472F /* nocommands.cpp */, + A7DA20AD113FECD400BF472F /* nocommands.h */, + A7DA20B8113FECD400BF472F /* otuhierarchycommand.cpp */, + A7DA20B9113FECD400BF472F /* otuhierarchycommand.h */, + A7DA20BC113FECD400BF472F /* parselistscommand.cpp */, + A7DA20BD113FECD400BF472F /* parselistscommand.h */, + A7DA20C0113FECD400BF472F /* parsimonycommand.cpp */, + A7DA20C1113FECD400BF472F /* parsimonycommand.h */, + A7DA20C2113FECD400BF472F /* pcacommand.cpp */, + A7DA20C3113FECD400BF472F /* pcacommand.h */, + A7DA20C6113FECD400BF472F /* phylotypecommand.cpp */, + A7DA20C7113FECD400BF472F /* phylotypecommand.h */, + A7DA20CA113FECD400BF472F /* preclustercommand.cpp */, + A7DA20CB113FECD400BF472F /* preclustercommand.h */, + A7DA20D0113FECD400BF472F /* quitcommand.cpp */, + A7DA20D1113FECD400BF472F /* quitcommand.h */, + A7DA20DA113FECD400BF472F /* rarefactcommand.cpp */, + A7DA20DB113FECD400BF472F /* rarefactcommand.h */, + A7DA20DD113FECD400BF472F /* rarefactsharedcommand.cpp */, + A7DA20DE113FECD400BF472F /* rarefactsharedcommand.h */, + A7DA20E5113FECD400BF472F /* readdistcommand.cpp */, + A7DA20E6113FECD400BF472F /* readdistcommand.h */, + A7DA20EA113FECD400BF472F /* readotucommand.cpp */, + A7DA20EB113FECD400BF472F /* readotucommand.h */, + A7DA20F0113FECD400BF472F /* readtreecommand.cpp */, + A7DA20F1113FECD400BF472F /* readtreecommand.h */, + A7DA20F2113FECD400BF472F /* removeseqscommand.cpp */, + A7DA20F3113FECD400BF472F /* removeseqscommand.h */, + A7DA20F4113FECD400BF472F /* reversecommand.cpp */, + A7DA20F5113FECD400BF472F /* reversecommand.h */, + A7DA20F8113FECD400BF472F /* screenseqscommand.cpp */, + A7DA20F9113FECD400BF472F /* screenseqscommand.h */, + A7DA20FA113FECD400BF472F /* secondarystructurecommand.cpp */, + A7DA20FB113FECD400BF472F /* secondarystructurecommand.h */, + A7DA20FC113FECD400BF472F /* seqsummarycommand.cpp */, + A7DA20FD113FECD400BF472F /* seqsummarycommand.h */, + A7DA2102113FECD400BF472F /* setdircommand.cpp */, + A7DA2103113FECD400BF472F /* setdircommand.h */, + A7DA210F113FECD400BF472F /* sharedcommand.cpp */, + A7DA2110113FECD400BF472F /* sharedcommand.h */, + A7DA2154113FECD400BF472F /* summarycommand.cpp */, + A7DA2155113FECD400BF472F /* summarycommand.h */, + A7DA2158113FECD400BF472F /* summarysharedcommand.cpp */, + A7DA2159113FECD400BF472F /* summarysharedcommand.h */, + A7DA215A113FECD400BF472F /* systemcommand.cpp */, + A7DA215B113FECD400BF472F /* systemcommand.h */, + A7DA2161113FECD400BF472F /* treegroupscommand.cpp */, + A7DA2162113FECD400BF472F /* treegroupscommand.h */, + A7DA2167113FECD400BF472F /* trimseqscommand.cpp */, + A7DA2168113FECD400BF472F /* trimseqscommand.h */, + A7DA2169113FECD400BF472F /* unifracunweightedcommand.cpp */, + A7DA216A113FECD400BF472F /* unifracunweightedcommand.h */, + A7DA216B113FECD400BF472F /* unifracweightedcommand.cpp */, + A7DA216C113FECD400BF472F /* unifracweightedcommand.h */, + A7DA2177113FECD400BF472F /* venncommand.cpp */, + A7DA2178113FECD400BF472F /* venncommand.h */, ); name = commands; sourceTree = ""; }; - 37D928AC0F213420001D4494 /* containers */ = { + A7CB594211402F430010EB83 /* containers */ = { isa = PBXGroup; children = ( - 373C68A10FC1C07D00137ACD /* alignment.hpp */, - 373C68A00FC1C07D00137ACD /* alignment.cpp */, - 373C68A30FC1C07D00137ACD /* alignmentcell.hpp */, - 373C68A20FC1C07D00137ACD /* alignmentcell.cpp */, - A78782A910A1B1CB0086103D /* alignmentdb.h */, - A78782AA10A1B1CB0086103D /* alignmentdb.cpp */, - 373C69170FC1C8AF00137ACD /* blastdb.hpp */, - 373C69160FC1C8AF00137ACD /* blastdb.cpp */, - 37D927D40F21331F001D4494 /* database.hpp */, - 37D927D30F21331F001D4494 /* database.cpp */, - 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All rights reserved. - * - */ - - -#include "chimera.h" -#include "decalc.h" - -//This class was created using the algorythms described in the -// "New Screening Software Shows that Most Recent Large 16SrRNA Gene Clone Libraries Contain Chimeras" paper -//by Kevin E. Ashelford 1, Nadia A. Chuzhanova 2, John C. Fry 1, Antonia J. Jones 3 and Andrew J. Weightman 1. - -/***********************************************************/ - -class Mallard : public Chimera { - - public: - Mallard(string); - ~Mallard(); - - void getChimeras(); - void print(ostream&); - - void setCons(string c) {}; - void setQuantiles(string q) {}; - - private: - - struct linePair { - int start; - int end; - linePair(int i, int j) : start(i), end(j) {} - linePair(){} - }; - - DeCalculator* decalc; - int iters; - string fastafile; - - vector lines; - vector querySeqs; - vector windowSizes; //windowSizes[0] = window size of querySeqs[0] - vector marked; - vector highestDE; - - vector probabilityProfile; - vector< vector > quantilesMembers; //quantiles[0] is the vector of deviations with ceiling score of 1, quantiles[1] is the vector of deviations with ceiling score of 2... - - void createProcessesQuan(); - -}; - -/***********************************************************/ - -#endif - diff --git a/summarydata.h b/summarydata.h deleted file mode 100644 index 4620337..0000000 --- a/summarydata.h +++ /dev/null @@ -1,36 +0,0 @@ -#ifndef SUMMARYDATA_H -#define SUMMARYDATA_H - -#include "mothur.h" -#include "sabundvector.hpp" -#include "display.h" -#include "observable.h" - -/***********************************************************************/ - -class SummaryData : public Observable { - -public: - SummaryData() : sabund(0) {}; - - void registerDisplay(Display* o) { displays.insert(o); }; - void removeDisplay(Display* o) { displays.erase(o); delete o; }; - SAbundVector* getSabundData() { return sabund; }; - void sabundDataChanged() { notifyDisplays(); }; - void updatesabundData(SAbundVector* rv) { sabund = rv; sabundDataChanged(); }; - - void notifyDisplays(){ - for(set::iterator pos=displays.begin();pos!=displays.end();pos++){ - (*pos)->update(sabund); - } - }; - -private: - set displays; - SAbundVector* sabund; - -}; - -/***********************************************************************/ - -#endif diff --git a/summarydisplay.h b/summarydisplay.h deleted file mode 100644 index 90d8960..0000000 --- a/summarydisplay.h +++ /dev/null @@ -1,32 +0,0 @@ -#ifndef SUMMARY_H -#define SUMMARY_H - -#include "mothur.h" -#include "display.h" - - - -class SummaryDisplay : public Display { - -public: - SummaryDisplay(Calculator* calc, FileOutput* file) : estimate(calc), output(file){ }; - - void update(SAbundVector* sabund) { output->output(sabund->getLabel(), estimate->getValues(rank)); }; - void init(string s) { output->initFile(s); }; - void reset() { output->resetFile(); }; - void close(){}; - string getLabel(){ return estimate->getName(); } - -private: - Calculator* estimate; - FileOutput* output; - - int nIters; - string tempInName, tempOutName; - ifstream tempInFile; - ofstream tempOutFile; -}; - -/***********************************************************************/ - -#endif -- 2.39.2