X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=4d37747693cceafd0d66ea97075c0ca07cc94ec0;hb=4160a27002f4a3ca436fcd62eca0366b09f8e901;hp=1b87a4f360376eb978f94c7a1e846ec2a18ffb7c;hpb=d04f948b1a2a1a2984fc4a45d04403b8c121c5bc;p=mothur.git diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index 1b87a4f..4d37747 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -7,10 +7,18 @@ objects = { /* Begin PBXBuildFile section */ + 7E6BE10A12F710D8007ADDBE /* refchimeratest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */; }; 8DD76FB00486AB0100D96B5E /* mothur.1 in CopyFiles */ = {isa = PBXBuildFile; fileRef = C6A0FF2C0290799A04C91782 /* mothur.1 */; }; A70332B712D3A13400761E33 /* makefile in Sources */ = {isa = PBXBuildFile; fileRef = A70332B512D3A13400761E33 /* makefile */; }; A713EBAC12DC7613000092AC /* readphylipvector.cpp in 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path = setcurrentcommand.h; sourceTree = ""; }; + A7FE7E6C13311EA400F7B327 /* setcurrentcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = setcurrentcommand.cpp; sourceTree = ""; }; C6A0FF2C0290799A04C91782 /* mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = mothur.1; sourceTree = ""; }; /* End PBXFileReference section */ @@ -899,6 +927,7 @@ 08FB7795FE84155DC02AAC07 /* Source */ = { isa = PBXGroup; children = ( + A7A61F1A130035C800E05B6B /* LICENSE */, A70332B512D3A13400761E33 /* makefile */, A7E9B65912D37EC300DA6239 /* averagelinkage.cpp */, A7E9BA4F12D398D700DA6239 /* clearcut */, @@ -918,8 +947,10 @@ A7E9B6B012D37EC400DA6239 /* commandfactory.hpp */, A7E9B6B112D37EC400DA6239 /* commandoptionparser.cpp */, A7E9B6B212D37EC400DA6239 /* commandoptionparser.hpp */, + A7DAAFA3133A254E003956EB /* commandparameter.h */, A7E9B6B412D37EC400DA6239 /* completelinkage.cpp */, A7E9BA4212D3960D00DA6239 /* containers */, + A7AACFBA132FE008003D6C4D /* currentfile.h */, A7E9B6C912D37EC400DA6239 /* display.h */, A7E9B6D112D37EC400DA6239 /* dlibshuff.cpp */, A7E9B6D212D37EC400DA6239 /* dlibshuff.h */, @@ -928,8 +959,6 @@ A7E9B6DB12D37EC400DA6239 /* engine.hpp */, A7E9B6E012D37EC400DA6239 /* fileoutput.cpp */, A7E9B6E112D37EC400DA6239 /* fileoutput.h */, - A7E9B70C12D37EC400DA6239 /* globaldata.cpp */, - A7E9B70D12D37EC400DA6239 /* globaldata.hpp */, A7E9B71112D37EC400DA6239 /* gotohoverlap.hpp */, A7E9B71012D37EC400DA6239 /* gotohoverlap.cpp */, A7E9B71812D37EC400DA6239 /* hcluster.cpp */, @@ -949,6 +978,12 @@ A7E9B75C12D37EC400DA6239 /* mothur.h */, A7E9B75D12D37EC400DA6239 /* mothurout.cpp */, A7E9B75E12D37EC400DA6239 /* mothurout.h */, + A7E9B76112D37EC400DA6239 /* nast.cpp */, + A7E9B76212D37EC400DA6239 /* nast.hpp */, + A7E9B76312D37EC400DA6239 /* nastreport.cpp */, + A7E9B76412D37EC400DA6239 /* nastreport.hpp */, + A7E9B76712D37EC400DA6239 /* noalign.cpp */, + A7E9B76812D37EC400DA6239 /* noalign.hpp */, A7E9B76512D37EC400DA6239 /* needlemanoverlap.cpp */, A7E9B76612D37EC400DA6239 /* needlemanoverlap.hpp */, A7E9B77012D37EC400DA6239 /* observable.h */, @@ -965,19 +1000,15 @@ A7E9B7A912D37EC400DA6239 /* rarefact.cpp */, A7E9B7AA12D37EC400DA6239 /* rarefact.h */, A7E9B7AD12D37EC400DA6239 /* rarefactioncurvedata.h */, + 7E6BE10812F710D8007ADDBE /* refchimeratest.h */, + 7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */, 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 */, + A7E9B83112D37EC400DA6239 /* slibshuff.h */, A7E9B85212D37EC400DA6239 /* suffixdb.hpp */, A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */, A7E9B85412D37EC400DA6239 /* suffixnodes.hpp */, @@ -1006,204 +1037,222 @@ isa = PBXGroup; children = ( A7E9B6AE12D37EC400DA6239 /* command.hpp */, - A7E9B65112D37EC300DA6239 /* aligncommand.cpp */, A7E9B65212D37EC300DA6239 /* aligncommand.h */, - A7E9B66012D37EC300DA6239 /* binsequencecommand.cpp */, + A7E9B65112D37EC300DA6239 /* aligncommand.cpp */, + A7A61F2B130062E000E05B6B /* amovacommand.h */, + A7A61F2C130062E000E05B6B /* amovacommand.cpp */, + A71CB15F130B04A2001E7287 /* anosimcommand.h */, + A71CB15E130B04A2001E7287 /* anosimcommand.cpp */, A7E9B66112D37EC300DA6239 /* binsequencecommand.h */, - A7E9B66A12D37EC400DA6239 /* bootstrapsharedcommand.cpp */, + A7E9B66012D37EC300DA6239 /* binsequencecommand.cpp */, A7E9B66B12D37EC400DA6239 /* bootstrapsharedcommand.h */, - A7E9B67212D37EC400DA6239 /* catchallcommand.cpp */, + A7E9B66A12D37EC400DA6239 /* bootstrapsharedcommand.cpp */, A7E9B67312D37EC400DA6239 /* catchallcommand.h */, - A7E9B67A12D37EC400DA6239 /* chimerabellerophoncommand.cpp */, + A7E9B67212D37EC400DA6239 /* catchallcommand.cpp */, A7E9B67B12D37EC400DA6239 /* chimerabellerophoncommand.h */, - A7E9B67C12D37EC400DA6239 /* chimeraccodecommand.cpp */, + A7E9B67A12D37EC400DA6239 /* chimerabellerophoncommand.cpp */, A7E9B67D12D37EC400DA6239 /* chimeraccodecommand.h */, - A7E9B67E12D37EC400DA6239 /* chimeracheckcommand.cpp */, + A7E9B67C12D37EC400DA6239 /* chimeraccodecommand.cpp */, A7E9B67F12D37EC400DA6239 /* chimeracheckcommand.h */, - A7E9B68212D37EC400DA6239 /* chimerapintailcommand.cpp */, + A7E9B67E12D37EC400DA6239 /* chimeracheckcommand.cpp */, A7E9B68312D37EC400DA6239 /* chimerapintailcommand.h */, - A7E9B68612D37EC400DA6239 /* chimeraseqscommand.cpp */, - A7E9B68712D37EC400DA6239 /* chimeraseqscommand.h */, - A7E9B68A12D37EC400DA6239 /* chimeraslayercommand.cpp */, + A7E9B68212D37EC400DA6239 /* chimerapintailcommand.cpp */, A7E9B68B12D37EC400DA6239 /* chimeraslayercommand.h */, - A7E9B68C12D37EC400DA6239 /* chopseqscommand.cpp */, + A7E9B68A12D37EC400DA6239 /* chimeraslayercommand.cpp */, A7E9B68D12D37EC400DA6239 /* chopseqscommand.h */, - A7E9B69012D37EC400DA6239 /* classifyotucommand.cpp */, + A7E9B68C12D37EC400DA6239 /* chopseqscommand.cpp */, A7E9B69112D37EC400DA6239 /* classifyotucommand.h */, - A7E9B69212D37EC400DA6239 /* classifyseqscommand.cpp */, + A7E9B69012D37EC400DA6239 /* classifyotucommand.cpp */, A7E9B69312D37EC400DA6239 /* classifyseqscommand.h */, - A7E9B69612D37EC400DA6239 /* clearcutcommand.cpp */, + A7E9B69212D37EC400DA6239 /* classifyseqscommand.cpp */, A7E9B69712D37EC400DA6239 /* clearcutcommand.h */, - A7E9B69C12D37EC400DA6239 /* clustercommand.cpp */, + A7E9B69612D37EC400DA6239 /* clearcutcommand.cpp */, A7E9B69D12D37EC400DA6239 /* clustercommand.h */, - A7E9B69E12D37EC400DA6239 /* clusterdoturcommand.cpp */, + A7E9B69C12D37EC400DA6239 /* clustercommand.cpp */, A7E9B69F12D37EC400DA6239 /* clusterdoturcommand.h */, - A7E9B6A012D37EC400DA6239 /* clusterfragmentscommand.cpp */, + A7E9B69E12D37EC400DA6239 /* clusterdoturcommand.cpp */, A7E9B6A112D37EC400DA6239 /* clusterfragmentscommand.h */, - A7E9B6A212D37EC400DA6239 /* clustersplitcommand.cpp */, + A7E9B6A012D37EC400DA6239 /* clusterfragmentscommand.cpp */, A7E9B6A312D37EC400DA6239 /* clustersplitcommand.h */, - A7E9B6A812D37EC400DA6239 /* collectcommand.cpp */, + A7E9B6A212D37EC400DA6239 /* clustersplitcommand.cpp */, A7E9B6A912D37EC400DA6239 /* collectcommand.h */, - A7E9B6AC12D37EC400DA6239 /* collectsharedcommand.cpp */, + A7E9B6A812D37EC400DA6239 /* collectcommand.cpp */, A7E9B6AD12D37EC400DA6239 /* collectsharedcommand.h */, - A7E9B6B512D37EC400DA6239 /* consensuscommand.cpp */, + A7E9B6AC12D37EC400DA6239 /* collectsharedcommand.cpp */, A7E9B6B612D37EC400DA6239 /* consensuscommand.h */, - A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */, + A7E9B6B512D37EC400DA6239 /* consensuscommand.cpp */, A7E9B6B812D37EC400DA6239 /* consensusseqscommand.h */, - A7E9B6B912D37EC400DA6239 /* corraxescommand.cpp */, + A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */, A7E9B6BA12D37EC400DA6239 /* corraxescommand.h */, - A7E9B6C312D37EC400DA6239 /* deconvolutecommand.cpp */, + A7E9B6B912D37EC400DA6239 /* corraxescommand.cpp */, A7E9B6C412D37EC400DA6239 /* deconvolutecommand.h */, - A7E9B6C512D37EC400DA6239 /* degapseqscommand.cpp */, + A7E9B6C312D37EC400DA6239 /* deconvolutecommand.cpp */, A7E9B6C612D37EC400DA6239 /* degapseqscommand.h */, - A7E9B6C712D37EC400DA6239 /* deuniqueseqscommand.cpp */, + A7E9B6C512D37EC400DA6239 /* degapseqscommand.cpp */, A7E9B6C812D37EC400DA6239 /* deuniqueseqscommand.h */, - A7E9B6CB12D37EC400DA6239 /* distancecommand.cpp */, + A7E9B6C712D37EC400DA6239 /* deuniqueseqscommand.cpp */, A7E9B6CC12D37EC400DA6239 /* distancecommand.h */, - A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */, + A7E9B6CB12D37EC400DA6239 /* distancecommand.cpp */, A7E9B6E412D37EC400DA6239 /* filterseqscommand.h */, - A7E9B6F212D37EC400DA6239 /* getgroupcommand.cpp */, + A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */, + A778FE69134CA6CA00C0BA33 /* getcommandinfocommand.h */, + A778FE6A134CA6CA00C0BA33 /* getcommandinfocommand.cpp */, + A7FE7C3E1330EA1000F7B327 /* getcurrentcommand.h */, + A7FE7C3F1330EA1000F7B327 /* getcurrentcommand.cpp */, A7E9B6F312D37EC400DA6239 /* getgroupcommand.h */, - A7E9B6F412D37EC400DA6239 /* getgroupscommand.cpp */, + A7E9B6F212D37EC400DA6239 /* getgroupcommand.cpp */, A7E9B6F512D37EC400DA6239 /* getgroupscommand.h */, - A7E9B6F612D37EC400DA6239 /* getlabelcommand.cpp */, + A7E9B6F412D37EC400DA6239 /* getgroupscommand.cpp */, A7E9B6F712D37EC400DA6239 /* getlabelcommand.h */, - A7E9B6F812D37EC400DA6239 /* getlineagecommand.cpp */, + A7E9B6F612D37EC400DA6239 /* getlabelcommand.cpp */, A7E9B6F912D37EC400DA6239 /* getlineagecommand.h */, - A7E9B6FA12D37EC400DA6239 /* getlistcountcommand.cpp */, + A7E9B6F812D37EC400DA6239 /* getlineagecommand.cpp */, A7E9B6FB12D37EC400DA6239 /* getlistcountcommand.h */, - A7E9B6FE12D37EC400DA6239 /* getoturepcommand.cpp */, + A7E9B6FA12D37EC400DA6239 /* getlistcountcommand.cpp */, A7E9B6FF12D37EC400DA6239 /* getoturepcommand.h */, - A7E9B70012D37EC400DA6239 /* getotuscommand.cpp */, + A7E9B6FE12D37EC400DA6239 /* getoturepcommand.cpp */, A7E9B70112D37EC400DA6239 /* getotuscommand.h */, - A7E9B70212D37EC400DA6239 /* getrabundcommand.cpp */, + A7E9B70012D37EC400DA6239 /* getotuscommand.cpp */, A7E9B70312D37EC400DA6239 /* getrabundcommand.h */, - A7E9B70412D37EC400DA6239 /* getrelabundcommand.cpp */, + A7E9B70212D37EC400DA6239 /* getrabundcommand.cpp */, A7E9B70512D37EC400DA6239 /* getrelabundcommand.h */, - A7E9B70612D37EC400DA6239 /* getsabundcommand.cpp */, + A7E9B70412D37EC400DA6239 /* getrelabundcommand.cpp */, A7E9B70712D37EC400DA6239 /* getsabundcommand.h */, - A7E9B70812D37EC400DA6239 /* getseqscommand.cpp */, + A7E9B70612D37EC400DA6239 /* getsabundcommand.cpp */, A7E9B70912D37EC400DA6239 /* getseqscommand.h */, - A7E9B70A12D37EC400DA6239 /* getsharedotucommand.cpp */, + A7E9B70812D37EC400DA6239 /* getseqscommand.cpp */, A7E9B70B12D37EC400DA6239 /* getsharedotucommand.h */, - A7E9B71A12D37EC400DA6239 /* hclustercommand.cpp */, + A7E9B70A12D37EC400DA6239 /* getsharedotucommand.cpp */, A7E9B71B12D37EC400DA6239 /* hclustercommand.h */, - A7E9B71E12D37EC400DA6239 /* heatmapcommand.cpp */, + A7E9B71A12D37EC400DA6239 /* hclustercommand.cpp */, A7E9B71F12D37EC400DA6239 /* heatmapcommand.h */, - A7E9B72212D37EC400DA6239 /* heatmapsimcommand.cpp */, + A7E9B71E12D37EC400DA6239 /* heatmapcommand.cpp */, A7E9B72312D37EC400DA6239 /* heatmapsimcommand.h */, - A7E9B72812D37EC400DA6239 /* helpcommand.cpp */, + A7E9B72212D37EC400DA6239 /* heatmapsimcommand.cpp */, A7E9B72912D37EC400DA6239 /* helpcommand.h */, - A7E9B72B12D37EC400DA6239 /* indicatorcommand.cpp */, + A7E9B72812D37EC400DA6239 /* helpcommand.cpp */, + A75790571301749D00A30DAB /* homovacommand.h */, + A75790581301749D00A30DAB /* homovacommand.cpp */, A7E9B72C12D37EC400DA6239 /* indicatorcommand.h */, - A7E9B73B12D37EC400DA6239 /* libshuffcommand.cpp */, + A7E9B72B12D37EC400DA6239 /* indicatorcommand.cpp */, A7E9B73C12D37EC400DA6239 /* libshuffcommand.h */, - A7E9B73D12D37EC400DA6239 /* listseqscommand.cpp */, + A7E9B73B12D37EC400DA6239 /* libshuffcommand.cpp */, A7E9B73E12D37EC400DA6239 /* listseqscommand.h */, - A7E9B74312D37EC400DA6239 /* makegroupcommand.cpp */, + A7E9B73D12D37EC400DA6239 /* listseqscommand.cpp */, + A7FA10001302E096003860FE /* mantelcommand.h */, + A7FA10011302E096003860FE /* mantelcommand.cpp */, + A799F5B71309A3E000AEEFA0 /* makefastqcommand.h */, + A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */, A7E9B74412D37EC400DA6239 /* makegroupcommand.h */, - A7E9B74912D37EC400DA6239 /* matrixoutputcommand.cpp */, + A7E9B74312D37EC400DA6239 /* makegroupcommand.cpp */, A7E9B74A12D37EC400DA6239 /* matrixoutputcommand.h */, - A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */, + A7E9B74912D37EC400DA6239 /* matrixoutputcommand.cpp */, A7E9B75412D37EC400DA6239 /* mergefilecommand.h */, - A7E9B75712D37EC400DA6239 /* metastatscommand.cpp */, + A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */, + A71FE12A12EDF72400963CA7 /* mergegroupscommand.h */, + A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */, A7E9B75812D37EC400DA6239 /* metastatscommand.h */, - A7E9B75912D37EC400DA6239 /* mgclustercommand.cpp */, + A7E9B75712D37EC400DA6239 /* metastatscommand.cpp */, A7E9B75A12D37EC400DA6239 /* mgclustercommand.h */, + A7E9B75912D37EC400DA6239 /* mgclustercommand.cpp */, A7E9B76A12D37EC400DA6239 /* nocommands.h */, A7E9B76912D37EC400DA6239 /* nocommands.cpp */, - A7E9B76B12D37EC400DA6239 /* normalizesharedcommand.cpp */, A7E9B76C12D37EC400DA6239 /* normalizesharedcommand.h */, + A7E9B76B12D37EC400DA6239 /* normalizesharedcommand.cpp */, A713EBEB12DC7C5E000092AC /* nmdscommand.h */, A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */, - A7E9B77912D37EC400DA6239 /* otuhierarchycommand.cpp */, A7E9B77A12D37EC400DA6239 /* otuhierarchycommand.h */, - A7E9B77D12D37EC400DA6239 /* pairwiseseqscommand.cpp */, + A7E9B77912D37EC400DA6239 /* otuhierarchycommand.cpp */, A7E9B77E12D37EC400DA6239 /* pairwiseseqscommand.h */, - A7E9B77F12D37EC400DA6239 /* parsefastaqcommand.cpp */, + A7E9B77D12D37EC400DA6239 /* pairwiseseqscommand.cpp */, A7E9B78012D37EC400DA6239 /* parsefastaqcommand.h */, - A7E9B78112D37EC400DA6239 /* parselistscommand.cpp */, + A7E9B77F12D37EC400DA6239 /* parsefastaqcommand.cpp */, A7E9B78212D37EC400DA6239 /* parselistscommand.h */, - A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */, + A7E9B78112D37EC400DA6239 /* parselistscommand.cpp */, A7E9B78612D37EC400DA6239 /* parsimonycommand.h */, + A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */, A7FC486512D795D60055BC5C /* pcacommand.h */, A7FC486612D795D60055BC5C /* pcacommand.cpp */, - A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */, A7E9B78812D37EC400DA6239 /* pcoacommand.h */, - A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */, + A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */, A7E9B78C12D37EC400DA6239 /* phylodiversitycommand.h */, - A7E9B79112D37EC400DA6239 /* phylotypecommand.cpp */, + A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */, A7E9B79212D37EC400DA6239 /* phylotypecommand.h */, - A7E9B79512D37EC400DA6239 /* pipelinepdscommand.cpp */, + A7E9B79112D37EC400DA6239 /* phylotypecommand.cpp */, A7E9B79612D37EC400DA6239 /* pipelinepdscommand.h */, - A7E9B79712D37EC400DA6239 /* preclustercommand.cpp */, + A7E9B79512D37EC400DA6239 /* pipelinepdscommand.cpp */, A7E9B79812D37EC400DA6239 /* preclustercommand.h */, - A7E9B7A112D37EC400DA6239 /* quitcommand.cpp */, + A7E9B79712D37EC400DA6239 /* preclustercommand.cpp */, A7E9B7A212D37EC400DA6239 /* quitcommand.h */, - A7E9B7AB12D37EC400DA6239 /* rarefactcommand.cpp */, + A7E9B7A112D37EC400DA6239 /* quitcommand.cpp */, A7E9B7AC12D37EC400DA6239 /* rarefactcommand.h */, - A7E9B7AE12D37EC400DA6239 /* rarefactsharedcommand.cpp */, + A7E9B7AB12D37EC400DA6239 /* rarefactcommand.cpp */, A7E9B7AF12D37EC400DA6239 /* rarefactsharedcommand.h */, - A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */, + A7E9B7AE12D37EC400DA6239 /* rarefactsharedcommand.cpp */, A7E9B7B712D37EC400DA6239 /* readdistcommand.h */, - A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */, + A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */, A7E9B7BC12D37EC400DA6239 /* readotucommand.h */, - A7E9B7C112D37EC400DA6239 /* readtreecommand.cpp */, + A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */, A7E9B7C212D37EC400DA6239 /* readtreecommand.h */, - A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */, + A7E9B7C112D37EC400DA6239 /* readtreecommand.cpp */, A7E9B7C412D37EC400DA6239 /* removegroupscommand.h */, - A7E9B7C512D37EC400DA6239 /* removelineagecommand.cpp */, + A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */, A7E9B7C612D37EC400DA6239 /* removelineagecommand.h */, - A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */, + A7E9B7C512D37EC400DA6239 /* removelineagecommand.cpp */, A7E9B7C812D37EC400DA6239 /* removeotuscommand.h */, - A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */, + A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */, + A727864212E9E28C00F86ABA /* removerarecommand.h */, + A727864312E9E28C00F86ABA /* removerarecommand.cpp */, A7E9B7CA12D37EC400DA6239 /* removeseqscommand.h */, - A7E9B7CD12D37EC400DA6239 /* reversecommand.cpp */, + A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */, A7E9B7CE12D37EC400DA6239 /* reversecommand.h */, - A7E9B7D112D37EC400DA6239 /* screenseqscommand.cpp */, + A7E9B7CD12D37EC400DA6239 /* reversecommand.cpp */, A7E9B7D212D37EC400DA6239 /* screenseqscommand.h */, - A7E9B7D312D37EC400DA6239 /* secondarystructurecommand.cpp */, + A7E9B7D112D37EC400DA6239 /* screenseqscommand.cpp */, A7E9B7D412D37EC400DA6239 /* secondarystructurecommand.h */, - A7E9B7D512D37EC400DA6239 /* sensspeccommand.cpp */, + A7E9B7D312D37EC400DA6239 /* secondarystructurecommand.cpp */, A7E9B7D612D37EC400DA6239 /* sensspeccommand.h */, - A7E9B7D712D37EC400DA6239 /* seqerrorcommand.cpp */, + A7E9B7D512D37EC400DA6239 /* sensspeccommand.cpp */, A7E9B7D812D37EC400DA6239 /* seqerrorcommand.h */, - A7E9B7D912D37EC400DA6239 /* seqsummarycommand.cpp */, + A7E9B7D712D37EC400DA6239 /* seqerrorcommand.cpp */, A7E9B7DA12D37EC400DA6239 /* seqsummarycommand.h */, - A7E9B7DF12D37EC400DA6239 /* setdircommand.cpp */, + A7E9B7D912D37EC400DA6239 /* seqsummarycommand.cpp */, + A7FE7E6B13311EA400F7B327 /* setcurrentcommand.h */, + A7FE7E6C13311EA400F7B327 /* setcurrentcommand.cpp */, A7E9B7E012D37EC400DA6239 /* setdircommand.h */, - A7E9B7E112D37EC400DA6239 /* setlogfilecommand.cpp */, + A7E9B7DF12D37EC400DA6239 /* setdircommand.cpp */, A7E9B7E212D37EC400DA6239 /* setlogfilecommand.h */, - A7E9B7E312D37EC400DA6239 /* sffinfocommand.cpp */, + A7E9B7E112D37EC400DA6239 /* setlogfilecommand.cpp */, A7E9B7E412D37EC400DA6239 /* sffinfocommand.h */, - A7E9B7F212D37EC400DA6239 /* sharedcommand.cpp */, + A7E9B7E312D37EC400DA6239 /* sffinfocommand.cpp */, A7E9B7F312D37EC400DA6239 /* sharedcommand.h */, - A7E9B82712D37EC400DA6239 /* shhhercommand.cpp */, + A7E9B7F212D37EC400DA6239 /* sharedcommand.cpp */, A7E9B82812D37EC400DA6239 /* shhhercommand.h */, - A7E9B83F12D37EC400DA6239 /* splitabundcommand.cpp */, + A7E9B82712D37EC400DA6239 /* shhhercommand.cpp */, A7E9B84012D37EC400DA6239 /* splitabundcommand.h */, - A7E9B84112D37EC400DA6239 /* splitgroupscommand.cpp */, + A7E9B83F12D37EC400DA6239 /* splitabundcommand.cpp */, A7E9B84212D37EC400DA6239 /* splitgroupscommand.h */, - A7E9B84F12D37EC400DA6239 /* subsamplecommand.cpp */, + A7E9B84112D37EC400DA6239 /* splitgroupscommand.cpp */, A7E9B85012D37EC400DA6239 /* subsamplecommand.h */, - A7E9B85712D37EC400DA6239 /* summarycommand.cpp */, + A7E9B84F12D37EC400DA6239 /* subsamplecommand.cpp */, A7E9B85812D37EC400DA6239 /* summarycommand.h */, - A7E9B85912D37EC400DA6239 /* summarysharedcommand.cpp */, + A7E9B85712D37EC400DA6239 /* summarycommand.cpp */, A7E9B85A12D37EC400DA6239 /* summarysharedcommand.h */, - A7E9B85B12D37EC400DA6239 /* systemcommand.cpp */, + A7E9B85912D37EC400DA6239 /* summarysharedcommand.cpp */, A7E9B85C12D37EC400DA6239 /* systemcommand.h */, - A7E9B86212D37EC400DA6239 /* treegroupscommand.cpp */, + A7E9B85B12D37EC400DA6239 /* systemcommand.cpp */, A7E9B86312D37EC400DA6239 /* treegroupscommand.h */, - A7E9B86812D37EC400DA6239 /* trimflowscommand.cpp */, + A7E9B86212D37EC400DA6239 /* treegroupscommand.cpp */, A7E9B86912D37EC400DA6239 /* trimflowscommand.h */, - A7E9B86A12D37EC400DA6239 /* trimseqscommand.cpp */, + A7E9B86812D37EC400DA6239 /* trimflowscommand.cpp */, A7E9B86B12D37EC400DA6239 /* trimseqscommand.h */, - A7E9B86C12D37EC400DA6239 /* unifracunweightedcommand.cpp */, + A7E9B86A12D37EC400DA6239 /* trimseqscommand.cpp */, A7E9B86D12D37EC400DA6239 /* unifracunweightedcommand.h */, - A7E9B86E12D37EC400DA6239 /* unifracweightedcommand.cpp */, + A7E9B86C12D37EC400DA6239 /* unifracunweightedcommand.cpp */, A7E9B86F12D37EC400DA6239 /* unifracweightedcommand.h */, - A7E9B87A12D37EC400DA6239 /* venncommand.cpp */, + A7E9B86E12D37EC400DA6239 /* unifracweightedcommand.cpp */, A7E9B87B12D37EC400DA6239 /* venncommand.h */, + A7E9B87A12D37EC400DA6239 /* venncommand.cpp */, ); name = commands; sourceTree = ""; @@ -1211,6 +1260,7 @@ A7E9BA3F12D395F700DA6239 /* calculators */ = { isa = PBXGroup; children = ( + 7E78911B135F3E8600E725D2 /* eachgapdistignorens.h */, A7E9B64F12D37EC300DA6239 /* ace.cpp */, A7E9B65012D37EC300DA6239 /* ace.h */, A7E9B65E12D37EC300DA6239 /* bergerparker.cpp */, @@ -1360,12 +1410,12 @@ A7E9B84D12D37EC400DA6239 /* structpearson.cpp */, A7E9B84E12D37EC400DA6239 /* structpearson.h */, A7E9B86112D37EC400DA6239 /* treecalculator.h */, - A7E9B87012D37EC400DA6239 /* unweighted.cpp */, A7E9B87112D37EC400DA6239 /* unweighted.h */, + A7E9B87012D37EC400DA6239 /* unweighted.cpp */, A7E9B87212D37EC400DA6239 /* uvest.cpp */, A7E9B87312D37EC400DA6239 /* uvest.h */, - A7E9B87C12D37EC400DA6239 /* weighted.cpp */, A7E9B87D12D37EC400DA6239 /* weighted.h */, + A7E9B87C12D37EC400DA6239 /* weighted.cpp */, A7E9B87F12D37EC400DA6239 /* whittaker.cpp */, A7E9B88012D37EC400DA6239 /* whittaker.h */, ); @@ -1422,8 +1472,8 @@ A7E9B7DE12D37EC400DA6239 /* sequencedb.h */, A7E9B80412D37EC400DA6239 /* sharedlistvector.cpp */, A7E9B80512D37EC400DA6239 /* sharedlistvector.h */, - A7E9B80D12D37EC400DA6239 /* sharedordervector.cpp */, A7E9B80E12D37EC400DA6239 /* sharedordervector.h */, + A7E9B80D12D37EC400DA6239 /* sharedordervector.cpp */, A7E9B80F12D37EC400DA6239 /* sharedrabundfloatvector.cpp */, A7E9B81012D37EC400DA6239 /* sharedrabundfloatvector.h */, A7E9B81112D37EC400DA6239 /* sharedrabundvector.cpp */, @@ -1455,10 +1505,10 @@ A7E9B68112D37EC400DA6239 /* chimeracheckrdp.h */, A7E9B68412D37EC400DA6239 /* chimerarealigner.cpp */, A7E9B68512D37EC400DA6239 /* chimerarealigner.h */, + A7E9B6C212D37EC400DA6239 /* decalc.h */, + A7E9B6C112D37EC400DA6239 /* decalc.cpp */, A7E9B68812D37EC400DA6239 /* chimeraslayer.cpp */, A7E9B68912D37EC400DA6239 /* chimeraslayer.h */, - A7E9B6C112D37EC400DA6239 /* decalc.cpp */, - A7E9B6C212D37EC400DA6239 /* decalc.h */, A7E9B74612D37EC400DA6239 /* maligner.h */, A7E9B74512D37EC400DA6239 /* maligner.cpp */, A7E9B79312D37EC400DA6239 /* pintail.cpp */, @@ -1523,8 +1573,6 @@ A7E9B7B412D37EC400DA6239 /* readcolumn.cpp */, A7E9B7B512D37EC400DA6239 /* readcolumn.h */, A7E9B7B812D37EC400DA6239 /* readmatrix.hpp */, - A7E9B7B912D37EC400DA6239 /* readotu.cpp */, - A7E9B7BA12D37EC400DA6239 /* readotu.h */, A7E9B7BD12D37EC400DA6239 /* readphylip.cpp */, A7E9B7BE12D37EC400DA6239 /* readphylip.h */, A7E9B7BF12D37EC400DA6239 /* readtree.cpp */, @@ -1580,7 +1628,10 @@ /* Begin PBXProject section */ 08FB7793FE84155DC02AAC07 /* Project object */ = { isa = PBXProject; - buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */; + attributes = { + ORGANIZATIONNAME = "Schloss Lab"; + }; + buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */; compatibilityVersion = "Xcode 3.1"; developmentRegion = English; hasScannedForEncodings = 1; @@ -1632,7 +1683,6 @@ A7E9B89A12D37EC400DA6239 /* chimeracheckrdp.cpp in Sources */, A7E9B89B12D37EC400DA6239 /* chimerapintailcommand.cpp in Sources */, A7E9B89C12D37EC400DA6239 /* chimerarealigner.cpp in Sources */, - A7E9B89D12D37EC400DA6239 /* chimeraseqscommand.cpp in Sources */, A7E9B89E12D37EC400DA6239 /* chimeraslayer.cpp in Sources */, A7E9B89F12D37EC400DA6239 /* chimeraslayercommand.cpp in Sources */, A7E9B8A012D37EC400DA6239 /* chopseqscommand.cpp in Sources */, @@ -1693,7 +1743,6 @@ A7E9B8D712D37EC400DA6239 /* getsabundcommand.cpp in Sources */, A7E9B8D812D37EC400DA6239 /* getseqscommand.cpp in Sources */, A7E9B8D912D37EC400DA6239 /* getsharedotucommand.cpp in Sources */, - A7E9B8DA12D37EC400DA6239 /* globaldata.cpp in Sources */, A7E9B8DB12D37EC400DA6239 /* goodscoverage.cpp in Sources */, A7E9B8DC12D37EC400DA6239 /* gotohoverlap.cpp in Sources */, A7E9B8DD12D37EC400DA6239 /* gower.cpp in Sources */, @@ -1776,7 +1825,6 @@ A7E9B92A12D37EC400DA6239 /* readcluster.cpp in Sources */, A7E9B92B12D37EC400DA6239 /* readcolumn.cpp in Sources */, A7E9B92C12D37EC400DA6239 /* readdistcommand.cpp in Sources */, - A7E9B92D12D37EC400DA6239 /* readotu.cpp in Sources */, A7E9B92E12D37EC400DA6239 /* readotucommand.cpp in Sources */, A7E9B92F12D37EC400DA6239 /* readphylip.cpp in Sources */, A7E9B93012D37EC400DA6239 /* readtree.cpp in Sources */, @@ -1880,6 +1928,17 @@ A7FC486712D795D60055BC5C /* pcacommand.cpp in Sources */, A713EBAC12DC7613000092AC /* readphylipvector.cpp in Sources */, A713EBED12DC7C5E000092AC /* nmdscommand.cpp in Sources */, + A727864412E9E28C00F86ABA /* removerarecommand.cpp in Sources */, + A71FE12C12EDF72400963CA7 /* mergegroupscommand.cpp in Sources */, + 7E6BE10A12F710D8007ADDBE /* refchimeratest.cpp in Sources */, + A7A61F2D130062E000E05B6B /* amovacommand.cpp in Sources */, + A75790591301749D00A30DAB /* homovacommand.cpp in Sources */, + A7FA10021302E097003860FE /* mantelcommand.cpp in Sources */, + A799F5B91309A3E000AEEFA0 /* makefastqcommand.cpp in Sources */, + A71CB160130B04A2001E7287 /* anosimcommand.cpp in Sources */, + A7FE7C401330EA1000F7B327 /* getcurrentcommand.cpp in Sources */, + A7FE7E6D13311EA400F7B327 /* setcurrentcommand.cpp in Sources */, + A778FE6B134CA6CA00C0BA33 /* getcommandinfocommand.cpp in Sources */, ); runOnlyForDeploymentPostprocessing = 0; }; @@ -1897,6 +1956,7 @@ GCC_OPTIMIZATION_LEVEL = 0; INSTALL_PATH = /usr/local/bin; PRODUCT_NAME = Mothur; + SDKROOT = macosx10.6; }; name = Debug; }; @@ -1916,22 +1976,24 @@ 1DEB928A08733DD80010E9CD /* Debug */ = { isa = XCBuildConfiguration; buildSettings = { - ARCHS = "$(ARCHS_STANDARD_32_64_BIT)"; + ARCHS = "$(ARCHS_STANDARD_64_BIT)"; DEPLOYMENT_LOCATION = NO; GCC_C_LANGUAGE_STANDARD = gnu99; GCC_OPTIMIZATION_LEVEL = 0; GCC_PREPROCESSOR_DEFINITIONS = ( "MOTHUR_FILES=\"\\\"../release\\\"\"", - "VERSION=\"\\\"1.15.0\\\"\"", - "RELEASE_DATE=\"\\\"12/10/2010\\\"\"", + "VERSION=\"\\\"1.19.0\\\"\"", + "RELEASE_DATE=\"\\\"5/9/2011\\\"\"", ); + GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; GCC_WARN_UNUSED_VARIABLE = YES; INSTALL_PATH = ""; + MACH_O_TYPE = mh_execute; ONLY_ACTIVE_ARCH = YES; OTHER_CPLUSPLUSFLAGS = ( - "-DUSE_READLINE", "-DBIT_VERSION", + "-DUSE_READLINE", "$(OTHER_CFLAGS)", ); OTHER_LDFLAGS = ( @@ -1939,20 +2001,22 @@ "-lreadline", ); PREBINDING = NO; - SDKROOT = macosx10.5; + SDKROOT = macosx10.6; }; name = Debug; }; 1DEB928B08733DD80010E9CD /* Release */ = { isa = XCBuildConfiguration; buildSettings = { - ARCHS = "$(ARCHS_STANDARD_32_64_BIT)"; + ARCHS = "$(ARCHS_STANDARD_64_BIT)"; DEPLOYMENT_LOCATION = NO; GCC_C_LANGUAGE_STANDARD = gnu99; + GCC_GENERATE_DEBUGGING_SYMBOLS = NO; + GCC_MODEL_TUNING = ""; + GCC_OPTIMIZATION_LEVEL = 0; GCC_PREPROCESSOR_DEFINITIONS = ( - "MOTHUR_FILES=\"\\\"../release\\\"\"", - "VERSION=\"\\\"1.15.0\\\"\"", - "RELEASE_DATE=\"\\\"12/10/2010\\\"\"", + "VERSION=\"\\\"1.19.0\\\"\"", + "RELEASE_DATE=\"\\\"5/9/2011\\\"\"", ); GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; @@ -1963,6 +2027,7 @@ GCC_WARN_UNUSED_VALUE = YES; GCC_WARN_UNUSED_VARIABLE = YES; INSTALL_PATH = ""; + MACH_O_TYPE = mh_execute; OTHER_CPLUSPLUSFLAGS = ( "-DUSE_READLINE", "-DBIT_VERSION", @@ -1973,7 +2038,7 @@ "-lreadline", ); PREBINDING = NO; - SDKROOT = macosx10.5; + SDKROOT = macosx10.6; }; name = Release; }; @@ -1989,7 +2054,7 @@ defaultConfigurationIsVisible = 0; defaultConfigurationName = Release; }; - 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */ = { + 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */ = { isa = XCConfigurationList; buildConfigurations = ( 1DEB928A08733DD80010E9CD /* Debug */,