X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=24187d82fd0bff1934e3faeb458bb062fba6548b;hb=f598bd8389840cf030d61f5da7d0b2c3e37c06ba;hp=1e52e09f149fff725e5b5914e74b44f07525c52a;hpb=3cebc384d8b267156aef2d09ce578a66cd36f98e;p=mothur.git diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index 1e52e09..24187d8 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -9,6 +9,10 @@ /* Begin PBXBuildFile section */ 8DD76FB00486AB0100D96B5E /* mothur.1 in CopyFiles */ = {isa = PBXBuildFile; fileRef = C6A0FF2C0290799A04C91782 /* mothur.1 */; }; A70332B712D3A13400761E33 /* makefile in Sources */ = {isa = PBXBuildFile; fileRef = A70332B512D3A13400761E33 /* makefile */; }; + A713EBAC12DC7613000092AC /* readphylipvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A713EBAB12DC7613000092AC /* readphylipvector.cpp */; }; + A713EBED12DC7C5E000092AC /* nmdscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */; }; + A71FE12C12EDF72400963CA7 /* mergegroupscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */; }; + A727864412E9E28C00F86ABA /* removerarecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A727864312E9E28C00F86ABA /* removerarecommand.cpp */; }; A7E9B88112D37EC400DA6239 /* ace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B64F12D37EC300DA6239 /* ace.cpp */; }; A7E9B88212D37EC400DA6239 /* aligncommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B65112D37EC300DA6239 /* aligncommand.cpp */; }; A7E9B88312D37EC400DA6239 /* alignment.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B65312D37EC300DA6239 /* alignment.cpp */; }; @@ -157,7 +161,7 @@ A7E9B91212D37EC400DA6239 /* parselistscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78112D37EC400DA6239 /* parselistscommand.cpp */; }; A7E9B91312D37EC400DA6239 /* parsimony.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78312D37EC400DA6239 /* parsimony.cpp */; }; A7E9B91412D37EC400DA6239 /* parsimonycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */; }; - A7E9B91512D37EC400DA6239 /* pcacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78712D37EC400DA6239 /* pcacommand.cpp */; }; + A7E9B91512D37EC400DA6239 /* pcoacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */; }; A7E9B91612D37EC400DA6239 /* phylodiversity.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78912D37EC400DA6239 /* phylodiversity.cpp */; }; A7E9B91712D37EC400DA6239 /* phylodiversitycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */; }; A7E9B91812D37EC400DA6239 /* phylosummary.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78D12D37EC400DA6239 /* phylosummary.cpp */; }; @@ -280,6 +284,8 @@ A7E9B98D12D37EC400DA6239 /* weighted.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87C12D37EC400DA6239 /* weighted.cpp */; }; A7E9B98E12D37EC400DA6239 /* weightedlinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87E12D37EC400DA6239 /* weightedlinkage.cpp */; }; A7E9B98F12D37EC400DA6239 /* whittaker.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87F12D37EC400DA6239 /* whittaker.cpp */; }; + A7FC480E12D788F20055BC5C /* linearalgebra.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FC480D12D788F20055BC5C /* linearalgebra.cpp */; }; + A7FC486712D795D60055BC5C /* pcacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FC486612D795D60055BC5C /* pcacommand.cpp */; }; /* End PBXBuildFile section */ /* Begin PBXCopyFilesBuildPhase section */ @@ -296,8 +302,16 @@ /* End PBXCopyFilesBuildPhase section */ /* Begin PBXFileReference section */ - 8DD76FB20486AB0100D96B5E /* mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = mothur; sourceTree = BUILT_PRODUCTS_DIR; }; + 8DD76FB20486AB0100D96B5E /* Mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = Mothur; sourceTree = BUILT_PRODUCTS_DIR; }; A70332B512D3A13400761E33 /* makefile */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.make; path = makefile; sourceTree = ""; }; + A713EBAA12DC7613000092AC /* readphylipvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylipvector.h; sourceTree = ""; }; + A713EBAB12DC7613000092AC /* readphylipvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylipvector.cpp; sourceTree = ""; }; + A713EBEB12DC7C5E000092AC /* nmdscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nmdscommand.h; sourceTree = ""; }; + A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nmdscommand.cpp; sourceTree = ""; }; + A71FE12A12EDF72400963CA7 /* mergegroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mergegroupscommand.h; sourceTree = ""; }; + A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mergegroupscommand.cpp; sourceTree = ""; }; + A727864212E9E28C00F86ABA /* removerarecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removerarecommand.h; sourceTree = ""; }; + A727864312E9E28C00F86ABA /* removerarecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removerarecommand.cpp; sourceTree = ""; }; A7E9B64F12D37EC300DA6239 /* ace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ace.cpp; sourceTree = ""; }; A7E9B65012D37EC300DA6239 /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = ""; }; A7E9B65112D37EC300DA6239 /* aligncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = aligncommand.cpp; sourceTree = ""; }; @@ -610,8 +624,8 @@ A7E9B78412D37EC400DA6239 /* parsimony.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimony.h; sourceTree = ""; }; A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimonycommand.cpp; sourceTree = ""; }; A7E9B78612D37EC400DA6239 /* parsimonycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimonycommand.h; sourceTree = ""; }; - A7E9B78712D37EC400DA6239 /* pcacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcacommand.cpp; sourceTree = ""; }; - A7E9B78812D37EC400DA6239 /* pcacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcacommand.h; sourceTree = ""; }; + A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcoacommand.cpp; sourceTree = ""; }; + A7E9B78812D37EC400DA6239 /* pcoacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcoacommand.h; sourceTree = ""; }; A7E9B78912D37EC400DA6239 /* phylodiversity.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversity.cpp; sourceTree = ""; }; A7E9B78A12D37EC400DA6239 /* phylodiversity.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylodiversity.h; sourceTree = ""; }; A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversitycommand.cpp; sourceTree = ""; }; @@ -860,6 +874,10 @@ A7E9B87E12D37EC400DA6239 /* weightedlinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = weightedlinkage.cpp; sourceTree = SOURCE_ROOT; }; A7E9B87F12D37EC400DA6239 /* whittaker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = whittaker.cpp; sourceTree = ""; }; A7E9B88012D37EC400DA6239 /* whittaker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = whittaker.h; sourceTree = ""; }; + A7FC480C12D788F20055BC5C /* linearalgebra.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = linearalgebra.h; sourceTree = ""; }; + A7FC480D12D788F20055BC5C /* linearalgebra.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = linearalgebra.cpp; sourceTree = ""; }; + A7FC486512D795D60055BC5C /* pcacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcacommand.h; sourceTree = ""; }; + A7FC486612D795D60055BC5C /* pcacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcacommand.cpp; sourceTree = ""; }; C6A0FF2C0290799A04C91782 /* mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = mothur.1; sourceTree = ""; }; /* End PBXFileReference section */ @@ -930,6 +948,8 @@ A7E9B72D12D37EC400DA6239 /* inputdata.cpp */, A7E9B73912D37EC400DA6239 /* libshuff.cpp */, A7E9B73A12D37EC400DA6239 /* libshuff.h */, + A7FC480C12D788F20055BC5C /* linearalgebra.h */, + A7FC480D12D788F20055BC5C /* linearalgebra.cpp */, A7E9BA5612D39BD800DA6239 /* metastats */, A7E9B75B12D37EC400DA6239 /* mothur.cpp */, A7E9B75C12D37EC400DA6239 /* mothur.h */, @@ -983,7 +1003,7 @@ 1AB674ADFE9D54B511CA2CBB /* Products */ = { isa = PBXGroup; children = ( - 8DD76FB20486AB0100D96B5E /* mothur */, + 8DD76FB20486AB0100D96B5E /* Mothur */, ); name = Products; sourceTree = ""; @@ -1092,6 +1112,8 @@ A7E9B74A12D37EC400DA6239 /* matrixoutputcommand.h */, A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */, A7E9B75412D37EC400DA6239 /* mergefilecommand.h */, + A71FE12A12EDF72400963CA7 /* mergegroupscommand.h */, + A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */, A7E9B75712D37EC400DA6239 /* metastatscommand.cpp */, A7E9B75812D37EC400DA6239 /* metastatscommand.h */, A7E9B75912D37EC400DA6239 /* mgclustercommand.cpp */, @@ -1100,6 +1122,8 @@ A7E9B76912D37EC400DA6239 /* nocommands.cpp */, A7E9B76B12D37EC400DA6239 /* normalizesharedcommand.cpp */, A7E9B76C12D37EC400DA6239 /* normalizesharedcommand.h */, + A713EBEB12DC7C5E000092AC /* nmdscommand.h */, + A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */, A7E9B77912D37EC400DA6239 /* otuhierarchycommand.cpp */, A7E9B77A12D37EC400DA6239 /* otuhierarchycommand.h */, A7E9B77D12D37EC400DA6239 /* pairwiseseqscommand.cpp */, @@ -1110,8 +1134,10 @@ A7E9B78212D37EC400DA6239 /* parselistscommand.h */, A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */, A7E9B78612D37EC400DA6239 /* parsimonycommand.h */, - A7E9B78712D37EC400DA6239 /* pcacommand.cpp */, - A7E9B78812D37EC400DA6239 /* pcacommand.h */, + A7FC486512D795D60055BC5C /* pcacommand.h */, + A7FC486612D795D60055BC5C /* pcacommand.cpp */, + A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */, + A7E9B78812D37EC400DA6239 /* pcoacommand.h */, A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */, A7E9B78C12D37EC400DA6239 /* phylodiversitycommand.h */, A7E9B79112D37EC400DA6239 /* phylotypecommand.cpp */, @@ -1138,6 +1164,8 @@ A7E9B7C612D37EC400DA6239 /* removelineagecommand.h */, A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */, A7E9B7C812D37EC400DA6239 /* removeotuscommand.h */, + A727864212E9E28C00F86ABA /* removerarecommand.h */, + A727864312E9E28C00F86ABA /* removerarecommand.cpp */, A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */, A7E9B7CA12D37EC400DA6239 /* removeseqscommand.h */, A7E9B7CD12D37EC400DA6239 /* reversecommand.cpp */, @@ -1511,6 +1539,8 @@ A7E9B7BE12D37EC400DA6239 /* readphylip.h */, A7E9B7BF12D37EC400DA6239 /* readtree.cpp */, A7E9B7C012D37EC400DA6239 /* readtree.h */, + A713EBAA12DC7613000092AC /* readphylipvector.h */, + A713EBAB12DC7613000092AC /* readphylipvector.cpp */, A7E9B84312D37EC400DA6239 /* splitmatrix.cpp */, A7E9B84412D37EC400DA6239 /* splitmatrix.h */, ); @@ -1537,9 +1567,9 @@ /* End PBXGroup section */ /* Begin PBXNativeTarget section */ - 8DD76FA90486AB0100D96B5E /* mothur */ = { + 8DD76FA90486AB0100D96B5E /* Mothur */ = { isa = PBXNativeTarget; - buildConfigurationList = 1DEB928508733DD80010E9CD /* Build configuration list for PBXNativeTarget "mothur" */; + buildConfigurationList = 1DEB928508733DD80010E9CD /* Build configuration list for PBXNativeTarget "Mothur" */; buildPhases = ( 8DD76FAB0486AB0100D96B5E /* Sources */, 8DD76FAD0486AB0100D96B5E /* Frameworks */, @@ -1549,10 +1579,10 @@ ); dependencies = ( ); - name = mothur; + name = Mothur; productInstallPath = "$(HOME)/bin"; productName = mothur; - productReference = 8DD76FB20486AB0100D96B5E /* mothur */; + productReference = 8DD76FB20486AB0100D96B5E /* Mothur */; productType = "com.apple.product-type.tool"; }; /* End PBXNativeTarget section */ @@ -1560,6 +1590,9 @@ /* Begin PBXProject section */ 08FB7793FE84155DC02AAC07 /* Project object */ = { isa = PBXProject; + attributes = { + ORGANIZATIONNAME = "Schloss Lab"; + }; buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */; compatibilityVersion = "Xcode 3.1"; developmentRegion = English; @@ -1574,7 +1607,7 @@ projectDirPath = ""; projectRoot = ""; targets = ( - 8DD76FA90486AB0100D96B5E /* mothur */, + 8DD76FA90486AB0100D96B5E /* Mothur */, ); }; /* End PBXProject section */ @@ -1732,7 +1765,7 @@ A7E9B91212D37EC400DA6239 /* parselistscommand.cpp in Sources */, A7E9B91312D37EC400DA6239 /* parsimony.cpp in Sources */, A7E9B91412D37EC400DA6239 /* parsimonycommand.cpp in Sources */, - A7E9B91512D37EC400DA6239 /* pcacommand.cpp in Sources */, + A7E9B91512D37EC400DA6239 /* pcoacommand.cpp in Sources */, A7E9B91612D37EC400DA6239 /* phylodiversity.cpp in Sources */, A7E9B91712D37EC400DA6239 /* phylodiversitycommand.cpp in Sources */, A7E9B91812D37EC400DA6239 /* phylosummary.cpp in Sources */, @@ -1856,6 +1889,12 @@ A7E9B98E12D37EC400DA6239 /* weightedlinkage.cpp in Sources */, A7E9B98F12D37EC400DA6239 /* whittaker.cpp in Sources */, A70332B712D3A13400761E33 /* makefile in Sources */, + A7FC480E12D788F20055BC5C /* linearalgebra.cpp in Sources */, + 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 */, ); runOnlyForDeploymentPostprocessing = 0; }; @@ -1872,7 +1911,7 @@ GCC_MODEL_TUNING = G5; GCC_OPTIMIZATION_LEVEL = 0; INSTALL_PATH = /usr/local/bin; - PRODUCT_NAME = mothur; + PRODUCT_NAME = Mothur; }; name = Debug; }; @@ -1885,7 +1924,7 @@ GCC_MODEL_TUNING = G5; GCC_WARN_UNUSED_VALUE = YES; INSTALL_PATH = ./; - PRODUCT_NAME = mothur; + PRODUCT_NAME = Mothur; }; name = Release; }; @@ -1901,6 +1940,7 @@ "VERSION=\"\\\"1.15.0\\\"\"", "RELEASE_DATE=\"\\\"12/10/2010\\\"\"", ); + GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; GCC_WARN_UNUSED_VARIABLE = YES; INSTALL_PATH = ""; @@ -1956,7 +1996,7 @@ /* End XCBuildConfiguration section */ /* Begin XCConfigurationList section */ - 1DEB928508733DD80010E9CD /* Build configuration list for PBXNativeTarget "mothur" */ = { + 1DEB928508733DD80010E9CD /* Build configuration list for PBXNativeTarget "Mothur" */ = { isa = XCConfigurationList; buildConfigurations = ( 1DEB928608733DD80010E9CD /* Debug */,