X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=f1b584195d2fecf3d7ba250b3a4001a738f46633;hb=dbd5da8043df1cb9f5ff7c6ddb5f550ea49b52c2;hp=b8a10577b717fc26f6d167c0fec1589b24bbc3d4;hpb=7e354c9abb09ea3cf5b500a16cc7f6dd79ccb6f5;p=mothur.git diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index b8a1057..f1b5841 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -13,6 +13,7 @@ 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 */; }; + 372A55551017922B00C5194B /* decalc.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372A55541017922B00C5194B /* decalc.cpp */; }; 372E12700F26365B0095CF7E /* readotucommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372E126F0F26365B0095CF7E /* readotucommand.cpp */; }; 372E12960F263D5A0095CF7E /* readdistcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372E12950F263D5A0095CF7E /* readdistcommand.cpp */; }; 372E12ED0F264D320095CF7E /* commandfactory.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372E12EC0F264D320095CF7E /* commandfactory.cpp */; }; @@ -38,6 +39,8 @@ 3746109D0F40657600460C57 /* unifracunweightedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */; }; 3749271D0FD58C840031C06B /* getsabundcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3749271C0FD58C840031C06B /* 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 */; }; @@ -76,6 +79,10 @@ 37AD4DCA0F28F3DD00AA2D49 /* readtree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */; }; 37AFC71F0F445386005F492D /* sharedsobscollectsummary.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */; }; 37B28F680F27590100808A62 /* deconvolutecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B28F670F27590100808A62 /* deconvolutecommand.cpp */; }; + 37B73C761004BEFD008C4B41 /* listseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B73C751004BEFD008C4B41 /* listseqscommand.cpp */; }; + 37B73CA61004D89A008C4B41 /* getseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B73CA51004D89A008C4B41 /* getseqscommand.cpp */; }; + 37B73CC01004EB38008C4B41 /* removeseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B73CBF1004EB38008C4B41 /* removeseqscommand.cpp */; }; + 37B73CCF1004F5E0008C4B41 /* systemcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B73CCE1004F5E0008C4B41 /* systemcommand.cpp */; }; 37C1D9730F86506E0059E3F0 /* binsequencecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */; }; 37C753CE0FB3415200DBD02E /* distancecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37C753CD0FB3415200DBD02E /* distancecommand.cpp */; }; 37D928550F21331F001D4494 /* ace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927B80F21331F001D4494 /* ace.cpp */; }; @@ -189,6 +196,8 @@ 370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getoturepcommand.cpp; sourceTree = SOURCE_ROOT; }; 371B30B20FD7EE67000414CA /* screenseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = screenseqscommand.cpp; sourceTree = SOURCE_ROOT; }; 371B30B30FD7EE67000414CA /* screenseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = screenseqscommand.h; sourceTree = SOURCE_ROOT; }; + 372A55531017922B00C5194B /* decalc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = decalc.h; sourceTree = ""; }; + 372A55541017922B00C5194B /* decalc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = decalc.cpp; sourceTree = ""; }; 372E126E0F26365B0095CF7E /* readotucommand.h */ = {isa = PBXFileReference; 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sourceTree = SOURCE_ROOT; }; + 37B73C741004BEFD008C4B41 /* listseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = listseqscommand.h; sourceTree = ""; }; + 37B73C751004BEFD008C4B41 /* listseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listseqscommand.cpp; sourceTree = ""; }; + 37B73CA41004D89A008C4B41 /* getseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getseqscommand.h; sourceTree = ""; }; + 37B73CA51004D89A008C4B41 /* getseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getseqscommand.cpp; sourceTree = ""; }; + 37B73CBE1004EB38008C4B41 /* removeseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removeseqscommand.h; sourceTree = ""; }; + 37B73CBF1004EB38008C4B41 /* removeseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removeseqscommand.cpp; sourceTree = ""; }; + 37B73CCD1004F5E0008C4B41 /* systemcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = systemcommand.h; sourceTree = ""; }; + 37B73CCE1004F5E0008C4B41 /* systemcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = systemcommand.cpp; sourceTree = ""; }; 37C1D9710F86506E0059E3F0 /* binsequencecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = binsequencecommand.h; sourceTree = SOURCE_ROOT; }; 37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = binsequencecommand.cpp; sourceTree = SOURCE_ROOT; }; 37C753CC0FB3415200DBD02E /* distancecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = distancecommand.h; sourceTree = SOURCE_ROOT; }; @@ -534,6 +556,7 @@ 373C68DC0FC1C38D00137ACD /* blastalign.hpp */, 373C68DB0FC1C38D00137ACD /* blastalign.cpp */, 37D928A60F2133C0001D4494 /* calculators */, + 374F2FE81006346600E97C66 /* chimera */, 37D927C20F21331F001D4494 /* cluster.hpp */, 37D927C10F21331F001D4494 /* cluster.cpp */, 37D928A90F2133E5001D4494 /* commands */, @@ -613,6 +636,20 @@ name = Products; sourceTree = ""; }; + 374F2FE81006346600E97C66 /* chimera */ = { + isa = PBXGroup; + children = ( + 374F2FD51006320200E97C66 /* chimera.h */, + 374F2FE9100634B600E97C66 /* bellerophon.h */, + 374F2FEA100634B600E97C66 /* bellerophon.cpp */, + 372A55531017922B00C5194B /* decalc.h */, + 372A55541017922B00C5194B /* decalc.cpp */, + 374F301110063B6F00E97C66 /* pintail.h */, + 374F301210063B6F00E97C66 /* pintail.cpp */, + ); + name = chimera; + sourceTree = ""; + }; 3796441D0FB9B9650081FDB6 /* read */ = { isa = PBXGroup; children = ( @@ -780,6 +817,8 @@ 3749273E0FD5956B0031C06B /* getrabundcommand.cpp */, 3749271B0FD58C840031C06B /* getsabundcommand.h */, 3749271C0FD58C840031C06B /* getsabundcommand.cpp */, + 37B73CA41004D89A008C4B41 /* getseqscommand.h */, + 37B73CA51004D89A008C4B41 /* getseqscommand.cpp */, 375873F10F7D64800040F377 /* heatmapcommand.h */, 375873F00F7D64800040F377 /* heatmapcommand.cpp */, 378598640FDD497000EF9D03 /* heatmapsimcommand.h */, @@ -788,6 +827,8 @@ 37D927E30F21331F001D4494 /* helpcommand.cpp */, 375873F40F7D648F0040F377 /* libshuffcommand.h */, 375873F30F7D648F0040F377 /* libshuffcommand.cpp */, + 37B73C741004BEFD008C4B41 /* listseqscommand.h */, + 37B73C751004BEFD008C4B41 /* listseqscommand.cpp */, 21E859D60FC4632E005E1A48 /* matrixoutputcommand.h */, 21E859D70FC4632E005E1A48 /* matrixoutputcommand.cpp */, 7E5A17AD0FE57292003C6A03 /* mergefilecommand.h */, @@ -808,6 +849,8 @@ 372E126F0F26365B0095CF7E /* readotucommand.cpp */, 37E5F4900F2A3DA800F8D827 /* readtreecommand.h */, 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */, + 37B73CBE1004EB38008C4B41 /* removeseqscommand.h */, + 37B73CBF1004EB38008C4B41 /* removeseqscommand.cpp */, 7E09C5120FDA79C5002ECAE5 /* reversecommand.h */, 7E09C5130FDA79C5002ECAE5 /* reversecommand.cpp */, 371B30B30FD7EE67000414CA /* screenseqscommand.h */, @@ -820,6 +863,8 @@ 37D928460F21331F001D4494 /* summarycommand.cpp */, 37D9284B0F21331F001D4494 /* summarysharedcommand.h */, 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */, + 37B73CCD1004F5E0008C4B41 /* systemcommand.h */, + 37B73CCE1004F5E0008C4B41 /* systemcommand.cpp */, 211C38370F961E1F00FEE541 /* treegroupscommand.h */, 211C38360F961E1F00FEE541 /* treegroupscommand.cpp */, 7E09C5340FDA7F65002ECAE5 /* trimseqscommand.h */, @@ -1111,6 +1156,13 @@ 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 */, ); runOnlyForDeploymentPostprocessing = 0; }; @@ -1170,11 +1222,20 @@ ); 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"; WARNING_CFLAGS = "";