X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=b04bf2a564483a942f68eda44fe2412bc5cfc83e;hb=29c0d3ec01be5372807eb86261100d77de253787;hp=3f1cd9953b270c8f686650a0936d384f31f75885;hpb=f15f7092c97277337d4fdd9ef674015c15a13220;p=mothur.git diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index 3f1cd99..b04bf2a 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -58,6 +58,7 @@ 377326650FAF16E0007ABB8B /* concensuscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 377326630FAF16E0007ABB8B /* concensuscommand.cpp */; }; 378598660FDD497000EF9D03 /* heatmapsimcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378598650FDD497000EF9D03 /* heatmapsimcommand.cpp */; }; 378598740FDD4C1500EF9D03 /* heatmapsim.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378598730FDD4C1500EF9D03 /* heatmapsim.cpp */; }; + 378599100FDD7E8E00EF9D03 /* optionparser.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3785990F0FDD7E8E00EF9D03 /* optionparser.cpp */; }; 378C1B030FB0644E004D63F5 /* filterseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378C1AEE0FB0644D004D63F5 /* filterseqscommand.cpp */; }; 378C1B040FB0644E004D63F5 /* goodscoverage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378C1AF00FB0644D004D63F5 /* goodscoverage.cpp */; }; 378C1B0A0FB0644E004D63F5 /* sequencedb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378C1AFD0FB0644D004D63F5 /* sequencedb.cpp */; }; @@ -90,7 +91,6 @@ 37D928610F21331F001D4494 /* completelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D20F21331F001D4494 /* completelinkage.cpp */; }; 37D928620F21331F001D4494 /* database.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D30F21331F001D4494 /* database.cpp */; }; 37D928630F21331F001D4494 /* engine.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D70F21331F001D4494 /* engine.cpp */; }; - 37D928640F21331F001D4494 /* errorchecking.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D90F21331F001D4494 /* errorchecking.cpp */; }; 37D928650F21331F001D4494 /* fastamap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927DB0F21331F001D4494 /* fastamap.cpp */; }; 37D928660F21331F001D4494 /* fileoutput.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927DD0F21331F001D4494 /* fileoutput.cpp */; }; 37D928670F21331F001D4494 /* globaldata.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927DF0F21331F001D4494 /* globaldata.cpp */; }; @@ -105,7 +105,6 @@ 37D928700F21331F001D4494 /* nameassignment.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F00F21331F001D4494 /* nameassignment.cpp */; }; 37D928720F21331F001D4494 /* npshannon.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F40F21331F001D4494 /* npshannon.cpp */; }; 37D928730F21331F001D4494 /* ordervector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F70F21331F001D4494 /* ordervector.cpp */; }; - 37D928740F21331F001D4494 /* parselistcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F90F21331F001D4494 /* parselistcommand.cpp */; }; 37D928750F21331F001D4494 /* progress.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927FB0F21331F001D4494 /* progress.cpp */; }; 37D928760F21331F001D4494 /* quitcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927FD0F21331F001D4494 /* quitcommand.cpp */; }; 37D928770F21331F001D4494 /* rabundvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927FF0F21331F001D4494 /* rabundvector.cpp */; }; @@ -117,7 +116,6 @@ 37D928840F21331F001D4494 /* sabundvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9281A0F21331F001D4494 /* sabundvector.cpp */; }; 37D928850F21331F001D4494 /* sequence.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9281C0F21331F001D4494 /* sequence.cpp */; }; 37D928860F21331F001D4494 /* shannon.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9281E0F21331F001D4494 /* shannon.cpp */; }; - 37D928870F21331F001D4494 /* shared.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928200F21331F001D4494 /* shared.cpp */; }; 37D928880F21331F001D4494 /* sharedace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928220F21331F001D4494 /* sharedace.cpp */; }; 37D928890F21331F001D4494 /* sharedchao1.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928240F21331F001D4494 /* sharedchao1.cpp */; }; 37D9288A0F21331F001D4494 /* sharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928260F21331F001D4494 /* sharedcommand.cpp */; }; @@ -140,7 +138,6 @@ 37D9289B0F21331F001D4494 /* summarysharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */; }; 37D9289C0F21331F001D4494 /* uvest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9284D0F21331F001D4494 /* uvest.cpp */; }; 37D9289D0F21331F001D4494 /* validcalculator.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9284F0F21331F001D4494 /* validcalculator.cpp */; }; - 37D9289E0F21331F001D4494 /* validcommands.cpp in Sources */ = {isa = PBXBuildFile; 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}; 37D927F70F21331F001D4494 /* ordervector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ordervector.cpp; sourceTree = SOURCE_ROOT; }; 37D927F80F21331F001D4494 /* ordervector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = ordervector.hpp; sourceTree = SOURCE_ROOT; }; - 37D927F90F21331F001D4494 /* parselistcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parselistcommand.cpp; sourceTree = SOURCE_ROOT; }; - 37D927FA0F21331F001D4494 /* parselistcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parselistcommand.h; sourceTree = SOURCE_ROOT; }; 37D927FB0F21331F001D4494 /* progress.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = progress.cpp; sourceTree = SOURCE_ROOT; }; 37D927FC0F21331F001D4494 /* progress.hpp */ = {isa = PBXFileReference; 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sourceTree = SOURCE_ROOT; }; 7EC3D4500FA0FFF900338DA5 /* coverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = coverage.cpp; sourceTree = SOURCE_ROOT; }; 7EC3D4510FA0FFF900338DA5 /* coverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = coverage.h; sourceTree = SOURCE_ROOT; }; 7EC3D4520FA0FFF900338DA5 /* sharedanderberg.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderberg.h; sourceTree = SOURCE_ROOT; }; @@ -582,6 +576,8 @@ 373C68E40FC1C4A500137ACD /* noalign.hpp */, 373C68E30FC1C4A500137ACD /* noalign.cpp */, 37D927F60F21331F001D4494 /* observable.h */, + 3785990E0FDD7E8E00EF9D03 /* optionparser.h */, + 3785990F0FDD7E8E00EF9D03 /* optionparser.cpp */, 373C68C40FC1C25F00137ACD /* overlap.hpp */, 373C68C30FC1C25F00137ACD /* overlap.cpp */, 37D927FC0F21331F001D4494 /* progress.hpp */, @@ -592,8 +588,6 @@ 37D928050F21331F001D4494 /* rarefact.cpp */, 37D928090F21331F001D4494 /* rarefactioncurvedata.h */, 3796441D0FB9B9650081FDB6 /* read */, - 37D928210F21331F001D4494 /* shared.h */, - 37D928200F21331F001D4494 /* shared.cpp */, 211C38310F961DD400FEE541 /* sharedutilities.h */, 211C38300F961DD400FEE541 /* sharedutilities.cpp */, 37D928420F21331F001D4494 /* singlelinkage.cpp */, @@ -789,10 +783,10 @@ 375873F30F7D648F0040F377 /* libshuffcommand.cpp */, 21E859D60FC4632E005E1A48 /* matrixoutputcommand.h */, 21E859D70FC4632E005E1A48 /* matrixoutputcommand.cpp */, - 375873F60F7D649C0040F377 /* nocommands.cpp */, + 7E5A17AD0FE57292003C6A03 /* mergefilecommand.h */, + 7E5A17AE0FE57292003C6A03 /* mergefilecommand.cpp */, 375873F70F7D649C0040F377 /* nocommands.h */, - 37D927FA0F21331F001D4494 /* parselistcommand.h */, - 37D927F90F21331F001D4494 /* parselistcommand.cpp */, + 375873F60F7D649C0040F377 /* nocommands.cpp */, 3792946E0F2E191800B9034A /* parsimonycommand.h */, 3792946F0F2E191800B9034A /* parsimonycommand.cpp */, 37D927FE0F21331F001D4494 /* quitcommand.h */, @@ -811,8 +805,8 @@ 7E09C5130FDA79C5002ECAE5 /* reversecommand.cpp */, 371B30B30FD7EE67000414CA /* screenseqscommand.h */, 371B30B20FD7EE67000414CA /* screenseqscommand.cpp */, - 3799A94E0FD6A58C00E33EDE /* seqsummarycommand.cpp */, 3799A94F0FD6A58C00E33EDE /* seqsummarycommand.h */, + 3799A94E0FD6A58C00E33EDE /* seqsummarycommand.cpp */, 37D928270F21331F001D4494 /* sharedcommand.h */, 37D928260F21331F001D4494 /* sharedcommand.cpp */, 37D928470F21331F001D4494 /* summarycommand.h */, @@ -898,12 +892,8 @@ 37D928B10F213472001D4494 /* errorcheckor */ = { isa = PBXGroup; children = ( - 37D927DA0F21331F001D4494 /* errorchecking.h */, - 37D927D90F21331F001D4494 /* errorchecking.cpp */, 37D928500F21331F001D4494 /* validcalculator.h */, 37D9284F0F21331F001D4494 /* validcalculator.cpp */, - 37D928520F21331F001D4494 /* validcommands.h */, - 37D928510F21331F001D4494 /* validcommands.cpp */, 37D928540F21331F001D4494 /* validparameter.h */, 37D928530F21331F001D4494 /* validparameter.cpp */, ); @@ -975,7 +965,6 @@ 37D928610F21331F001D4494 /* completelinkage.cpp in Sources */, 37D928620F21331F001D4494 /* database.cpp in Sources */, 37D928630F21331F001D4494 /* engine.cpp in Sources */, - 37D928640F21331F001D4494 /* errorchecking.cpp in Sources */, 37D928650F21331F001D4494 /* fastamap.cpp in Sources */, 37D928660F21331F001D4494 /* fileoutput.cpp in Sources */, 37D928670F21331F001D4494 /* globaldata.cpp in Sources */, @@ -990,7 +979,6 @@ 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 */, @@ -1002,7 +990,6 @@ 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 */, @@ -1025,7 +1012,6 @@ 37D9289B0F21331F001D4494 /* summarysharedcommand.cpp in Sources */, 37D9289C0F21331F001D4494 /* uvest.cpp in Sources */, 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 */, @@ -1115,6 +1101,8 @@ 7E09C5360FDA7F65002ECAE5 /* trimseqscommand.cpp in Sources */, 378598660FDD497000EF9D03 /* heatmapsimcommand.cpp in Sources */, 378598740FDD4C1500EF9D03 /* heatmapsim.cpp in Sources */, + 378599100FDD7E8E00EF9D03 /* optionparser.cpp in Sources */, + 7E5A17AF0FE57292003C6A03 /* mergefilecommand.cpp in Sources */, ); runOnlyForDeploymentPostprocessing = 0; }; @@ -1153,10 +1141,15 @@ isa = XCBuildConfiguration; buildSettings = { GCC_OPTIMIZATION_LEVEL = 3; + GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; + GCC_WARN_ALLOW_INCOMPLETE_PROTOCOL = NO; + GCC_WARN_PEDANTIC = NO; GCC_WARN_UNUSED_VARIABLE = YES; + OTHER_CPLUSPLUSFLAGS = ""; PREBINDING = NO; SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk"; + WARNING_CFLAGS = ""; }; name = Debug; }; @@ -1168,10 +1161,15 @@ i386, ); GCC_OPTIMIZATION_LEVEL = 3; + GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; + GCC_WARN_ALLOW_INCOMPLETE_PROTOCOL = NO; + GCC_WARN_PEDANTIC = NO; GCC_WARN_UNUSED_VARIABLE = YES; + OTHER_CPLUSPLUSFLAGS = ""; PREBINDING = NO; SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk"; + WARNING_CFLAGS = ""; }; name = Release; };