From: westcott Date: Tue, 4 Jan 2011 18:35:45 +0000 (+0000) Subject: Changed back to xcode build. X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=73fb1fe84d565ea9a0ff793de990546b177310c8 Changed back to xcode build. --- diff --git a/Mothur.1 b/Mothur.1 index 42e748c..e8070f8 100644 --- a/Mothur.1 +++ b/Mothur.1 @@ -1,79 +1,79 @@ -.\"Modified from man(1) of FreeBSD, the NetBSD mdoc.template, and mdoc.samples. -.\"See Also: -.\"man mdoc.samples for a complete listing of options -.\"man mdoc for the short list of editing options -.\"/usr/share/misc/mdoc.template -.Dd 1/16/09 \" DATE -.Dt Mothur 1 \" Program name and manual section number -.Os Darwin -.Sh NAME \" Section Header - required - don't modify -.Nm Mothur, -.\" The following lines are read in generating the apropos(man -k) database. Use only key -.\" words here as the database is built based on the words here and in the .ND line. -.Nm Other_name_for_same_program(), -.Nm Yet another name for the same program. -.\" Use .Nm macro to designate other names for the documented program. -.Nd This line parsed for whatis database. -.Sh SYNOPSIS \" Section Header - required - don't modify -.Nm -.Op Fl abcd \" [-abcd] -.Op Fl a Ar path \" [-a path] -.Op Ar file \" [file] -.Op Ar \" [file ...] -.Ar arg0 \" Underlined argument - use .Ar anywhere to underline -arg2 ... \" Arguments -.Sh DESCRIPTION \" Section Header - required - don't modify -Use the .Nm macro to refer to your program throughout the man page like such: -.Nm -Underlining is accomplished with the .Ar macro like this: -.Ar underlined text . -.Pp \" Inserts a space -A list of items with descriptions: -.Bl -tag -width -indent \" Begins a tagged list -.It item a \" Each item preceded by .It macro -Description of item a -.It item b -Description of item b -.El \" Ends the list -.Pp -A list of flags and their descriptions: -.Bl -tag -width -indent \" Differs from above in tag removed -.It Fl a \"-a flag as a list item -Description of -a flag -.It Fl b -Description of -b flag -.El \" Ends the list -.Pp -.\" .Sh ENVIRONMENT \" May not be needed -.\" .Bl -tag -width "ENV_VAR_1" -indent \" ENV_VAR_1 is width of the string ENV_VAR_1 -.\" .It Ev ENV_VAR_1 -.\" Description of ENV_VAR_1 -.\" .It Ev ENV_VAR_2 -.\" Description of ENV_VAR_2 -.\" .El -.Sh FILES \" File used or created by the topic of the man page -.Bl -tag -width "/Users/joeuser/Library/really_long_file_name" -compact -.It Pa /usr/share/file_name -FILE_1 description -.It Pa /Users/joeuser/Library/really_long_file_name -FILE_2 description -.El \" Ends the list -.\" .Sh DIAGNOSTICS \" May not be needed -.\" .Bl -diag -.\" .It Diagnostic Tag -.\" Diagnostic informtion here. -.\" .It Diagnostic Tag -.\" Diagnostic informtion here. -.\" .El -.Sh SEE ALSO -.\" List links in ascending order by section, alphabetically within a section. -.\" Please do not reference files that do not exist without filing a bug report -.Xr a 1 , -.Xr b 1 , -.Xr c 1 , -.Xr a 2 , -.Xr b 2 , -.Xr a 3 , -.Xr b 3 -.\" .Sh BUGS \" Document known, unremedied bugs -.\" .Sh HISTORY \" Document history if command behaves in a unique manner \ No newline at end of file +.\"Modified from man(1) of FreeBSD, the NetBSD mdoc.template, and mdoc.samples. +.\"See Also: +.\"man mdoc.samples for a complete listing of options +.\"man mdoc for the short list of editing options +.\"/usr/share/misc/mdoc.template +.Dd 1/4/11 \" DATE +.Dt mothur 1 \" Program name and manual section number +.Os Darwin +.Sh NAME \" Section Header - required - don't modify +.Nm mothur, +.\" The following lines are read in generating the apropos(man -k) database. Use only key +.\" words here as the database is built based on the words here and in the .ND line. +.Nm Other_name_for_same_program(), +.Nm Yet another name for the same program. +.\" Use .Nm macro to designate other names for the documented program. +.Nd This line parsed for whatis database. +.Sh SYNOPSIS \" Section Header - required - don't modify +.Nm +.Op Fl abcd \" [-abcd] +.Op Fl a Ar path \" [-a path] +.Op Ar file \" [file] +.Op Ar \" [file ...] +.Ar arg0 \" Underlined argument - use .Ar anywhere to underline +arg2 ... \" Arguments +.Sh DESCRIPTION \" Section Header - required - don't modify +Use the .Nm macro to refer to your program throughout the man page like such: +.Nm +Underlining is accomplished with the .Ar macro like this: +.Ar underlined text . +.Pp \" Inserts a space +A list of items with descriptions: +.Bl -tag -width -indent \" Begins a tagged list +.It item a \" Each item preceded by .It macro +Description of item a +.It item b +Description of item b +.El \" Ends the list +.Pp +A list of flags and their descriptions: +.Bl -tag -width -indent \" Differs from above in tag removed +.It Fl a \"-a flag as a list item +Description of -a flag +.It Fl b +Description of -b flag +.El \" Ends the list +.Pp +.\" .Sh ENVIRONMENT \" May not be needed +.\" .Bl -tag -width "ENV_VAR_1" -indent \" ENV_VAR_1 is width of the string ENV_VAR_1 +.\" .It Ev ENV_VAR_1 +.\" Description of ENV_VAR_1 +.\" .It Ev ENV_VAR_2 +.\" Description of ENV_VAR_2 +.\" .El +.Sh FILES \" File used or created by the topic of the man page +.Bl -tag -width "/Users/joeuser/Library/really_long_file_name" -compact +.It Pa /usr/share/file_name +FILE_1 description +.It Pa /Users/joeuser/Library/really_long_file_name +FILE_2 description +.El \" Ends the list +.\" .Sh DIAGNOSTICS \" May not be needed +.\" .Bl -diag +.\" .It Diagnostic Tag +.\" Diagnostic informtion here. +.\" .It Diagnostic Tag +.\" Diagnostic informtion here. +.\" .El +.Sh SEE ALSO +.\" List links in ascending order by section, alphabetically within a section. +.\" Please do not reference files that do not exist without filing a bug report +.Xr a 1 , +.Xr b 1 , +.Xr c 1 , +.Xr a 2 , +.Xr b 2 , +.Xr a 3 , +.Xr b 3 +.\" .Sh BUGS \" Document known, unremedied bugs +.\" .Sh HISTORY \" Document history if command behaves in a unique manner \ No newline at end of file diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index edb26d3..34bc7d9 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -3,1239 +3,1562 @@ archiveVersion = 1; classes = { }; - objectVersion = 44; + objectVersion = 45; objects = { +/* Begin PBXBuildFile section */ + 8DD76FB00486AB0100D96B5E /* mothur.1 in CopyFiles */ = {isa = PBXBuildFile; fileRef = C6A0FF2C0290799A04C91782 /* mothur.1 */; }; + A7E9B88112D37EC400DA6239 /* ace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B64F12D37EC300DA6239 /* ace.cpp */; }; + A7E9B88212D37EC400DA6239 /* aligncommand.cpp in Sources */ = 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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 */, - 7E4EBD43122018FB00D85E7B /* simpsoneven.h */, - 7E4EBD44122018FB00D85E7B /* simpsoneven.cpp */, - 7E5B294A121FFADC0005339C /* smithwilson.h */, - 7E5B294B121FFADC0005339C /* smithwilson.cpp */, - A7DA2143113FECD400BF472F /* simpson.h */, - A7DA2142113FECD400BF472F /* simpson.cpp */, - A7DA2149113FECD400BF472F /* sobs.h */, - A7460ADB12B914B700866BB6 /* soergel.h */, - A7460ADC12B914B700866BB6 /* soergel.cpp */, - A7DA214A113FECD400BF472F /* solow.cpp */, - A7DA214B113FECD400BF472F /* solow.h */, - A7460B5912B93F1F00866BB6 /* speciesprofile.h */, - A7460B5A12B93F1F00866BB6 /* speciesprofile.cpp */, - A7460AF712B9218400866BB6 /* spearman.h */, - A7460AF812B9218400866BB6 /* spearman.cpp */, - A7BB555212BB87F30041F26F /* structchi2.h */, - A7BB555312BB87F30041F26F /* structchi2.cpp */, - A7460A3F12B8EF1C00866BB6 /* structchord.h */, - A7460A4012B8EF1C00866BB6 /* structchord.cpp */, - A7F0C10112B80EEC0048BC64 /* structeuclidean.h */, - A7F0C10212B80EEC0048BC64 /* structeuclidean.cpp */, - A7460B3612B9377400866BB6 /* structkulczynski.h */, - A7460B3712B9377400866BB6 /* structkulczynski.cpp */, - A7460AC912B90C5600866BB6 /* structpearson.h */, - A7460ACA12B90C5600866BB6 /* structpearson.cpp */, - A7DA2160113FECD400BF472F /* treecalculator.h */, - A7DA216D113FECD400BF472F /* unweighted.cpp */, - A7DA216E113FECD400BF472F /* unweighted.h */, - A7DA216F113FECD400BF472F /* uvest.cpp */, - A7DA2170113FECD400BF472F /* uvest.h */, - A7DA2179113FECD400BF472F /* weighted.cpp */, - A7DA217A113FECD400BF472F /* weighted.h */, - 7EC61A0911BEA6AF00F668D9 /* weightedlinkage.cpp */, - A7DA217B113FECD400BF472F /* whittaker.cpp */, - A7DA217C113FECD400BF472F /* whittaker.h */, + A7E9B65912D37EC300DA6239 /* averagelinkage.cpp */, + A7E9BA4F12D398D700DA6239 /* clearcut */, + A7E9B69812D37EC400DA6239 /* cluster.cpp */, + A7E9B69912D37EC400DA6239 /* cluster.hpp */, + A7E9B69A12D37EC400DA6239 /* clusterclassic.cpp */, + A7E9B69B12D37EC400DA6239 /* clusterclassic.h */, + A7E9BA3F12D395F700DA6239 /* calculators */, + A7E9BA4512D3965600DA6239 /* chimera */, + A7E9BA4B12D3966900DA6239 /* classifier */, + A7E9B6A612D37EC400DA6239 /* collect.cpp */, + A7E9B6A712D37EC400DA6239 /* collect.h */, + A7E9B6AA12D37EC400DA6239 /* collectdisplay.h */, + A7E9B6AB12D37EC400DA6239 /* collectorscurvedata.h */, + A7E9BA3812D3956100DA6239 /* commands */, + A7E9B6AF12D37EC400DA6239 /* commandfactory.cpp */, + A7E9B6B012D37EC400DA6239 /* commandfactory.hpp */, + A7E9B6B112D37EC400DA6239 /* commandoptionparser.cpp */, + A7E9B6B212D37EC400DA6239 /* commandoptionparser.hpp */, + A7E9B6B412D37EC400DA6239 /* completelinkage.cpp */, + A7E9BA4212D3960D00DA6239 /* containers */, + A7E9B6C912D37EC400DA6239 /* display.h */, + A7E9B6D112D37EC400DA6239 /* dlibshuff.cpp */, + A7E9B6D212D37EC400DA6239 /* dlibshuff.h */, + A7E9B6D912D37EC400DA6239 /* endiannessmacros.h */, + A7E9B6DA12D37EC400DA6239 /* engine.cpp */, + A7E9B6DB12D37EC400DA6239 /* engine.hpp */, + A7E9B6E012D37EC400DA6239 /* fileoutput.cpp */, + A7E9B6E112D37EC400DA6239 /* fileoutput.h */, + A7E9B70C12D37EC400DA6239 /* globaldata.cpp */, + A7E9B70D12D37EC400DA6239 /* globaldata.hpp */, + A7E9B71112D37EC400DA6239 /* gotohoverlap.hpp */, + A7E9B71012D37EC400DA6239 /* gotohoverlap.cpp */, + A7E9B71812D37EC400DA6239 /* hcluster.cpp */, + A7E9B71912D37EC400DA6239 /* hcluster.h */, + A7E9B71C12D37EC400DA6239 /* heatmap.cpp */, + A7E9B71D12D37EC400DA6239 /* heatmap.h */, + A7E9B72012D37EC400DA6239 /* heatmapsim.cpp */, + A7E9B72112D37EC400DA6239 /* heatmapsim.h */, + A7E9B72E12D37EC400DA6239 /* inputdata.h */, + A7E9B72D12D37EC400DA6239 /* inputdata.cpp */, + A7E9B73912D37EC400DA6239 /* libshuff.cpp */, + A7E9B73A12D37EC400DA6239 /* libshuff.h */, + A7E9BA5612D39BD800DA6239 /* metastats */, + A7E9B75B12D37EC400DA6239 /* mothur.cpp */, + A7E9B75C12D37EC400DA6239 /* mothur.h */, + A7E9B75D12D37EC400DA6239 /* mothurout.cpp */, + A7E9B75E12D37EC400DA6239 /* mothurout.h */, + A7E9B76512D37EC400DA6239 /* needlemanoverlap.cpp */, + A7E9B76612D37EC400DA6239 /* needlemanoverlap.hpp */, + A7E9B77012D37EC400DA6239 /* observable.h */, + A7E9B77512D37EC400DA6239 /* optionparser.cpp */, + A7E9B77612D37EC400DA6239 /* optionparser.h */, + A7E9B77B12D37EC400DA6239 /* overlap.cpp */, + A7E9B77C12D37EC400DA6239 /* overlap.hpp */, + A7E9B79B12D37EC400DA6239 /* progress.cpp */, + A7E9B79C12D37EC400DA6239 /* progress.hpp */, + A7E9B7A512D37EC400DA6239 /* rarecalc.cpp */, + A7E9B7A612D37EC400DA6239 /* rarecalc.h */, + A7E9B7A712D37EC400DA6239 /* raredisplay.cpp */, + A7E9B7A812D37EC400DA6239 /* raredisplay.h */, + A7E9B7A912D37EC400DA6239 /* rarefact.cpp */, + A7E9B7AA12D37EC400DA6239 /* rarefact.h */, + A7E9B7AD12D37EC400DA6239 /* rarefactioncurvedata.h */, + A7E9BA5312D39A5E00DA6239 /* read */, + A7E9B76112D37EC400DA6239 /* nast.cpp */, + A7E9B76212D37EC400DA6239 /* nast.hpp */, + A7E9B76312D37EC400DA6239 /* nastreport.cpp */, + A7E9B76412D37EC400DA6239 /* nastreport.hpp */, + A7E9B76712D37EC400DA6239 /* noalign.cpp */, + A7E9B76812D37EC400DA6239 /* noalign.hpp */, + A7E9B82312D37EC400DA6239 /* sharedutilities.cpp */, + A7E9B82412D37EC400DA6239 /* sharedutilities.h */, + A7E9B82D12D37EC400DA6239 /* singlelinkage.cpp */, + A7E9B83012D37EC400DA6239 /* slibshuff.cpp */, + A7E9B83112D37EC400DA6239 /* slibshuff.h */, + A7E9B85112D37EC400DA6239 /* suffixdb.cpp */, + A7E9B85212D37EC400DA6239 /* suffixdb.hpp */, + A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */, + A7E9B85412D37EC400DA6239 /* suffixnodes.hpp */, + A7E9B85512D37EC400DA6239 /* suffixtree.cpp */, + A7E9B85612D37EC400DA6239 /* suffixtree.hpp */, + A7E9B87412D37EC400DA6239 /* validcalculator.cpp */, + A7E9B87512D37EC400DA6239 /* validcalculator.h */, + A7E9B87612D37EC400DA6239 /* validparameter.cpp */, + A7E9B87712D37EC400DA6239 /* validparameter.h */, + A7E9B87812D37EC400DA6239 /* venn.cpp */, + A7E9B87912D37EC400DA6239 /* venn.h */, + A7E9B87E12D37EC400DA6239 /* weightedlinkage.cpp */, ); - name = calculators; + name = Source; sourceTree = ""; }; - A7CB593E11402F110010EB83 /* commands */ = { + 1AB674ADFE9D54B511CA2CBB /* Products */ = { isa = PBXGroup; children = ( - 7E1CA7D912C2A425003F10B2 /* trimflowscommand.h */, - 7E1CA7DA12C2A425003F10B2 /* trimflowscommand.cpp */, - A7DA202B113FECD400BF472F /* command.hpp */, - A7DA1FEF113FECD400BF472F /* aligncommand.h */, - A7DA1FEE113FECD400BF472F /* aligncommand.cpp */, - A7DA1FFE113FECD400BF472F /* binsequencecommand.h */, - A7DA1FFD113FECD400BF472F /* binsequencecommand.cpp */, - A7DA2008113FECD400BF472F /* bootstrapsharedcommand.h */, - A7DA2007113FECD400BF472F /* bootstrapsharedcommand.cpp */, - A7D216061199C47F00F13F13 /* catchallcommand.h */, - A7D216071199C47F00F13F13 /* catchallcommand.cpp */, - A7DA2018113FECD400BF472F /* chimeraseqscommand.h */, - A7DA2017113FECD400BF472F /* chimeraseqscommand.cpp */, - A7825502116519F70002E2DD /* chimerabellerophoncommand.h */, - A7825503116519F70002E2DD /* chimerabellerophoncommand.cpp */, - A747E79B1163442A00FB9042 /* chimeracheckcommand.h */, - A747E79C1163442A00FB9042 /* chimeracheckcommand.cpp */, - A78434881162224F00100BE0 /* chimeraccodecommand.h */, - A78434891162224F00100BE0 /* chimeraccodecommand.cpp */, - A78254461164D7790002E2DD /* chimerapintailcommand.h */, - A78254471164D7790002E2DD /* chimerapintailcommand.cpp */, - A747E81C116365E000FB9042 /* chimeraslayercommand.h */, - A747E81D116365E000FB9042 /* chimeraslayercommand.cpp */, - A73953DA11987ED100B0B160 /* chopseqscommand.h */, - A73953DB11987ED100B0B160 /* chopseqscommand.cpp */, - A7DA201E113FECD400BF472F /* classifyseqscommand.h */, - A7DA201D113FECD400BF472F /* classifyseqscommand.cpp */, - A7BBDA7B11B5694E006E6551 /* classifyotucommand.h */, - A7BBDA7C11B5694E006E6551 /* classifyotucommand.cpp */, - A7D215C811996C6E00F13F13 /* clearcutcommand.h */, - A7D215C911996C6E00F13F13 /* clearcutcommand.cpp */, - A7DA2022113FECD400BF472F /* clustercommand.h */, - A7DA2021113FECD400BF472F /* clustercommand.cpp */, - A7653D111278B09C009D6C09 /* clusterdoturcommand.h */, - A7653D121278B09C009D6C09 /* clusterdoturcommand.cpp */, - A74A9C03124B72DB000D5D25 /* clusterfragmentscommand.h */, - A74A9C04124B72DB000D5D25 /* clusterfragmentscommand.cpp */, - A71D924311AEB42400D00CBC /* clustersplitcommand.h */, - A71D924211AEB42400D00CBC /* clustersplitcommand.cpp */, - A7DA2026113FECD400BF472F /* collectcommand.h */, - A7DA2025113FECD400BF472F /* collectcommand.cpp */, - A7DA202A113FECD400BF472F /* collectsharedcommand.h */, - A7DA2029113FECD400BF472F /* collectsharedcommand.cpp */, - A7DA2032113FECD400BF472F /* consensuscommand.h */, - A7DA2031113FECD400BF472F /* consensuscommand.cpp */, - A71FF438129BDC35004397E6 /* consensusseqscommand.h */, - A71FF439129BDC35004397E6 /* consensusseqscommand.cpp */, - A7D9006D12C2544A00D8F543 /* corraxescommand.h */, - A7D9006E12C2544A00D8F543 /* corraxescommand.cpp */, - A7118EE511CFCAC000CFDE03 /* degapseqscommand.h */, - A7118EE611CFCAC000CFDE03 /* degapseqscommand.cpp */, - A7DA203B113FECD400BF472F /* deconvolutecommand.h */, - A7DA203A113FECD400BF472F /* deconvolutecommand.cpp */, - A7DA203F113FECD400BF472F /* distancecommand.h */, - A7DA203E113FECD400BF472F /* distancecommand.cpp */, - A76714DD126DE45A003F359A /* deuniqueseqscommand.h */, - A76714DE126DE45A003F359A /* deuniqueseqscommand.cpp */, - A7DA2050113FECD400BF472F /* filterseqscommand.h */, - A7DA204F113FECD400BF472F /* filterseqscommand.cpp */, - A7DA205B113FECD400BF472F /* getgroupcommand.h */, - A7DA205A113FECD400BF472F /* getgroupcommand.cpp */, - A75103D6128AE34100ABB831 /* getgroupscommand.h */, - A75103D7128AE34100ABB831 /* getgroupscommand.cpp */, - A7DA205D113FECD400BF472F /* getlabelcommand.h */, - A7DA205C113FECD400BF472F /* getlabelcommand.cpp */, - A787A24F124CB46C0076EB84 /* getlineagecommand.h */, - A787A250124CB46C0076EB84 /* getlineagecommand.cpp */, - A7DA205F113FECD400BF472F /* getlistcountcommand.h */, - A7DA205E113FECD400BF472F /* getlistcountcommand.cpp */, - A7510407128AFCC100ABB831 /* getotuscommand.h */, - A7510408128AFCC100ABB831 /* getotuscommand.cpp */, - A7DA2061113FECD400BF472F /* getoturepcommand.h */, - A7DA2060113FECD400BF472F /* getoturepcommand.cpp */, - A7DA2063113FECD400BF472F /* getrabundcommand.h */, - A7DA2062113FECD400BF472F /* getrabundcommand.cpp */, - A7118F0F11CFD5DC00CFDE03 /* getrelabundcommand.h */, - A7118F1011CFD5DC00CFDE03 /* getrelabundcommand.cpp */, - A7DA2065113FECD400BF472F /* getsabundcommand.h */, - A7DA2064113FECD400BF472F /* getsabundcommand.cpp */, - A7DA2067113FECD400BF472F /* getseqscommand.h */, - A7DA2066113FECD400BF472F /* getseqscommand.cpp */, - A7DA2069113FECD400BF472F /* getsharedotucommand.h */, - A7DA2068113FECD400BF472F /* getsharedotucommand.cpp */, - A7DA2075113FECD400BF472F /* hclustercommand.h */, - A7DA2074113FECD400BF472F /* hclustercommand.cpp */, - A7DA2079113FECD400BF472F /* heatmapcommand.h */, - A7DA2078113FECD400BF472F /* heatmapcommand.cpp */, - A7DA207D113FECD400BF472F /* heatmapsimcommand.h */, - A7DA207C113FECD400BF472F /* heatmapsimcommand.cpp */, - A7DA207F113FECD400BF472F /* helpcommand.h */, - A7DA207E113FECD400BF472F /* helpcommand.cpp */, - A76D1473128D9DA2005D4DFE /* indicatorcommand.h */, - A76D1474128D9DA2005D4DFE /* indicatorcommand.cpp */, - A7DA208E113FECD400BF472F /* libshuffcommand.h */, - A7DA208D113FECD400BF472F /* libshuffcommand.cpp */, - A7DA2090113FECD400BF472F /* listseqscommand.h */, - A7DA208F113FECD400BF472F /* listseqscommand.cpp */, - A703FE931194645F002C397E /* makegroupcommand.h */, - A703FE941194645F002C397E /* makegroupcommand.cpp */, - A7DA2099113FECD400BF472F /* matrixoutputcommand.h */, - A7DA2098113FECD400BF472F /* matrixoutputcommand.cpp */, - A7DA209B113FECD400BF472F /* mergefilecommand.h */, - A7DA209A113FECD400BF472F /* mergefilecommand.cpp */, - A7F6C8EA12423C0300299875 /* metastatscommand.h */, - A7F6C8EB12423C0300299875 /* metastatscommand.cpp */, - A7DA209D113FECD400BF472F /* mgclustercommand.h */, - A7DA209C113FECD400BF472F /* mgclustercommand.cpp */, - A7DA20AD113FECD400BF472F /* nocommands.h */, - A7DA20AC113FECD400BF472F /* nocommands.cpp */, - A798626D1240D91B005FC847 /* normalizesharedcommand.h */, - A798626E1240D91B005FC847 /* normalizesharedcommand.cpp */, - A7DA20B9113FECD400BF472F /* otuhierarchycommand.h */, - A7DA20B8113FECD400BF472F /* otuhierarchycommand.cpp */, - A77D787B126F387700F351BD /* pairwiseseqscommand.h */, - A77D787C126F387700F351BD /* pairwiseseqscommand.cpp */, - A724C2B61254961E006BB1C7 /* parsefastaqcommand.h */, - A724C2B71254961E006BB1C7 /* parsefastaqcommand.cpp */, - A7DA20BD113FECD400BF472F /* parselistscommand.h */, - A7DA20BC113FECD400BF472F /* parselistscommand.cpp */, - A7DA20C1113FECD400BF472F /* parsimonycommand.h */, - A7DA20C0113FECD400BF472F /* parsimonycommand.cpp */, - A7DA20C3113FECD400BF472F /* pcacommand.h */, - A7DA20C2113FECD400BF472F /* pcacommand.cpp */, - A72B3A62118B37FD004B9F8D /* phylodiversitycommand.h */, - A72B3A63118B37FD004B9F8D /* phylodiversitycommand.cpp */, - A7DA20C7113FECD400BF472F /* phylotypecommand.h */, - A7DA20C6113FECD400BF472F /* phylotypecommand.cpp */, - A72C66A1125B356F0058C2F9 /* pipelinepdscommand.h */, - A72C66A2125B356F0058C2F9 /* pipelinepdscommand.cpp */, - A7DA20CB113FECD400BF472F /* preclustercommand.h */, - A7DA20CA113FECD400BF472F /* preclustercommand.cpp */, - A7DA20D1113FECD400BF472F /* quitcommand.h */, - A7DA20D0113FECD400BF472F /* quitcommand.cpp */, - A7DA20DB113FECD400BF472F /* rarefactcommand.h */, - A7DA20DA113FECD400BF472F /* rarefactcommand.cpp */, - A7DA20DE113FECD400BF472F /* rarefactsharedcommand.h */, - A7DA20DD113FECD400BF472F /* rarefactsharedcommand.cpp */, - A7DA20E6113FECD400BF472F /* readdistcommand.h */, - A7DA20E5113FECD400BF472F /* readdistcommand.cpp */, - A7DA20EB113FECD400BF472F /* readotucommand.h */, - A7DA20EA113FECD400BF472F /* readotucommand.cpp */, - A7DA20F1113FECD400BF472F /* readtreecommand.h */, - A7DA20F0113FECD400BF472F /* readtreecommand.cpp */, - A751032A128AC93F00ABB831 /* removegroupscommand.h */, - A751032B128AC93F00ABB831 /* removegroupscommand.cpp */, - A787A28E124CE1470076EB84 /* removelineagecommand.h */, - A787A28F124CE1470076EB84 /* removelineagecommand.cpp */, - A76D1451128D6A03005D4DFE /* removeotuscommand.h */, - A76D1452128D6A03005D4DFE /* removeotuscommand.cpp */, - A7DA20F3113FECD400BF472F /* removeseqscommand.h */, - A7DA20F2113FECD400BF472F /* removeseqscommand.cpp */, - A7DA20F5113FECD400BF472F /* reversecommand.h */, - A7DA20F4113FECD400BF472F /* reversecommand.cpp */, - A7DA20F9113FECD400BF472F /* screenseqscommand.h */, - A7DA20F8113FECD400BF472F /* screenseqscommand.cpp */, - A7DA20FB113FECD400BF472F /* secondarystructurecommand.h */, - A7DA20FA113FECD400BF472F /* secondarystructurecommand.cpp */, - 7EA299BA11E384940022D8D3 /* sensspeccommand.h */, - 7EA299BB11E384940022D8D3 /* sensspeccommand.cpp */, - 7E84528511EF4BEB00564975 /* seqerrorcommand.h */, - 7E84528611EF4BEB00564975 /* seqerrorcommand.cpp */, - A7DA20FD113FECD400BF472F /* seqsummarycommand.h */, - A7DA20FC113FECD400BF472F /* seqsummarycommand.cpp */, - A7DA2103113FECD400BF472F /* setdircommand.h */, - A7DA2102113FECD400BF472F /* setdircommand.cpp */, - A76C4A1011876BAF0009460B /* setlogfilecommand.h */, - A76C4A1111876BAF0009460B /* setlogfilecommand.cpp */, - A732505E11E49EF100484B90 /* sffinfocommand.h */, - A732505F11E49EF100484B90 /* sffinfocommand.cpp */, - A7DA2110113FECD400BF472F /* sharedcommand.h */, - A7DA210F113FECD400BF472F /* sharedcommand.cpp */, - A71D924511AEB42400D00CBC /* splitabundcommand.h */, - A71D924411AEB42400D00CBC /* splitabundcommand.cpp */, - A7F139481247C3CB0033324C /* splitgroupscommand.h */, - A7F139491247C3CB0033324C /* splitgroupscommand.cpp */, - A7653CB112789EFD009D6C09 /* subsamplecommand.h */, - A7653CB212789EFD009D6C09 /* subsamplecommand.cpp */, - A7DA2155113FECD400BF472F /* summarycommand.h */, - A7DA2154113FECD400BF472F /* summarycommand.cpp */, - A7DA2159113FECD400BF472F /* summarysharedcommand.h */, - A7DA2158113FECD400BF472F /* summarysharedcommand.cpp */, - A7DA215B113FECD400BF472F /* systemcommand.h */, - A7DA215A113FECD400BF472F /* systemcommand.cpp */, - A7DA2162113FECD400BF472F /* treegroupscommand.h */, - A7DA2161113FECD400BF472F /* treegroupscommand.cpp */, - A7DA2168113FECD400BF472F /* trimseqscommand.h */, - A7DA2167113FECD400BF472F /* trimseqscommand.cpp */, - A7DA216A113FECD400BF472F /* unifracunweightedcommand.h */, - A7DA2169113FECD400BF472F /* unifracunweightedcommand.cpp */, - A7DA216C113FECD400BF472F /* unifracweightedcommand.h */, - A7DA216B113FECD400BF472F /* unifracweightedcommand.cpp */, - A7DA2178113FECD400BF472F /* venncommand.h */, - A7DA2177113FECD400BF472F /* venncommand.cpp */, + 8DD76FB20486AB0100D96B5E /* mothur */, + ); + name = Products; + sourceTree = ""; + }; + A7E9BA3812D3956100DA6239 /* commands */ = { + isa = PBXGroup; + children = ( + A7E9B6AE12D37EC400DA6239 /* command.hpp */, + A7E9B65112D37EC300DA6239 /* aligncommand.cpp */, + A7E9B65212D37EC300DA6239 /* aligncommand.h */, + A7E9B66012D37EC300DA6239 /* binsequencecommand.cpp */, + A7E9B66112D37EC300DA6239 /* binsequencecommand.h */, + A7E9B66A12D37EC400DA6239 /* bootstrapsharedcommand.cpp */, + A7E9B66B12D37EC400DA6239 /* bootstrapsharedcommand.h */, + A7E9B67212D37EC400DA6239 /* catchallcommand.cpp */, + A7E9B67312D37EC400DA6239 /* catchallcommand.h */, + A7E9B67A12D37EC400DA6239 /* chimerabellerophoncommand.cpp */, + A7E9B67B12D37EC400DA6239 /* chimerabellerophoncommand.h */, + A7E9B67C12D37EC400DA6239 /* chimeraccodecommand.cpp */, + A7E9B67D12D37EC400DA6239 /* chimeraccodecommand.h */, + A7E9B67E12D37EC400DA6239 /* chimeracheckcommand.cpp */, + A7E9B67F12D37EC400DA6239 /* chimeracheckcommand.h */, + A7E9B68212D37EC400DA6239 /* chimerapintailcommand.cpp */, + A7E9B68312D37EC400DA6239 /* chimerapintailcommand.h */, + A7E9B68612D37EC400DA6239 /* chimeraseqscommand.cpp */, + A7E9B68712D37EC400DA6239 /* chimeraseqscommand.h */, + A7E9B68A12D37EC400DA6239 /* chimeraslayercommand.cpp */, + A7E9B68B12D37EC400DA6239 /* chimeraslayercommand.h */, + A7E9B68C12D37EC400DA6239 /* chopseqscommand.cpp */, + A7E9B68D12D37EC400DA6239 /* chopseqscommand.h */, + A7E9B69012D37EC400DA6239 /* classifyotucommand.cpp */, + A7E9B69112D37EC400DA6239 /* classifyotucommand.h */, + A7E9B69212D37EC400DA6239 /* classifyseqscommand.cpp */, + A7E9B69312D37EC400DA6239 /* classifyseqscommand.h */, + A7E9B69612D37EC400DA6239 /* clearcutcommand.cpp */, + A7E9B69712D37EC400DA6239 /* clearcutcommand.h */, + A7E9B69C12D37EC400DA6239 /* clustercommand.cpp */, + A7E9B69D12D37EC400DA6239 /* clustercommand.h */, + A7E9B69E12D37EC400DA6239 /* clusterdoturcommand.cpp */, + A7E9B69F12D37EC400DA6239 /* clusterdoturcommand.h */, + A7E9B6A012D37EC400DA6239 /* clusterfragmentscommand.cpp */, + A7E9B6A112D37EC400DA6239 /* clusterfragmentscommand.h */, + A7E9B6A212D37EC400DA6239 /* clustersplitcommand.cpp */, + A7E9B6A312D37EC400DA6239 /* clustersplitcommand.h */, + A7E9B6A812D37EC400DA6239 /* collectcommand.cpp */, + A7E9B6A912D37EC400DA6239 /* collectcommand.h */, + A7E9B6AC12D37EC400DA6239 /* collectsharedcommand.cpp */, + A7E9B6AD12D37EC400DA6239 /* collectsharedcommand.h */, + A7E9B6B512D37EC400DA6239 /* consensuscommand.cpp */, + A7E9B6B612D37EC400DA6239 /* consensuscommand.h */, + A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */, + A7E9B6B812D37EC400DA6239 /* consensusseqscommand.h */, + A7E9B6B912D37EC400DA6239 /* corraxescommand.cpp */, + A7E9B6BA12D37EC400DA6239 /* corraxescommand.h */, + A7E9B6C312D37EC400DA6239 /* deconvolutecommand.cpp */, + A7E9B6C412D37EC400DA6239 /* deconvolutecommand.h */, + A7E9B6C512D37EC400DA6239 /* degapseqscommand.cpp */, + A7E9B6C612D37EC400DA6239 /* degapseqscommand.h */, + A7E9B6C712D37EC400DA6239 /* deuniqueseqscommand.cpp */, + A7E9B6C812D37EC400DA6239 /* deuniqueseqscommand.h */, + A7E9B6CB12D37EC400DA6239 /* distancecommand.cpp */, + A7E9B6CC12D37EC400DA6239 /* distancecommand.h */, + A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */, + A7E9B6E412D37EC400DA6239 /* filterseqscommand.h */, + A7E9B6F212D37EC400DA6239 /* getgroupcommand.cpp */, + A7E9B6F312D37EC400DA6239 /* getgroupcommand.h */, + A7E9B6F412D37EC400DA6239 /* getgroupscommand.cpp */, + A7E9B6F512D37EC400DA6239 /* getgroupscommand.h */, + A7E9B6F612D37EC400DA6239 /* getlabelcommand.cpp */, + A7E9B6F712D37EC400DA6239 /* getlabelcommand.h */, + A7E9B6F812D37EC400DA6239 /* getlineagecommand.cpp */, + A7E9B6F912D37EC400DA6239 /* getlineagecommand.h */, + A7E9B6FA12D37EC400DA6239 /* getlistcountcommand.cpp */, + A7E9B6FB12D37EC400DA6239 /* getlistcountcommand.h */, + A7E9B6FE12D37EC400DA6239 /* getoturepcommand.cpp */, + A7E9B6FF12D37EC400DA6239 /* getoturepcommand.h */, + A7E9B70012D37EC400DA6239 /* getotuscommand.cpp */, + A7E9B70112D37EC400DA6239 /* getotuscommand.h */, + A7E9B70212D37EC400DA6239 /* getrabundcommand.cpp */, + A7E9B70312D37EC400DA6239 /* getrabundcommand.h */, + A7E9B70412D37EC400DA6239 /* getrelabundcommand.cpp */, + A7E9B70512D37EC400DA6239 /* getrelabundcommand.h */, + A7E9B70612D37EC400DA6239 /* getsabundcommand.cpp */, + A7E9B70712D37EC400DA6239 /* getsabundcommand.h */, + A7E9B70812D37EC400DA6239 /* getseqscommand.cpp */, + A7E9B70912D37EC400DA6239 /* getseqscommand.h */, + A7E9B70A12D37EC400DA6239 /* getsharedotucommand.cpp */, + A7E9B70B12D37EC400DA6239 /* getsharedotucommand.h */, + A7E9B71A12D37EC400DA6239 /* hclustercommand.cpp */, + A7E9B71B12D37EC400DA6239 /* hclustercommand.h */, + A7E9B71E12D37EC400DA6239 /* heatmapcommand.cpp */, + A7E9B71F12D37EC400DA6239 /* heatmapcommand.h */, + A7E9B72212D37EC400DA6239 /* heatmapsimcommand.cpp */, + A7E9B72312D37EC400DA6239 /* heatmapsimcommand.h */, + A7E9B72812D37EC400DA6239 /* helpcommand.cpp */, + A7E9B72912D37EC400DA6239 /* helpcommand.h */, + A7E9B72B12D37EC400DA6239 /* indicatorcommand.cpp */, + A7E9B72C12D37EC400DA6239 /* indicatorcommand.h */, + A7E9B73B12D37EC400DA6239 /* libshuffcommand.cpp */, + A7E9B73C12D37EC400DA6239 /* libshuffcommand.h */, + A7E9B73D12D37EC400DA6239 /* listseqscommand.cpp */, + A7E9B73E12D37EC400DA6239 /* listseqscommand.h */, + A7E9B74312D37EC400DA6239 /* makegroupcommand.cpp */, + A7E9B74412D37EC400DA6239 /* makegroupcommand.h */, + A7E9B74912D37EC400DA6239 /* matrixoutputcommand.cpp */, + A7E9B74A12D37EC400DA6239 /* matrixoutputcommand.h */, + A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */, + A7E9B75412D37EC400DA6239 /* mergefilecommand.h */, + A7E9B75712D37EC400DA6239 /* metastatscommand.cpp */, + A7E9B75812D37EC400DA6239 /* metastatscommand.h */, + A7E9B75912D37EC400DA6239 /* mgclustercommand.cpp */, + A7E9B75A12D37EC400DA6239 /* mgclustercommand.h */, + A7E9B76A12D37EC400DA6239 /* nocommands.h */, + A7E9B76912D37EC400DA6239 /* nocommands.cpp */, + A7E9B76B12D37EC400DA6239 /* normalizesharedcommand.cpp */, + A7E9B76C12D37EC400DA6239 /* normalizesharedcommand.h */, + A7E9B77912D37EC400DA6239 /* otuhierarchycommand.cpp */, + A7E9B77A12D37EC400DA6239 /* otuhierarchycommand.h */, + A7E9B77D12D37EC400DA6239 /* pairwiseseqscommand.cpp */, + A7E9B77E12D37EC400DA6239 /* pairwiseseqscommand.h */, + A7E9B77F12D37EC400DA6239 /* parsefastaqcommand.cpp */, + A7E9B78012D37EC400DA6239 /* parsefastaqcommand.h */, + A7E9B78112D37EC400DA6239 /* parselistscommand.cpp */, + A7E9B78212D37EC400DA6239 /* parselistscommand.h */, + A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */, + A7E9B78612D37EC400DA6239 /* parsimonycommand.h */, + A7E9B78712D37EC400DA6239 /* pcacommand.cpp */, + A7E9B78812D37EC400DA6239 /* pcacommand.h */, + A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */, + A7E9B78C12D37EC400DA6239 /* phylodiversitycommand.h */, + A7E9B79112D37EC400DA6239 /* phylotypecommand.cpp */, + A7E9B79212D37EC400DA6239 /* phylotypecommand.h */, + A7E9B79512D37EC400DA6239 /* pipelinepdscommand.cpp */, + A7E9B79612D37EC400DA6239 /* pipelinepdscommand.h */, + A7E9B79712D37EC400DA6239 /* preclustercommand.cpp */, + A7E9B79812D37EC400DA6239 /* preclustercommand.h */, + A7E9B7A112D37EC400DA6239 /* quitcommand.cpp */, + A7E9B7A212D37EC400DA6239 /* quitcommand.h */, + A7E9B7AB12D37EC400DA6239 /* rarefactcommand.cpp */, + A7E9B7AC12D37EC400DA6239 /* rarefactcommand.h */, + A7E9B7AE12D37EC400DA6239 /* rarefactsharedcommand.cpp */, + A7E9B7AF12D37EC400DA6239 /* rarefactsharedcommand.h */, + A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */, + A7E9B7B712D37EC400DA6239 /* readdistcommand.h */, + A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */, + A7E9B7BC12D37EC400DA6239 /* readotucommand.h */, + A7E9B7C112D37EC400DA6239 /* readtreecommand.cpp */, + A7E9B7C212D37EC400DA6239 /* readtreecommand.h */, + A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */, + A7E9B7C412D37EC400DA6239 /* removegroupscommand.h */, + A7E9B7C512D37EC400DA6239 /* removelineagecommand.cpp */, + A7E9B7C612D37EC400DA6239 /* removelineagecommand.h */, + A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */, + A7E9B7C812D37EC400DA6239 /* removeotuscommand.h */, + A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */, + A7E9B7CA12D37EC400DA6239 /* removeseqscommand.h */, + A7E9B7CD12D37EC400DA6239 /* reversecommand.cpp */, + A7E9B7CE12D37EC400DA6239 /* reversecommand.h */, + A7E9B7D112D37EC400DA6239 /* screenseqscommand.cpp */, + A7E9B7D212D37EC400DA6239 /* screenseqscommand.h */, + A7E9B7D312D37EC400DA6239 /* secondarystructurecommand.cpp */, + A7E9B7D412D37EC400DA6239 /* secondarystructurecommand.h */, + A7E9B7D512D37EC400DA6239 /* sensspeccommand.cpp */, + A7E9B7D612D37EC400DA6239 /* sensspeccommand.h */, + A7E9B7D712D37EC400DA6239 /* seqerrorcommand.cpp */, + A7E9B7D812D37EC400DA6239 /* seqerrorcommand.h */, + A7E9B7D912D37EC400DA6239 /* seqsummarycommand.cpp */, + A7E9B7DA12D37EC400DA6239 /* seqsummarycommand.h */, + A7E9B7DF12D37EC400DA6239 /* setdircommand.cpp */, + A7E9B7E012D37EC400DA6239 /* setdircommand.h */, + A7E9B7E112D37EC400DA6239 /* setlogfilecommand.cpp */, + A7E9B7E212D37EC400DA6239 /* setlogfilecommand.h */, + A7E9B7E312D37EC400DA6239 /* sffinfocommand.cpp */, + A7E9B7E412D37EC400DA6239 /* sffinfocommand.h */, + A7E9B7F212D37EC400DA6239 /* sharedcommand.cpp */, + A7E9B7F312D37EC400DA6239 /* sharedcommand.h */, + A7E9B82712D37EC400DA6239 /* shhhercommand.cpp */, + A7E9B82812D37EC400DA6239 /* shhhercommand.h */, + A7E9B83F12D37EC400DA6239 /* splitabundcommand.cpp */, + A7E9B84012D37EC400DA6239 /* splitabundcommand.h */, + A7E9B84112D37EC400DA6239 /* splitgroupscommand.cpp */, + A7E9B84212D37EC400DA6239 /* splitgroupscommand.h */, + A7E9B84F12D37EC400DA6239 /* subsamplecommand.cpp */, + A7E9B85012D37EC400DA6239 /* subsamplecommand.h */, + A7E9B85712D37EC400DA6239 /* summarycommand.cpp */, + A7E9B85812D37EC400DA6239 /* summarycommand.h */, + A7E9B85912D37EC400DA6239 /* summarysharedcommand.cpp */, + A7E9B85A12D37EC400DA6239 /* summarysharedcommand.h */, + A7E9B85B12D37EC400DA6239 /* systemcommand.cpp */, + A7E9B85C12D37EC400DA6239 /* systemcommand.h */, + A7E9B86212D37EC400DA6239 /* treegroupscommand.cpp */, + A7E9B86312D37EC400DA6239 /* treegroupscommand.h */, + A7E9B86812D37EC400DA6239 /* trimflowscommand.cpp */, + A7E9B86912D37EC400DA6239 /* trimflowscommand.h */, + A7E9B86A12D37EC400DA6239 /* trimseqscommand.cpp */, + A7E9B86B12D37EC400DA6239 /* trimseqscommand.h */, + A7E9B86C12D37EC400DA6239 /* unifracunweightedcommand.cpp */, + A7E9B86D12D37EC400DA6239 /* unifracunweightedcommand.h */, + A7E9B86E12D37EC400DA6239 /* unifracweightedcommand.cpp */, + A7E9B86F12D37EC400DA6239 /* unifracweightedcommand.h */, + A7E9B87A12D37EC400DA6239 /* venncommand.cpp */, + A7E9B87B12D37EC400DA6239 /* venncommand.h */, ); name = commands; sourceTree = ""; }; - A7CB594211402F430010EB83 /* containers */ = { + A7E9BA3F12D395F700DA6239 /* calculators */ = { isa = PBXGroup; children = ( - A7DA1FF3113FECD400BF472F /* alignmentcell.hpp */, - A7DA1FF2113FECD400BF472F /* alignmentcell.cpp */, - A7DA1FF4113FECD400BF472F /* alignmentdb.cpp */, - A7DA1FF5113FECD400BF472F /* alignmentdb.h */, - A7DA2001113FECD400BF472F /* blastdb.cpp */, - A7DA2002113FECD400BF472F /* blastdb.hpp */, - A7DA2035113FECD400BF472F /* database.cpp */, - A7DA2036113FECD400BF472F /* database.hpp */, - A7DA2037113FECD400BF472F /* datavector.hpp */, - A7DA2040113FECD400BF472F /* distancedb.cpp */, - A7DA2041113FECD400BF472F /* distancedb.hpp */, - A7DA204A113FECD400BF472F /* fastamap.cpp */, - A7DA204B113FECD400BF472F /* fastamap.h */, - A7DA2056113FECD400BF472F /* fullmatrix.cpp */, - A7DA2057113FECD400BF472F /* fullmatrix.h */, - A7DA2070113FECD400BF472F /* groupmap.cpp */, - A7DA2071113FECD400BF472F /* groupmap.h */, - A7DA2085113FECD400BF472F /* kmer.cpp */, - A7DA2086113FECD400BF472F /* kmer.hpp */, - A7DA2087113FECD400BF472F /* kmerdb.cpp */, - A7DA2088113FECD400BF472F /* kmerdb.hpp */, - A7DA2091113FECD400BF472F /* listvector.cpp */, - A7DA2092113FECD400BF472F /* listvector.hpp */, - A7DA20A2113FECD400BF472F /* nameassignment.cpp */, - A7DA20A3113FECD400BF472F /* nameassignment.hpp */, - A7DA20B6113FECD400BF472F /* ordervector.cpp */, - A7DA20B7113FECD400BF472F /* ordervector.hpp */, - 7E85BD1C11EB5E9B00FD37C0 /* qualityscores.h */, - 7E85BD1D11EB5E9B00FD37C0 /* qualityscores.cpp */, - A7DA20D3113FECD400BF472F /* rabundvector.hpp */, - A7DA20D2113FECD400BF472F /* rabundvector.cpp */, - A7DA20F6113FECD400BF472F /* sabundvector.cpp */, - A7DA20F7113FECD400BF472F /* sabundvector.hpp */, - A7DA20FE113FECD400BF472F /* sequence.cpp */, - A7DA20FF113FECD400BF472F /* sequence.hpp */, - A7DA2100113FECD400BF472F /* sequencedb.cpp */, - A7DA2101113FECD400BF472F /* sequencedb.h */, - A7DA2121113FECD400BF472F /* sharedlistvector.cpp */, - A7DA2122113FECD400BF472F /* sharedlistvector.h */, - A7DA212A113FECD400BF472F /* sharedordervector.cpp */, - A7DA212B113FECD400BF472F /* sharedordervector.h */, - A7DA212C113FECD400BF472F /* sharedrabundvector.cpp */, - A7DA212D113FECD400BF472F /* sharedrabundvector.h */, - A7AE6302121C3408001DE6FC /* sharedrabundfloatvector.h */, - A7AE6303121C3408001DE6FC /* sharedrabundfloatvector.cpp */, - A7DA212F113FECD400BF472F /* sharedsabundvector.h */, - A7DA212E113FECD400BF472F /* sharedsabundvector.cpp */, - A7DA214C113FECD400BF472F /* sparsematrix.cpp */, - A7DA214D113FECD400BF472F /* sparsematrix.hpp */, - A7DA214E113FECD400BF472F /* suffixdb.cpp */, - A7DA214F113FECD400BF472F /* suffixdb.hpp */, - A7DA2150113FECD400BF472F /* suffixnodes.cpp */, - A7DA2151113FECD400BF472F /* suffixnodes.hpp */, - A7DA2152113FECD400BF472F /* suffixtree.cpp */, - A7DA2153113FECD400BF472F /* suffixtree.hpp */, - A7DA215E113FECD400BF472F /* tree.cpp */, - A7DA215F113FECD400BF472F /* tree.h */, - A7DA2163113FECD400BF472F /* treemap.cpp */, - A7DA2164113FECD400BF472F /* treemap.h */, - A7DA2165113FECD400BF472F /* treenode.cpp */, - A7DA2166113FECD400BF472F /* treenode.h */, + A7E9B64F12D37EC300DA6239 /* ace.cpp */, + A7E9B65012D37EC300DA6239 /* ace.h */, + A7E9B65E12D37EC300DA6239 /* bergerparker.cpp */, + A7E9B65F12D37EC300DA6239 /* bergerparker.h */, + A7E9B66612D37EC400DA6239 /* boneh.cpp */, + A7E9B66712D37EC400DA6239 /* boneh.h */, + A7E9B66812D37EC400DA6239 /* bootstrap.cpp */, + A7E9B66912D37EC400DA6239 /* bootstrap.h */, + A7E9B66C12D37EC400DA6239 /* bstick.cpp */, + A7E9B66D12D37EC400DA6239 /* bstick.h */, + A7E9B66E12D37EC400DA6239 /* calculator.cpp */, + A7E9B66F12D37EC400DA6239 /* calculator.h */, + A7E9B67012D37EC400DA6239 /* canberra.cpp */, + A7E9B67112D37EC400DA6239 /* canberra.h */, + A7E9B67612D37EC400DA6239 /* chao1.cpp */, + A7E9B67712D37EC400DA6239 /* chao1.h */, + A7E9B6A412D37EC400DA6239 /* cmdargs.cpp */, + A7E9B6A512D37EC400DA6239 /* cmdargs.h */, + A7E9B6BB12D37EC400DA6239 /* coverage.cpp */, + A7E9B6BC12D37EC400DA6239 /* coverage.h */, + A7E9B6CA12D37EC400DA6239 /* dist.h */, + A7E9B6C012D37EC400DA6239 /* dayhoff.h */, + A7E9B6D512D37EC400DA6239 /* eachgapdist.h */, + A7E9B6D612D37EC400DA6239 /* eachgapignore.h */, + A7E9B6D712D37EC400DA6239 /* efron.cpp */, + A7E9B6D812D37EC400DA6239 /* efron.h */, + A7E9B6E212D37EC400DA6239 /* filters.h */, + A7E9B6E512D37EC400DA6239 /* fisher2.c */, + A7E9B6E612D37EC400DA6239 /* fisher2.h */, + A7E9B6F012D37EC400DA6239 /* geom.cpp */, + A7E9B6F112D37EC400DA6239 /* geom.h */, + A7E9B70E12D37EC400DA6239 /* goodscoverage.cpp */, + A7E9B70F12D37EC400DA6239 /* goodscoverage.h */, + A7E9B71212D37EC400DA6239 /* gower.cpp */, + A7E9B71312D37EC400DA6239 /* gower.h */, + A7E9B71612D37EC400DA6239 /* hamming.cpp */, + A7E9B71712D37EC400DA6239 /* hamming.h */, + A7E9B72412D37EC400DA6239 /* heip.cpp */, + A7E9B72512D37EC400DA6239 /* heip.h */, + A7E9B72612D37EC400DA6239 /* hellinger.cpp */, + A7E9B72712D37EC400DA6239 /* hellinger.h */, + A7E9B72A12D37EC400DA6239 /* ignoregaps.h */, + A7E9B72F12D37EC400DA6239 /* invsimpson.cpp */, + A7E9B73012D37EC400DA6239 /* invsimpson.h */, + A7E9B73112D37EC400DA6239 /* jackknife.cpp */, + A7E9B73212D37EC400DA6239 /* jackknife.h */, + A7E9B74112D37EC400DA6239 /* logsd.cpp */, + A7E9B74212D37EC400DA6239 /* logsd.h */, + A7E9B74712D37EC400DA6239 /* manhattan.cpp */, + A7E9B74812D37EC400DA6239 /* manhattan.h */, + A7E9B74B12D37EC400DA6239 /* memchi2.cpp */, + A7E9B74C12D37EC400DA6239 /* memchi2.h */, + A7E9B74D12D37EC400DA6239 /* memchord.cpp */, + A7E9B74E12D37EC400DA6239 /* memchord.h */, + A7E9B74F12D37EC400DA6239 /* memeuclidean.cpp */, + A7E9B75012D37EC400DA6239 /* memeuclidean.h */, + A7E9B75112D37EC400DA6239 /* mempearson.cpp */, + A7E9B75212D37EC400DA6239 /* mempearson.h */, + A7E9B76D12D37EC400DA6239 /* npshannon.cpp */, + A7E9B76E12D37EC400DA6239 /* npshannon.h */, + A7E9B76F12D37EC400DA6239 /* nseqs.h */, + A7E9B77112D37EC400DA6239 /* odum.cpp */, + A7E9B77212D37EC400DA6239 /* odum.h */, + A7E9B77312D37EC400DA6239 /* onegapdist.h */, + A7E9B77412D37EC400DA6239 /* onegapignore.h */, + A7E9B78412D37EC400DA6239 /* parsimony.h */, + A7E9B78312D37EC400DA6239 /* parsimony.cpp */, + A7E9B79912D37EC400DA6239 /* prng.cpp */, + A7E9B79A12D37EC400DA6239 /* prng.h */, + A7E9B79D12D37EC400DA6239 /* qstat.cpp */, + A7E9B79E12D37EC400DA6239 /* qstat.h */, + A7E9B7E512D37EC400DA6239 /* shannon.cpp */, + A7E9B7E612D37EC400DA6239 /* shannon.h */, + A7E9B7E712D37EC400DA6239 /* shannoneven.cpp */, + A7E9B7E812D37EC400DA6239 /* shannoneven.h */, + A7E9B7E912D37EC400DA6239 /* sharedace.cpp */, + A7E9B7EA12D37EC400DA6239 /* sharedace.h */, + A7E9B7EB12D37EC400DA6239 /* sharedanderberg.h */, + A7E9B7EC12D37EC400DA6239 /* sharedanderbergs.cpp */, + A7E9B7ED12D37EC400DA6239 /* sharedanderbergs.h */, + A7E9B7EE12D37EC400DA6239 /* sharedbraycurtis.cpp */, + A7E9B7EF12D37EC400DA6239 /* sharedbraycurtis.h */, + A7E9B7F012D37EC400DA6239 /* sharedchao1.cpp */, + A7E9B7F112D37EC400DA6239 /* sharedchao1.h */, + A7E9B7F412D37EC400DA6239 /* sharedjabund.cpp */, + A7E9B7F512D37EC400DA6239 /* sharedjabund.h */, + A7E9B7F612D37EC400DA6239 /* sharedjackknife.cpp */, + A7E9B7F712D37EC400DA6239 /* sharedjackknife.h */, + A7E9B7F812D37EC400DA6239 /* sharedjclass.cpp */, + A7E9B7F912D37EC400DA6239 /* sharedjclass.h */, + A7E9B7FA12D37EC400DA6239 /* sharedjest.cpp */, + A7E9B7FB12D37EC400DA6239 /* sharedjest.h */, + A7E9B7FC12D37EC400DA6239 /* sharedkstest.cpp */, + A7E9B7FD12D37EC400DA6239 /* sharedkstest.h */, + A7E9B7FE12D37EC400DA6239 /* sharedkulczynski.cpp */, + A7E9B7FF12D37EC400DA6239 /* sharedkulczynski.h */, + A7E9B80012D37EC400DA6239 /* sharedkulczynskicody.cpp */, + A7E9B80112D37EC400DA6239 /* sharedkulczynskicody.h */, + A7E9B80212D37EC400DA6239 /* sharedlennon.cpp */, + A7E9B80312D37EC400DA6239 /* sharedlennon.h */, + A7E9B80612D37EC400DA6239 /* sharedmarczewski.cpp */, + A7E9B80712D37EC400DA6239 /* sharedmarczewski.h */, + A7E9B80812D37EC400DA6239 /* sharedmorisitahorn.cpp */, + A7E9B80912D37EC400DA6239 /* sharedmorisitahorn.h */, + A7E9B80A12D37EC400DA6239 /* sharednseqs.h */, + A7E9B80B12D37EC400DA6239 /* sharedochiai.cpp */, + A7E9B80C12D37EC400DA6239 /* sharedochiai.h */, + A7E9B81512D37EC400DA6239 /* sharedsobs.cpp */, + A7E9B81612D37EC400DA6239 /* sharedsobs.h */, + A7E9B81712D37EC400DA6239 /* sharedsobscollectsummary.cpp */, + A7E9B81812D37EC400DA6239 /* sharedsobscollectsummary.h */, + A7E9B81912D37EC400DA6239 /* sharedsorabund.cpp */, + A7E9B81A12D37EC400DA6239 /* sharedsorabund.h */, + A7E9B81B12D37EC400DA6239 /* sharedsorclass.cpp */, + A7E9B81C12D37EC400DA6239 /* sharedsorclass.h */, + A7E9B81D12D37EC400DA6239 /* sharedsorest.cpp */, + A7E9B81E12D37EC400DA6239 /* sharedsorest.h */, + A7E9B81F12D37EC400DA6239 /* sharedthetan.cpp */, + A7E9B82012D37EC400DA6239 /* sharedthetan.h */, + A7E9B82112D37EC400DA6239 /* sharedthetayc.cpp */, + A7E9B82212D37EC400DA6239 /* sharedthetayc.h */, + A7E9B82512D37EC400DA6239 /* shen.cpp */, + A7E9B82612D37EC400DA6239 /* shen.h */, + A7E9B82912D37EC400DA6239 /* simpson.cpp */, + A7E9B82A12D37EC400DA6239 /* simpson.h */, + A7E9B82B12D37EC400DA6239 /* simpsoneven.cpp */, + A7E9B82C12D37EC400DA6239 /* simpsoneven.h */, + A7E9B83212D37EC400DA6239 /* smithwilson.cpp */, + A7E9B83312D37EC400DA6239 /* smithwilson.h */, + A7E9B83412D37EC400DA6239 /* sobs.h */, + A7E9B83512D37EC400DA6239 /* soergel.cpp */, + A7E9B83612D37EC400DA6239 /* soergel.h */, + A7E9B83712D37EC400DA6239 /* solow.cpp */, + A7E9B83812D37EC400DA6239 /* solow.h */, + A7E9B83B12D37EC400DA6239 /* spearman.cpp */, + A7E9B83C12D37EC400DA6239 /* spearman.h */, + A7E9B83D12D37EC400DA6239 /* speciesprofile.cpp */, + A7E9B83E12D37EC400DA6239 /* speciesprofile.h */, + A7E9B84512D37EC400DA6239 /* structchi2.cpp */, + A7E9B84612D37EC400DA6239 /* structchi2.h */, + A7E9B84712D37EC400DA6239 /* structchord.cpp */, + A7E9B84812D37EC400DA6239 /* structchord.h */, + A7E9B84912D37EC400DA6239 /* structeuclidean.cpp */, + A7E9B84A12D37EC400DA6239 /* structeuclidean.h */, + A7E9B84B12D37EC400DA6239 /* structkulczynski.cpp */, + A7E9B84C12D37EC400DA6239 /* structkulczynski.h */, + A7E9B84D12D37EC400DA6239 /* structpearson.cpp */, + A7E9B84E12D37EC400DA6239 /* structpearson.h */, + A7E9B86112D37EC400DA6239 /* treecalculator.h */, + A7E9B87012D37EC400DA6239 /* unweighted.cpp */, + A7E9B87112D37EC400DA6239 /* unweighted.h */, + A7E9B87212D37EC400DA6239 /* uvest.cpp */, + A7E9B87312D37EC400DA6239 /* uvest.h */, + A7E9B87C12D37EC400DA6239 /* weighted.cpp */, + A7E9B87D12D37EC400DA6239 /* weighted.h */, + A7E9B87F12D37EC400DA6239 /* whittaker.cpp */, + A7E9B88012D37EC400DA6239 /* whittaker.h */, + ); + name = calculators; + sourceTree = ""; + }; + A7E9BA4212D3960D00DA6239 /* containers */ = { + isa = PBXGroup; + children = ( + A7E9B65312D37EC300DA6239 /* alignment.cpp */, + A7E9B65412D37EC300DA6239 /* alignment.hpp */, + A7E9B65512D37EC300DA6239 /* alignmentcell.cpp */, + A7E9B65612D37EC300DA6239 /* alignmentcell.hpp */, + A7E9B65712D37EC300DA6239 /* alignmentdb.cpp */, + A7E9B65812D37EC300DA6239 /* alignmentdb.h */, + A7E9B66212D37EC300DA6239 /* blastalign.cpp */, + A7E9B66312D37EC400DA6239 /* blastalign.hpp */, + A7E9B66412D37EC400DA6239 /* blastdb.cpp */, + A7E9B66512D37EC400DA6239 /* blastdb.hpp */, + A7E9B6BD12D37EC400DA6239 /* database.cpp */, + A7E9B6BE12D37EC400DA6239 /* database.hpp */, + A7E9B6BF12D37EC400DA6239 /* datavector.hpp */, + A7E9B6CD12D37EC400DA6239 /* distancedb.cpp */, + A7E9B6CE12D37EC400DA6239 /* distancedb.hpp */, + A7E9B6DE12D37EC400DA6239 /* fastamap.cpp */, + A7E9B6DF12D37EC400DA6239 /* fastamap.h */, + A7E9B6E812D37EC400DA6239 /* flowdata.h */, + A7E9B6E712D37EC400DA6239 /* flowdata.cpp */, + A7E9B6EE12D37EC400DA6239 /* fullmatrix.cpp */, + A7E9B6EF12D37EC400DA6239 /* fullmatrix.h */, + A7E9B71412D37EC400DA6239 /* groupmap.cpp */, + A7E9B71512D37EC400DA6239 /* groupmap.h */, + A7E9B73312D37EC400DA6239 /* kmer.cpp */, + A7E9B73412D37EC400DA6239 /* kmer.hpp */, + A7E9B73512D37EC400DA6239 /* kmerdb.cpp */, + A7E9B73612D37EC400DA6239 /* kmerdb.hpp */, + A7E9B73F12D37EC400DA6239 /* listvector.cpp */, + A7E9B74012D37EC400DA6239 /* listvector.hpp */, + A7E9B75F12D37EC400DA6239 /* nameassignment.cpp */, + A7E9B76012D37EC400DA6239 /* nameassignment.hpp */, + A7E9B77712D37EC400DA6239 /* ordervector.cpp */, + A7E9B77812D37EC400DA6239 /* ordervector.hpp */, + A7E9B79F12D37EC400DA6239 /* qualityscores.cpp */, + A7E9B7A012D37EC400DA6239 /* qualityscores.h */, + A7E9B7A312D37EC400DA6239 /* rabundvector.cpp */, + A7E9B7A412D37EC400DA6239 /* rabundvector.hpp */, + A7E9B7CB12D37EC400DA6239 /* reportfile.cpp */, + A7E9B7CC12D37EC400DA6239 /* reportfile.h */, + A7E9B7CF12D37EC400DA6239 /* sabundvector.cpp */, + A7E9B7D012D37EC400DA6239 /* sabundvector.hpp */, + A7E9B7DB12D37EC400DA6239 /* sequence.cpp */, + A7E9B7DC12D37EC400DA6239 /* sequence.hpp */, + A7E9B7DD12D37EC400DA6239 /* sequencedb.cpp */, + A7E9B7DE12D37EC400DA6239 /* sequencedb.h */, + A7E9B80412D37EC400DA6239 /* sharedlistvector.cpp */, + A7E9B80512D37EC400DA6239 /* sharedlistvector.h */, + A7E9B80D12D37EC400DA6239 /* sharedordervector.cpp */, + A7E9B80E12D37EC400DA6239 /* sharedordervector.h */, + A7E9B80F12D37EC400DA6239 /* sharedrabundfloatvector.cpp */, + A7E9B81012D37EC400DA6239 /* sharedrabundfloatvector.h */, + A7E9B81112D37EC400DA6239 /* sharedrabundvector.cpp */, + A7E9B81212D37EC400DA6239 /* sharedrabundvector.h */, + A7E9B81312D37EC400DA6239 /* sharedsabundvector.cpp */, + A7E9B81412D37EC400DA6239 /* sharedsabundvector.h */, + A7E9B83912D37EC400DA6239 /* sparsematrix.cpp */, + A7E9B83A12D37EC400DA6239 /* sparsematrix.hpp */, + A7E9B85F12D37EC400DA6239 /* tree.cpp */, + A7E9B86012D37EC400DA6239 /* tree.h */, + A7E9B86412D37EC400DA6239 /* treemap.cpp */, + A7E9B86512D37EC400DA6239 /* treemap.h */, + A7E9B86612D37EC400DA6239 /* treenode.cpp */, + A7E9B86712D37EC400DA6239 /* treenode.h */, ); name = containers; sourceTree = ""; }; - A7CB594511402F6E0010EB83 /* classifers */ = { + A7E9BA4512D3965600DA6239 /* chimera */ = { + isa = PBXGroup; + children = ( + A7E9B65C12D37EC300DA6239 /* bellerophon.cpp */, + A7E9B65D12D37EC300DA6239 /* bellerophon.h */, + A7E9B67412D37EC400DA6239 /* ccode.cpp */, + A7E9B67512D37EC400DA6239 /* ccode.h */, + A7E9B67812D37EC400DA6239 /* chimera.cpp */, + A7E9B67912D37EC400DA6239 /* chimera.h */, + A7E9B68012D37EC400DA6239 /* chimeracheckrdp.cpp */, + A7E9B68112D37EC400DA6239 /* chimeracheckrdp.h */, + A7E9B68412D37EC400DA6239 /* chimerarealigner.cpp */, + A7E9B68512D37EC400DA6239 /* chimerarealigner.h */, + A7E9B68812D37EC400DA6239 /* chimeraslayer.cpp */, + A7E9B68912D37EC400DA6239 /* chimeraslayer.h */, + A7E9B6C112D37EC400DA6239 /* decalc.cpp */, + A7E9B6C212D37EC400DA6239 /* decalc.h */, + A7E9B74612D37EC400DA6239 /* maligner.h */, + A7E9B74512D37EC400DA6239 /* maligner.cpp */, + A7E9B79312D37EC400DA6239 /* pintail.cpp */, + A7E9B79412D37EC400DA6239 /* pintail.h */, + A7E9B82E12D37EC400DA6239 /* slayer.cpp */, + A7E9B82F12D37EC400DA6239 /* slayer.h */, + ); + name = chimera; + sourceTree = ""; + }; + A7E9BA4B12D3966900DA6239 /* classifier */ = { isa = PBXGroup; children = ( - A7DA201B113FECD400BF472F /* classify.cpp */, - A7DA201C113FECD400BF472F /* classify.h */, - A7DA1FF7113FECD400BF472F /* bayesian.cpp */, - A7DA1FF8113FECD400BF472F /* bayesian.h */, - A7DA2089113FECD400BF472F /* knn.cpp */, - A7DA208A113FECD400BF472F /* knn.h */, - A7DA20C4113FECD400BF472F /* phylotree.cpp */, - A7DA20C5113FECD400BF472F /* phylotree.h */, - A76AAD02117F322B003D8DA1 /* phylosummary.h */, - A76AAD03117F322B003D8DA1 /* phylosummary.cpp */, - A7DA215C113FECD400BF472F /* taxonomyequalizer.cpp */, - A7DA215D113FECD400BF472F /* taxonomyequalizer.h */, + A7E9B65A12D37EC300DA6239 /* bayesian.cpp */, + A7E9B65B12D37EC300DA6239 /* bayesian.h */, + A7E9B68E12D37EC400DA6239 /* classify.cpp */, + A7E9B68F12D37EC400DA6239 /* classify.h */, + A7E9B73812D37EC400DA6239 /* knn.h */, + A7E9B73712D37EC400DA6239 /* knn.cpp */, + A7E9B78912D37EC400DA6239 /* phylodiversity.cpp */, + A7E9B78A12D37EC400DA6239 /* phylodiversity.h */, + A7E9B78D12D37EC400DA6239 /* phylosummary.cpp */, + A7E9B78E12D37EC400DA6239 /* phylosummary.h */, + A7E9B78F12D37EC400DA6239 /* phylotree.cpp */, + A7E9B79012D37EC400DA6239 /* phylotree.h */, + A7E9B85D12D37EC400DA6239 /* taxonomyequalizer.cpp */, + A7E9B85E12D37EC400DA6239 /* taxonomyequalizer.h */, ); - name = classifers; + name = classifier; sourceTree = ""; }; - A7CB594A11402FB40010EB83 /* chimeras */ = { + A7E9BA4F12D398D700DA6239 /* clearcut */ = { isa = PBXGroup; children = ( - A7DA2011113FECD400BF472F /* chimera.cpp */, - A7DA2012113FECD400BF472F /* chimera.h */, - A7DA1FF9113FECD400BF472F /* bellerophon.cpp */, - A7DA1FFA113FECD400BF472F /* bellerophon.h */, - A7DA200D113FECD400BF472F /* ccode.cpp */, - A7DA200E113FECD400BF472F /* ccode.h */, - A7DA2013113FECD400BF472F /* chimeracheckrdp.cpp */, - A7DA2014113FECD400BF472F /* chimeracheckrdp.h */, - A7DA2015113FECD400BF472F /* chimerarealigner.cpp */, - A7DA2016113FECD400BF472F /* chimerarealigner.h */, - A7DA2019113FECD400BF472F /* chimeraslayer.cpp */, - A7DA201A113FECD400BF472F /* chimeraslayer.h */, - A7DA2038113FECD400BF472F /* decalc.cpp */, - A7DA2039113FECD400BF472F /* decalc.h */, - A7DA2095113FECD400BF472F /* maligner.cpp */, - A7DA2096113FECD400BF472F /* maligner.h */, - A7DA20C8113FECD400BF472F /* pintail.cpp */, - A7DA20C9113FECD400BF472F /* pintail.h */, - A7DA2145113FECD400BF472F /* slayer.cpp */, - A7DA2146113FECD400BF472F /* slayer.h */, + A7E9B69412D37EC400DA6239 /* clearcut.cpp */, + A7E9B69512D37EC400DA6239 /* clearcut.h */, + A7E9B6B312D37EC400DA6239 /* common.h */, + A7E9B6CF12D37EC400DA6239 /* distclearcut.cpp */, + A7E9B6D012D37EC400DA6239 /* distclearcut.h */, + A7E9B6D312D37EC400DA6239 /* dmat.cpp */, + A7E9B6D412D37EC400DA6239 /* dmat.h */, + A7E9B6DC12D37EC400DA6239 /* fasta.cpp */, + A7E9B6DD12D37EC400DA6239 /* fasta.h */, + A7E9B6FD12D37EC400DA6239 /* getopt_long.h */, + A7E9B6FC12D37EC400DA6239 /* getopt_long.cpp */, ); - name = chimeras; + name = clearcut; sourceTree = ""; }; - A7CB5953114033220010EB83 /* read */ = { + A7E9BA5312D39A5E00DA6239 /* read */ = { isa = PBXGroup; children = ( - A7DA2051113FECD400BF472F /* formatcolumn.cpp */, - A7DA2052113FECD400BF472F /* formatcolumn.h */, - A7DA2053113FECD400BF472F /* 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defaultConfigurationName = Release; diff --git a/bellerophon.cpp b/bellerophon.cpp index 761d291..6e1e242 100644 --- a/bellerophon.cpp +++ b/bellerophon.cpp @@ -535,7 +535,7 @@ int Bellerophon::createSparseMatrix(int startSeq, int endSeq, SparseMatrix* spar int Bellerophon::generatePreferences(vector left, vector right, int mid){ try { - float dme = 0.0; + //float dme = 0.0; SeqMap::iterator itR; SeqMap::iterator itL; diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp index 85c70f0..5998726 100644 --- a/clustersplitcommand.cpp +++ b/clustersplitcommand.cpp @@ -538,7 +538,6 @@ int ClusterSplitCommand::execute(){ //for each file group figure out which process will complete it //want to divide the load intelligently so the big files are spread between processes - int count = 1; for (int i = 0; i < distName.size(); i++) { int processToAssign = (i+1) % processors; if (processToAssign == 0) { processToAssign = processors; } @@ -991,9 +990,7 @@ vector ClusterSplitCommand::cluster(vector< map > distNa m->openOutputFile(fileroot+ tag + ".list", listFile); listFileNames.push_back(fileroot+ tag + ".list"); - - time_t estart = time(NULL); - + float previousDist = 0.00000; float rndPreviousDist = 0.00000; diff --git a/flowdata.cpp b/flowdata.cpp index a172a03..eb6f9bf 100644 --- a/flowdata.cpp +++ b/flowdata.cpp @@ -68,7 +68,7 @@ bool FlowData::getNext(ifstream& flowFile){ void FlowData::updateEndFlow(){ try{ - int currLength = 0; + //int currLength = 0; float maxIntensity = (float) maxHomoP + 0.49; int deadSpot = 0; diff --git a/getlineagecommand.cpp b/getlineagecommand.cpp index 8a825a1..4231435 100644 --- a/getlineagecommand.cpp +++ b/getlineagecommand.cpp @@ -542,7 +542,7 @@ int GetLineageCommand::readTax(){ m->openInputFile(taxfile, in); string name, tax; - bool wroteSomething = false; + //bool wroteSomething = false; bool taxonsHasConfidence = false; vector< map > searchTaxons; diff --git a/mothurout.cpp b/mothurout.cpp index 54cf25d..27b36ce 100644 --- a/mothurout.cpp +++ b/mothurout.cpp @@ -927,7 +927,7 @@ vector MothurOut::setFilePosFasta(string filename, int& num) in.seekg(size); - while(char c = in.get()){ + while(in.get()){ if(in.eof()) { break; } else { size++; } } diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp index 58140ab..fe6d4dd 100644 --- a/seqerrorcommand.cpp +++ b/seqerrorcommand.cpp @@ -355,9 +355,7 @@ int SeqErrorCommand::execute(){ } queryFile.close(); - - int total = 0; - + if(qualFileName != "" && reportFileName != ""){ string errorQualityFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.quality"; ofstream errorQualityFile; diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp index 3b21d31..b098f8f 100644 --- a/trimflowscommand.cpp +++ b/trimflowscommand.cpp @@ -775,7 +775,6 @@ int TrimFlowsCommand::stripForward(Sequence& seq, int& group){ oligo = oligo.substr(0,alnLength); temp = temp.substr(0,alnLength); - int newStart=0; int numDiff = countDiffs(oligo, temp); if(numDiff < minDiff){ diff --git a/weighted.cpp b/weighted.cpp index 1ce6230..24adbba 100644 --- a/weighted.cpp +++ b/weighted.cpp @@ -73,7 +73,6 @@ EstOutput Weighted::createProcesses(Tree* t, vector< vector > namesOfGro try { #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) int process = 1; - int num = 0; vector processIDS; EstOutput results; @@ -204,9 +203,7 @@ EstOutput Weighted::driver(Tree* t, vector< vector > namesOfGroupCombos, for (int h = start; h < (start+num); h++) { //report progress m->mothurOut("Processing combo: " + toString(h)); m->mothurOutEndLine(); - - int numLeaves = t->getNumLeaves(); - + string groupA = namesOfGroupCombos[h][0]; string groupB = namesOfGroupCombos[h][1];