X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=8dcff47032eb79dfd55eaff7658f1b52083d6abb;hb=d5c8caf2d08b7ac6de30e33b1d19cfd246d08f03;hp=a60c51468519eb4acaf570657ee083fcf58b9756;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index a60c514..8dcff47 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -7,6 +7,10 @@ objects = { /* Begin PBXBuildFile section */ + 372E12700F26365B0095CF7E /* readotucommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372E126F0F26365B0095CF7E /* readotucommand.cpp */; }; + 372E12960F263D5A0095CF7E /* readdistcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372E12950F263D5A0095CF7E /* readdistcommand.cpp */; }; + 372E12C10F2648250095CF7E /* readlistcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372E12C00F2648250095CF7E /* readlistcommand.cpp */; }; + 372E12ED0F264D320095CF7E /* commandfactory.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372E12EC0F264D320095CF7E /* commandfactory.cpp */; }; 37D928550F21331F001D4494 /* ace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927B80F21331F001D4494 /* ace.cpp */; }; 37D928560F21331F001D4494 /* averagelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927BA0F21331F001D4494 /* averagelinkage.cpp */; }; 37D928570F21331F001D4494 /* bootstrap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927BB0F21331F001D4494 /* bootstrap.cpp */; }; @@ -17,7 +21,6 @@ 37D9285C0F21331F001D4494 /* collect.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927C50F21331F001D4494 /* collect.cpp */; }; 37D9285D0F21331F001D4494 /* collectcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927C70F21331F001D4494 /* collectcommand.cpp */; }; 37D9285E0F21331F001D4494 /* collectsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */; }; - 37D9285F0F21331F001D4494 /* commandfactory.cpp in Sources */ = {isa = PBXBuildFile; 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fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = ""; }; 37D927BA0F21331F001D4494 /* averagelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = averagelinkage.cpp; sourceTree = ""; }; @@ -121,7 +125,6 @@ 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collectsharedcommand.cpp; sourceTree = ""; }; 37D927CC0F21331F001D4494 /* collectsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectsharedcommand.h; sourceTree = ""; }; 37D927CD0F21331F001D4494 /* command.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = command.hpp; sourceTree = ""; }; - 37D927CE0F21331F001D4494 /* commandfactory.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = commandfactory.cpp; sourceTree = ""; }; 37D927CF0F21331F001D4494 /* commandfactory.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandfactory.hpp; sourceTree = ""; }; 37D927D00F21331F001D4494 /* commandoptionparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = commandoptionparser.cpp; sourceTree = ""; }; 37D927D10F21331F001D4494 /* commandoptionparser.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandoptionparser.hpp; sourceTree = ""; }; @@ -183,20 +186,8 @@ 37D928090F21331F001D4494 /* rarefactioncurvedata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactioncurvedata.h; sourceTree = ""; }; 37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefactsharedcommand.cpp; sourceTree = ""; }; 37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */ = {isa = PBXFileReference; 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lastKnownFileType = sourcecode.cpp.cpp; path = readlistfilecommand.cpp; sourceTree = ""; }; - 37D928110F21331F001D4494 /* readlistfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readlistfilecommand.h; sourceTree = ""; }; 37D928120F21331F001D4494 /* readmatrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readmatrix.cpp; sourceTree = ""; }; 37D928130F21331F001D4494 /* readmatrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = readmatrix.hpp; sourceTree = ""; }; - 37D928140F21331F001D4494 /* readrabundfilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readrabundfilecommand.cpp; sourceTree = ""; }; - 37D928150F21331F001D4494 /* readrabundfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readrabundfilecommand.h; sourceTree = ""; }; - 37D928160F21331F001D4494 /* readsabundfilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readsabundfilecommand.cpp; sourceTree = ""; }; - 37D928170F21331F001D4494 /* readsabundfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readsabundfilecommand.h; sourceTree = ""; }; - 37D928180F21331F001D4494 /* readsharedfilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readsharedfilecommand.cpp; sourceTree = ""; }; - 37D928190F21331F001D4494 /* readsharedfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readsharedfilecommand.h; sourceTree = ""; }; 37D9281A0F21331F001D4494 /* sabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sabundvector.cpp; sourceTree = ""; }; 37D9281B0F21331F001D4494 /* sabundvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sabundvector.hpp; sourceTree = ""; }; 37D9281C0F21331F001D4494 /* sequence.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequence.cpp; sourceTree = ""; }; @@ -256,7 +247,7 @@ 37D928520F21331F001D4494 /* validcommands.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validcommands.h; sourceTree = ""; }; 37D928530F21331F001D4494 /* validparameter.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validparameter.cpp; sourceTree = ""; }; 37D928540F21331F001D4494 /* validparameter.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validparameter.h; sourceTree = ""; }; - 8DD76F6C0486A84900D96B5E /* Mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = Mothur; sourceTree = BUILT_PRODUCTS_DIR; }; + 8DD76F6C0486A84900D96B5E /* mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = mothur; sourceTree = BUILT_PRODUCTS_DIR; }; C6859E8B029090EE04C91782 /* Mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = Mothur.1; sourceTree = ""; }; /* End PBXFileReference section */ @@ -294,8 +285,8 @@ 37D927C90F21331F001D4494 /* collectdisplay.h */, 37D928AC0F213420001D4494 /* containers */, 37D927CA0F21331F001D4494 /* collectorscurvedata.h */, - 37D927CE0F21331F001D4494 /* commandfactory.cpp */, 37D927CF0F21331F001D4494 /* commandfactory.hpp */, + 372E12EC0F264D320095CF7E /* commandfactory.cpp */, 37D927D00F21331F001D4494 /* commandoptionparser.cpp */, 37D927D10F21331F001D4494 /* commandoptionparser.hpp */, 37D927D20F21331F001D4494 /* completelinkage.cpp */, @@ -345,7 +336,7 @@ 1AB674ADFE9D54B511CA2CBB /* Products */ = { isa = PBXGroup; children = ( - 8DD76F6C0486A84900D96B5E /* Mothur */, + 8DD76F6C0486A84900D96B5E /* mothur */, ); name = Products; sourceTree = ""; @@ -422,18 +413,12 @@ 37D928080F21331F001D4494 /* rarefactcommand.h */, 37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */, 37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */, - 37D9280C0F21331F001D4494 /* readdistcolumnfilecommand.cpp */, - 37D9280D0F21331F001D4494 /* readdistcolumnfilecommand.h */, - 37D9280E0F21331F001D4494 /* readdistphylipfilecommand.cpp */, - 37D9280F0F21331F001D4494 /* readdistphylipfilecommand.h */, - 37D928100F21331F001D4494 /* readlistfilecommand.cpp */, - 37D928110F21331F001D4494 /* readlistfilecommand.h */, - 37D928140F21331F001D4494 /* readrabundfilecommand.cpp */, - 37D928150F21331F001D4494 /* readrabundfilecommand.h */, - 37D928160F21331F001D4494 /* readsabundfilecommand.cpp */, - 37D928170F21331F001D4494 /* readsabundfilecommand.h */, - 37D928180F21331F001D4494 /* readsharedfilecommand.cpp */, - 37D928190F21331F001D4494 /* readsharedfilecommand.h */, + 372E12940F263D5A0095CF7E /* readdistcommand.h */, + 372E12950F263D5A0095CF7E /* readdistcommand.cpp */, + 372E126E0F26365B0095CF7E /* readotucommand.h */, + 372E126F0F26365B0095CF7E /* readotucommand.cpp */, + 372E12BF0F2648250095CF7E /* readlistcommand.h */, + 372E12C00F2648250095CF7E /* readlistcommand.cpp */, 37D928260F21331F001D4494 /* sharedcommand.cpp */, 37D928270F21331F001D4494 /* sharedcommand.h */, 37D928460F21331F001D4494 /* summarycommand.cpp */, @@ -496,9 +481,9 @@ /* End PBXGroup section */ /* Begin PBXNativeTarget section */ - 8DD76F620486A84900D96B5E /* Mothur */ = { + 8DD76F620486A84900D96B5E /* mothur */ = { isa = PBXNativeTarget; - buildConfigurationList = 1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "Mothur" */; + buildConfigurationList = 1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "mothur" */; buildPhases = ( 8DD76F640486A84900D96B5E /* Sources */, 8DD76F660486A84900D96B5E /* Frameworks */, @@ -508,10 +493,10 @@ ); dependencies = ( ); - name = Mothur; + name = mothur; productInstallPath = "$(HOME)/bin"; productName = Mothur; - productReference = 8DD76F6C0486A84900D96B5E /* Mothur */; + productReference = 8DD76F6C0486A84900D96B5E /* mothur */; productType = "com.apple.product-type.tool"; }; /* End PBXNativeTarget section */ @@ -526,7 +511,7 @@ projectDirPath = ""; projectRoot = ""; targets = ( - 8DD76F620486A84900D96B5E /* Mothur */, + 8DD76F620486A84900D96B5E /* mothur */, ); }; /* End PBXProject section */ @@ -546,7 +531,6 @@ 37D9285C0F21331F001D4494 /* collect.cpp in Sources */, 37D9285D0F21331F001D4494 /* collectcommand.cpp in Sources */, 37D9285E0F21331F001D4494 /* collectsharedcommand.cpp in Sources */, - 37D9285F0F21331F001D4494 /* commandfactory.cpp in Sources */, 37D928600F21331F001D4494 /* commandoptionparser.cpp in Sources */, 37D928610F21331F001D4494 /* completelinkage.cpp in Sources */, 37D928620F21331F001D4494 /* database.cpp in Sources */, @@ -576,13 +560,7 @@ 37D9287A0F21331F001D4494 /* rarefact.cpp in Sources */, 37D9287B0F21331F001D4494 /* rarefactcommand.cpp in Sources */, 37D9287C0F21331F001D4494 /* rarefactsharedcommand.cpp in Sources */, - 37D9287D0F21331F001D4494 /* readdistcolumnfilecommand.cpp in Sources */, - 37D9287E0F21331F001D4494 /* readdistphylipfilecommand.cpp in Sources */, - 37D9287F0F21331F001D4494 /* readlistfilecommand.cpp in Sources */, 37D928800F21331F001D4494 /* readmatrix.cpp in Sources */, - 37D928810F21331F001D4494 /* readrabundfilecommand.cpp in Sources */, - 37D928820F21331F001D4494 /* readsabundfilecommand.cpp in Sources */, - 37D928830F21331F001D4494 /* readsharedfilecommand.cpp in Sources */, 37D928840F21331F001D4494 /* sabundvector.cpp in Sources */, 37D928850F21331F001D4494 /* sequence.cpp in Sources */, 37D928860F21331F001D4494 /* shannon.cpp in Sources */, @@ -611,6 +589,10 @@ 37D9289D0F21331F001D4494 /* validcalculator.cpp in Sources */, 37D9289E0F21331F001D4494 /* validcommands.cpp in Sources */, 37D9289F0F21331F001D4494 /* validparameter.cpp in Sources */, + 372E12700F26365B0095CF7E /* readotucommand.cpp in Sources */, + 372E12960F263D5A0095CF7E /* readdistcommand.cpp in Sources */, + 372E12C10F2648250095CF7E /* readlistcommand.cpp in Sources */, + 372E12ED0F264D320095CF7E /* commandfactory.cpp in Sources */, ); runOnlyForDeploymentPostprocessing = 0; }; @@ -630,7 +612,7 @@ "_GLIBCXX_DEBUG_PEDANTIC=1", ); INSTALL_PATH = /usr/local/bin; - PRODUCT_NAME = Mothur; + PRODUCT_NAME = mothur; ZERO_LINK = YES; }; name = Debug; @@ -641,13 +623,14 @@ DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym"; GCC_MODEL_TUNING = G5; INSTALL_PATH = /usr/local/bin; - PRODUCT_NAME = Mothur; + PRODUCT_NAME = mothur; }; name = Release; }; 1DEB923608733DC60010E9CD /* Debug */ = { isa = XCBuildConfiguration; buildSettings = { + GCC_OPTIMIZATION_LEVEL = 3; GCC_WARN_ABOUT_RETURN_TYPE = YES; GCC_WARN_UNUSED_VARIABLE = YES; PREBINDING = NO; @@ -662,6 +645,7 @@ ppc, i386, ); + GCC_OPTIMIZATION_LEVEL = 3; GCC_WARN_ABOUT_RETURN_TYPE = YES; GCC_WARN_UNUSED_VARIABLE = YES; PREBINDING = NO; @@ -672,7 +656,7 @@ /* End XCBuildConfiguration section */ /* Begin XCConfigurationList section */ - 1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "Mothur" */ = { + 1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "mothur" */ = { isa = XCConfigurationList; buildConfigurations = ( 1DEB923208733DC60010E9CD /* Debug */,