mothur with external build

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 89ddb28bfee495e7145be65740f860460bae44d6..e30c0d4acd457fb66f0a21b289853eb7578b310a 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -6,1465 +6,965 @@
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+                               A7DA208B113FECD400BF472F /* libshuff.cpp */,
+                               A7DA208C113FECD400BF472F /* libshuff.h */,
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+                               A7DA20A0113FECD400BF472F /* mothurout.cpp */,
+                               A7DA20A1113FECD400BF472F /* mothurout.h */,
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+                               A7DA20A8113FECD400BF472F /* needlemanoverlap.cpp */,
+                               A7DA20A9113FECD400BF472F /* needlemanoverlap.hpp */,
+                               A7DA20AA113FECD400BF472F /* noalign.cpp */,
+                               A7DA20AB113FECD400BF472F /* noalign.hpp */,
+                               A7DA20B1113FECD400BF472F /* observable.h */,
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+                               A7DA20B5113FECD400BF472F /* optionparser.h */,
+                               A7DA20BA113FECD400BF472F /* overlap.cpp */,
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+                               A7DA20CC113FECD400BF472F /* progress.cpp */,
+                               A7DA20CD113FECD400BF472F /* progress.hpp */,
+                               A7DA20D4113FECD400BF472F /* rarecalc.cpp */,
+                               A7DA20D5113FECD400BF472F /* rarecalc.h */,
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+                               A7DA20D9113FECD400BF472F /* rarefact.h */,
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+                               A7CB5953114033220010EB83 /* read */,
+                               A7DA213E113FECD400BF472F /* sharedutilities.cpp */,
+                               A7DA213F113FECD400BF472F /* sharedutilities.h */,
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+                               A7DA2171113FECD400BF472F /* validcalculator.cpp */,
+                               A7DA2172113FECD400BF472F /* validcalculator.h */,
+                               A7DA2173113FECD400BF472F /* validparameter.cpp */,
+                               A7DA2174113FECD400BF472F /* validparameter.h */,
+                               A7DA2175113FECD400BF472F /* venn.cpp */,
+                               A7DA2176113FECD400BF472F /* venn.h */,
                        );
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-                               7EC3D4530FA0FFF900338DA5 /* whittaker.cpp */,
+                               A7DA200B113FECD400BF472F /* calculator.cpp */,
+                               A7DA200C113FECD400BF472F /* calculator.h */,
+                               A7DA1FED113FECD400BF472F /* ace.h */,
+                               A7DA1FEC113FECD400BF472F /* ace.cpp */,
+                               A7DA1FFB113FECD400BF472F /* bergerparker.cpp */,
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+                               A7DA2004113FECD400BF472F /* boneh.h */,
+                               A7DA2005113FECD400BF472F /* bootstrap.cpp */,
+                               A7DA2006113FECD400BF472F /* bootstrap.h */,
+                               A7DA2009113FECD400BF472F /* bstick.cpp */,
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+                               A7DA2094113FECD400BF472F /* logsd.h */,
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+                               A7DA20AF113FECD400BF472F /* npshannon.h */,
+                               A7DA20B0113FECD400BF472F /* nseqs.h */,
+                               A7DA20B2113FECD400BF472F /* onegapdist.h */,
+                               A7DA20B3113FECD400BF472F /* onegapignore.h */,
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+                               A7DA20BF113FECD400BF472F /* parsimony.h */,
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+                               A7DA20CF113FECD400BF472F /* qstat.h */,
+                               A7DA2104113FECD400BF472F /* shannon.cpp */,
+                               A7DA2105113FECD400BF472F /* shannon.h */,
+                               A7DA2106113FECD400BF472F /* sharedace.cpp */,
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+                               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 = "<group>";
                };
-               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 = "<group>";
                };
-               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 */,
-                               37D927D50F21331F001D4494 /* datavector.hpp */,
-                               A794201011107897003AECCD /* distancedb.hpp */,
-                               A794200F11107897003AECCD /* distancedb.cpp */,
-                               37D927DC0F21331F001D4494 /* fastamap.h */,
-                               37D927DB0F21331F001D4494 /* fastamap.cpp */,
-                               375873EA0F7D64520040F377 /* fullmatrix.h */,
-                               375873EB0F7D64520040F377 /* fullmatrix.cpp */,
-                               37D927E20F21331F001D4494 /* groupmap.h */,
-                               37D927E10F21331F001D4494 /* groupmap.cpp */,
-                               37D927EA0F21331F001D4494 /* kmer.hpp */,
-                               37D927E90F21331F001D4494 /* kmer.cpp */,
-                               37D927EC0F21331F001D4494 /* kmerdb.hpp */,
-                               37D927EB0F21331F001D4494 /* kmerdb.cpp */,
-                               37D927EE0F21331F001D4494 /* listvector.hpp */,
-                               37D927ED0F21331F001D4494 /* listvector.cpp */,
-                               37D927F10F21331F001D4494 /* nameassignment.hpp */,
-                               37D927F00F21331F001D4494 /* nameassignment.cpp */,
-                               37D927F80F21331F001D4494 /* ordervector.hpp */,
-                               37D927F70F21331F001D4494 /* ordervector.cpp */,
-                               37D928000F21331F001D4494 /* rabundvector.hpp */,
-                               37D927FF0F21331F001D4494 /* rabundvector.cpp */,
-                               37D9281B0F21331F001D4494 /* sabundvector.hpp */,
-                               37D9281A0F21331F001D4494 /* sabundvector.cpp */,
-                               37D9281D0F21331F001D4494 /* sequence.hpp */,
-                               37D9281C0F21331F001D4494 /* sequence.cpp */,
-                               378C1AFE0FB0644D004D63F5 /* sequencedb.h */,
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diff --git a/mallard.h b/mallard.h
deleted file mode 100644 (file)
index d356f17..0000000
--- a/mallard.h
+++ /dev/null
@@ -1,64 +0,0 @@
-#ifndef MALLARD_H
-#define MALLARD_H
-
-/*
- *  mallard.h
- *  Mothur
- *
- *  Created by Sarah Westcott on 8/11/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. 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<linePair*> lines;
-               vector<Sequence*> querySeqs;
-               vector<int> windowSizes;                        //windowSizes[0] = window size of querySeqs[0]
-               vector<int> marked;
-               vector<float> highestDE;
-       
-               vector<float> probabilityProfile;
-               vector< vector<quanMember> > 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 (file)
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<Display*>::iterator pos=displays.begin();pos!=displays.end();pos++){
-                       (*pos)->update(sabund);
-               }       
-       };
-       
-private:
-       set<Display*> displays;
-       SAbundVector* sabund;
-       
-};
-
-/***********************************************************************/
-
-#endif

diff --git a/summarydisplay.h b/summarydisplay.h
deleted file mode 100644 (file)
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