X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=c6d6c0ed29fa33724df4aae7934582ad63b14ddd;hb=f7fbd74ffedcf62217109c22e828453eaefa1458;hp=14071540ef2d94503de27fffe13bba2779fcbbb9;hpb=163b300cfd7d4ca4e70c454be20f07b1d8346650;p=mothur.git diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index 1407154..c6d6c0e 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -13,6 +13,8 @@ 21E859D80FC4632E005E1A48 /* matrixoutputcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 21E859D70FC4632E005E1A48 /* matrixoutputcommand.cpp */; }; 370B88070F8A4EE4005AB382 /* getoturepcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */; }; 371B30B40FD7EE67000414CA /* screenseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 371B30B20FD7EE67000414CA /* screenseqscommand.cpp */; }; + 372095C2103196D70004D347 /* chimera.cpp in 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getsabundcommand.cpp */; }; 3749273F0FD5956B0031C06B /* getrabundcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3749273E0FD5956B0031C06B /* getrabundcommand.cpp */; }; + 374F2FEB100634B600E97C66 /* bellerophon.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 374F2FEA100634B600E97C66 /* bellerophon.cpp */; }; + 374F301310063B6F00E97C66 /* pintail.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 374F301210063B6F00E97C66 /* pintail.cpp */; }; 37519A6B0F80E6EB00FED5E8 /* sharedanderbergs.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */; }; 37519AA10F810D0200FED5E8 /* venncommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37519AA00F810D0200FED5E8 /* venncommand.cpp */; }; 37519AB50F810FAE00FED5E8 /* venn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37519AB40F810FAE00FED5E8 /* venn.cpp */; }; @@ -55,7 +59,7 @@ 375AA1390F9E433D008EF9B8 /* readcolumn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 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37D928220F21331F001D4494 /* sharedace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedace.cpp; sourceTree = SOURCE_ROOT; }; 37D928230F21331F001D4494 /* sharedace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedace.h; sourceTree = SOURCE_ROOT; }; 37D928240F21331F001D4494 /* sharedchao1.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedchao1.cpp; sourceTree = SOURCE_ROOT; }; @@ -491,6 +515,10 @@ A70B53A70F4CD7AD0064797E /* getlabelcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlabelcommand.h; sourceTree = SOURCE_ROOT; }; A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlinecommand.cpp; sourceTree = SOURCE_ROOT; }; A70B53A90F4CD7AD0064797E /* getlinecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlinecommand.h; sourceTree = SOURCE_ROOT; }; + A75B8879104C16860083C454 /* alignedsimilarity.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alignedsimilarity.cpp; sourceTree = ""; }; + A75B887A104C16860083C454 /* alignedsimilarity.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = alignedsimilarity.h; sourceTree = ""; }; + A75B887B104C16860083C454 /* ccode.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ccode.cpp; sourceTree = ""; }; + A75B887C104C16860083C454 /* ccode.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ccode.h; sourceTree = ""; }; C6859E8B029090EE04C91782 /* Mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = Mothur.1; sourceTree = ""; }; EB1216860F619B83004A865F /* bergerparker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bergerparker.h; sourceTree = SOURCE_ROOT; }; EB1216870F619B83004A865F /* bergerparker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bergerparker.cpp; sourceTree = SOURCE_ROOT; }; @@ -536,6 +564,7 @@ 373C68DC0FC1C38D00137ACD /* blastalign.hpp */, 373C68DB0FC1C38D00137ACD /* blastalign.cpp */, 37D928A60F2133C0001D4494 /* calculators */, + 374F2FE81006346600E97C66 /* chimera */, 37D927C20F21331F001D4494 /* cluster.hpp */, 37D927C10F21331F001D4494 /* cluster.cpp */, 37D928A90F2133E5001D4494 /* commands */, @@ -594,8 +623,6 @@ 37D928050F21331F001D4494 /* rarefact.cpp */, 37D928090F21331F001D4494 /* rarefactioncurvedata.h */, 3796441D0FB9B9650081FDB6 /* read */, - 37D928210F21331F001D4494 /* shared.h */, - 37D928200F21331F001D4494 /* shared.cpp */, 211C38310F961DD400FEE541 /* sharedutilities.h */, 211C38300F961DD400FEE541 /* sharedutilities.cpp */, 37D928420F21331F001D4494 /* singlelinkage.cpp */, @@ -617,6 +644,25 @@ name = Products; sourceTree = ""; }; + 374F2FE81006346600E97C66 /* chimera */ = { + isa = PBXGroup; + children = ( + 374F2FD51006320200E97C66 /* chimera.h */, + 372095C1103196D70004D347 /* chimera.cpp */, + 374F2FE9100634B600E97C66 /* bellerophon.h */, + 374F2FEA100634B600E97C66 /* bellerophon.cpp */, + A75B8879104C16860083C454 /* alignedsimilarity.cpp */, + A75B887A104C16860083C454 /* alignedsimilarity.h */, + A75B887B104C16860083C454 /* ccode.cpp */, + A75B887C104C16860083C454 /* ccode.h */, + 372A55531017922B00C5194B /* decalc.h */, + 372A55541017922B00C5194B /* decalc.cpp */, + 374F301110063B6F00E97C66 /* pintail.h */, + 374F301210063B6F00E97C66 /* pintail.cpp */, + ); + name = chimera; + sourceTree = ""; + }; 3796441D0FB9B9650081FDB6 /* read */ = { isa = PBXGroup; children = ( @@ -658,6 +704,7 @@ 37C753F40FB34C0300DBD02E /* eachgapignore.h */, 373C69960FC1E63600137ACD /* efron.cpp */, 373C69970FC1E63600137ACD /* efron.h */, + 379D3D6B0FF917F40068C1C0 /* filters.h */, EB9303F70F53517300E8EF26 /* geom.h */, EB9303F80F53517300E8EF26 /* geom.cpp */, 378C1AF10FB0644D004D63F5 /* goodscoverage.h */, @@ -761,8 +808,10 @@ 37D927C70F21331F001D4494 /* collectcommand.cpp */, 37D927CC0F21331F001D4494 /* collectsharedcommand.h */, 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */, - 377326640FAF16E0007ABB8B /* concensuscommand.h */, - 377326630FAF16E0007ABB8B /* concensuscommand.cpp */, + 377326640FAF16E0007ABB8B /* consensuscommand.h */, + 377326630FAF16E0007ABB8B /* consensuscommand.cpp */, + 379D3D4F0FF90E090068C1C0 /* chimeraseqscommand.h */, + 379D3D500FF90E090068C1C0 /* chimeraseqscommand.cpp */, 37B28F660F27590100808A62 /* deconvolutecommand.h */, 37B28F670F27590100808A62 /* deconvolutecommand.cpp */, 37C753CC0FB3415200DBD02E /* distancecommand.h */, @@ -781,6 +830,8 @@ 3749273E0FD5956B0031C06B /* getrabundcommand.cpp */, 3749271B0FD58C840031C06B /* getsabundcommand.h */, 3749271C0FD58C840031C06B /* getsabundcommand.cpp */, + 37B73CA41004D89A008C4B41 /* getseqscommand.h */, + 37B73CA51004D89A008C4B41 /* getseqscommand.cpp */, 375873F10F7D64800040F377 /* heatmapcommand.h */, 375873F00F7D64800040F377 /* heatmapcommand.cpp */, 378598640FDD497000EF9D03 /* heatmapsimcommand.h */, @@ -789,14 +840,14 @@ 37D927E30F21331F001D4494 /* helpcommand.cpp */, 375873F40F7D648F0040F377 /* libshuffcommand.h */, 375873F30F7D648F0040F377 /* libshuffcommand.cpp */, + 37B73C741004BEFD008C4B41 /* listseqscommand.h */, + 37B73C751004BEFD008C4B41 /* listseqscommand.cpp */, 21E859D60FC4632E005E1A48 /* matrixoutputcommand.h */, 21E859D70FC4632E005E1A48 /* matrixoutputcommand.cpp */, 7E5A17AD0FE57292003C6A03 /* mergefilecommand.h */, 7E5A17AE0FE57292003C6A03 /* mergefilecommand.cpp */, 375873F70F7D649C0040F377 /* nocommands.h */, 375873F60F7D649C0040F377 /* nocommands.cpp */, - 37D927FA0F21331F001D4494 /* parselistcommand.h */, - 37D927F90F21331F001D4494 /* parselistcommand.cpp */, 3792946E0F2E191800B9034A /* parsimonycommand.h */, 3792946F0F2E191800B9034A /* parsimonycommand.cpp */, 37D927FE0F21331F001D4494 /* quitcommand.h */, @@ -811,6 +862,8 @@ 372E126F0F26365B0095CF7E /* readotucommand.cpp */, 37E5F4900F2A3DA800F8D827 /* readtreecommand.h */, 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */, + 37B73CBE1004EB38008C4B41 /* removeseqscommand.h */, + 37B73CBF1004EB38008C4B41 /* removeseqscommand.cpp */, 7E09C5120FDA79C5002ECAE5 /* reversecommand.h */, 7E09C5130FDA79C5002ECAE5 /* reversecommand.cpp */, 371B30B30FD7EE67000414CA /* screenseqscommand.h */, @@ -823,6 +876,8 @@ 37D928460F21331F001D4494 /* summarycommand.cpp */, 37D9284B0F21331F001D4494 /* summarysharedcommand.h */, 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */, + 37B73CCD1004F5E0008C4B41 /* systemcommand.h */, + 37B73CCE1004F5E0008C4B41 /* systemcommand.cpp */, 211C38370F961E1F00FEE541 /* treegroupscommand.h */, 211C38360F961E1F00FEE541 /* treegroupscommand.cpp */, 7E09C5340FDA7F65002ECAE5 /* trimseqscommand.h */, @@ -989,7 +1044,6 @@ 37D928700F21331F001D4494 /* nameassignment.cpp in Sources */, 37D928720F21331F001D4494 /* npshannon.cpp in Sources */, 37D928730F21331F001D4494 /* ordervector.cpp in Sources */, - 37D928740F21331F001D4494 /* parselistcommand.cpp in Sources */, 37D928750F21331F001D4494 /* progress.cpp in Sources */, 37D928760F21331F001D4494 /* quitcommand.cpp in Sources */, 37D928770F21331F001D4494 /* rabundvector.cpp in Sources */, @@ -1001,7 +1055,6 @@ 37D928840F21331F001D4494 /* sabundvector.cpp in Sources */, 37D928850F21331F001D4494 /* sequence.cpp in Sources */, 37D928860F21331F001D4494 /* shannon.cpp in Sources */, - 37D928870F21331F001D4494 /* shared.cpp in Sources */, 37D928880F21331F001D4494 /* sharedace.cpp in Sources */, 37D928890F21331F001D4494 /* sharedchao1.cpp in Sources */, 37D9288A0F21331F001D4494 /* sharedcommand.cpp in Sources */, @@ -1078,7 +1131,7 @@ 375AA13B0F9E433D008EF9B8 /* readphylip.cpp in Sources */, 7EC3D4550FA0FFF900338DA5 /* coverage.cpp in Sources */, 7EC3D4560FA0FFF900338DA5 /* whittaker.cpp in Sources */, - 377326650FAF16E0007ABB8B /* concensuscommand.cpp in Sources */, + 377326650FAF16E0007ABB8B /* consensuscommand.cpp in Sources */, 378C1B030FB0644E004D63F5 /* filterseqscommand.cpp in Sources */, 378C1B040FB0644E004D63F5 /* goodscoverage.cpp in Sources */, 378C1B0A0FB0644E004D63F5 /* sequencedb.cpp in Sources */, @@ -1115,6 +1168,17 @@ 378598740FDD4C1500EF9D03 /* heatmapsim.cpp in Sources */, 378599100FDD7E8E00EF9D03 /* optionparser.cpp in Sources */, 7E5A17AF0FE57292003C6A03 /* mergefilecommand.cpp in Sources */, + 379D3D510FF90E090068C1C0 /* chimeraseqscommand.cpp in Sources */, + 37B73C761004BEFD008C4B41 /* listseqscommand.cpp in Sources */, + 37B73CA61004D89A008C4B41 /* getseqscommand.cpp in Sources */, + 37B73CC01004EB38008C4B41 /* removeseqscommand.cpp in Sources */, + 37B73CCF1004F5E0008C4B41 /* systemcommand.cpp in Sources */, + 374F2FEB100634B600E97C66 /* bellerophon.cpp in Sources */, + 374F301310063B6F00E97C66 /* pintail.cpp in Sources */, + 372A55551017922B00C5194B /* decalc.cpp in Sources */, + 372095C2103196D70004D347 /* chimera.cpp in Sources */, + A75B887D104C16860083C454 /* alignedsimilarity.cpp in Sources */, + A75B887E104C16860083C454 /* ccode.cpp in Sources */, ); runOnlyForDeploymentPostprocessing = 0; }; @@ -1174,13 +1238,23 @@ ); GCC_OPTIMIZATION_LEVEL = 3; GCC_WARN_ABOUT_MISSING_NEWLINE = YES; + GCC_WARN_ABOUT_MISSING_PROTOTYPES = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; GCC_WARN_ALLOW_INCOMPLETE_PROTOCOL = NO; - GCC_WARN_PEDANTIC = NO; + GCC_WARN_MISSING_PARENTHESES = YES; + GCC_WARN_PEDANTIC = YES; + GCC_WARN_UNUSED_FUNCTION = YES; + GCC_WARN_UNUSED_PARAMETER = NO; + GCC_WARN_UNUSED_VALUE = YES; GCC_WARN_UNUSED_VARIABLE = YES; - OTHER_CPLUSPLUSFLAGS = ""; + OTHER_CPLUSPLUSFLAGS = ( + "-ansi", + "-pedantic", + "-wall", + ); PREBINDING = NO; SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk"; + SYMROOT = /Users/johnwestcott/Desktop; WARNING_CFLAGS = ""; }; name = Release;