X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=855dad891d3b9b4e3b0422e57a3a5be488aa3c12;hb=6cf9539162b0fb0b5c0b99673e999df3cd717c55;hp=ebe8a90115bbc86641664e6922ba39a23e92de25;hpb=d84bb41d7dadcfa2c67ce5edb9b94060e5659fa7;p=mothur.git

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index ebe8a90..855dad8 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -30,16 +30,23 @@
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 		A71D924711AEB42400D00CBC /* splitmatrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = splitmatrix.h; sourceTree = "<group>"; };
+		A724C2B61254961E006BB1C7 /* parsefastaqcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsefastaqcommand.h; sourceTree = "<group>"; };
+		A724C2B71254961E006BB1C7 /* parsefastaqcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsefastaqcommand.cpp; sourceTree = "<group>"; };
 		A72B3A62118B37FD004B9F8D /* phylodiversitycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylodiversitycommand.h; sourceTree = "<group>"; };
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+		A72C66A1125B356F0058C2F9 /* pipelinepdscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pipelinepdscommand.h; sourceTree = "<group>"; };
+		A72C66A2125B356F0058C2F9 /* pipelinepdscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pipelinepdscommand.cpp; sourceTree = "<group>"; };
+		A72E295D127ADCE300905B79 /* clusterclassic.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clusterclassic.h; sourceTree = "<group>"; };
+		A72E295E127ADCE300905B79 /* clusterclassic.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clusterclassic.cpp; sourceTree = "<group>"; };
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@@ -48,11 +55,22 @@
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+		A74A9C03124B72DB000D5D25 /* clusterfragmentscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clusterfragmentscommand.h; sourceTree = "<group>"; };
+		A74A9C04124B72DB000D5D25 /* clusterfragmentscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clusterfragmentscommand.cpp; sourceTree = "<group>"; };
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+		A7653CB212789EFD009D6C09 /* subsamplecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = subsamplecommand.cpp; sourceTree = "<group>"; };
+		A7653D111278B09C009D6C09 /* clusterdoturcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clusterdoturcommand.h; sourceTree = "<group>"; };
+		A7653D121278B09C009D6C09 /* clusterdoturcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clusterdoturcommand.cpp; sourceTree = "<group>"; };
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+		A77D787C126F387700F351BD /* pairwiseseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pairwiseseqscommand.cpp; sourceTree = "<group>"; };
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@@ -60,6 +78,12 @@
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+		A787A24F124CB46C0076EB84 /* getlineagecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlineagecommand.h; sourceTree = "<group>"; };
+		A787A250124CB46C0076EB84 /* getlineagecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlineagecommand.cpp; sourceTree = "<group>"; };
+		A787A28E124CE1470076EB84 /* removelineagecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removelineagecommand.h; sourceTree = "<group>"; };
+		A787A28F124CE1470076EB84 /* removelineagecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removelineagecommand.cpp; sourceTree = "<group>"; };
+		A798626D1240D91B005FC847 /* normalizesharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = normalizesharedcommand.h; sourceTree = "<group>"; };
+		A798626E1240D91B005FC847 /* normalizesharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = normalizesharedcommand.cpp; sourceTree = "<group>"; };
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@@ -466,30 +490,38 @@
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+		A7DF0AD5121EBB14004A03EA /* cmdargs.cpp */ = {isa = PBXFileReference; explicitFileType = sourcecode.cpp.cpp; fileEncoding = 4; path = cmdargs.cpp; sourceTree = "<group>"; };
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+		A7F139491247C3CB0033324C /* splitgroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = splitgroupscommand.cpp; sourceTree = "<group>"; };
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+		A7F6C8EA12423C0300299875 /* metastatscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = metastatscommand.h; sourceTree = "<group>"; };
+		A7F6C8EB12423C0300299875 /* metastatscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = metastatscommand.cpp; sourceTree = "<group>"; };
+		A7F6C9D512425D4600299875 /* metastats.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = metastats.h; sourceTree = "<group>"; };
 /* End PBXFileReference section */
 
 /* Begin PBXGroup section */
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 			isa = PBXGroup;
 			children = (
+				A768D95D1248FEAA008AB1D0 /* mothur */,
 				A7639F8D1175DF35008F5578 /* makefile */,
 				A7DA1FF0113FECD400BF472F /* alignment.cpp */,
 				A7DA1FF1113FECD400BF472F /* alignment.hpp */,
@@ -498,6 +530,8 @@
 				A7DA1FFF113FECD400BF472F /* blastalign.cpp */,
 				A7DA201F113FECD400BF472F /* cluster.cpp */,
 				A7DA2020113FECD400BF472F /* cluster.hpp */,
+				A72E295D127ADCE300905B79 /* clusterclassic.h */,
+				A72E295E127ADCE300905B79 /* clusterclassic.cpp */,
 				A7CB593B11402EF90010EB83 /* calculators */,
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@@ -535,6 +569,7 @@
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 				A7DA208B113FECD400BF472F /* libshuff.cpp */,
 				A7DA208C113FECD400BF472F /* libshuff.h */,
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@@ -709,12 +744,12 @@
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@@ -733,78 +768,96 @@
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 				A7DA203F113FECD400BF472F /* distancecommand.h */,
-				A7DA204F113FECD400BF472F /* filterseqscommand.cpp */,
+				A7DA203E113FECD400BF472F /* distancecommand.cpp */,
+				A76714DD126DE45A003F359A /* deuniqueseqscommand.h */,
+				A76714DE126DE45A003F359A /* deuniqueseqscommand.cpp */,
 				A7DA2050113FECD400BF472F /* filterseqscommand.h */,
-				A7DA205A113FECD400BF472F /* getgroupcommand.cpp */,
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 				A7DA205B113FECD400BF472F /* getgroupcommand.h */,
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+				A7DA205A113FECD400BF472F /* getgroupcommand.cpp */,
 				A7DA205D113FECD400BF472F /* getlabelcommand.h */,
+				A7DA205C113FECD400BF472F /* getlabelcommand.cpp */,
+				A787A24F124CB46C0076EB84 /* getlineagecommand.h */,
+				A787A250124CB46C0076EB84 /* getlineagecommand.cpp */,
 				A7DA205F113FECD400BF472F /* getlistcountcommand.h */,
 				A7DA205E113FECD400BF472F /* getlistcountcommand.cpp */,
 				A7DA2061113FECD400BF472F /* getoturepcommand.h */,
 				A7DA2060113FECD400BF472F /* getoturepcommand.cpp */,
-				A7DA2062113FECD400BF472F /* getrabundcommand.cpp */,
 				A7DA2063113FECD400BF472F /* getrabundcommand.h */,
+				A7DA2062113FECD400BF472F /* getrabundcommand.cpp */,
 				A7118F0F11CFD5DC00CFDE03 /* getrelabundcommand.h */,
 				A7118F1011CFD5DC00CFDE03 /* getrelabundcommand.cpp */,
-				A7DA2064113FECD400BF472F /* getsabundcommand.cpp */,
 				A7DA2065113FECD400BF472F /* getsabundcommand.h */,
+				A7DA2064113FECD400BF472F /* getsabundcommand.cpp */,
 				A7DA2067113FECD400BF472F /* getseqscommand.h */,
 				A7DA2066113FECD400BF472F /* getseqscommand.cpp */,
-				A7DA2068113FECD400BF472F /* getsharedotucommand.cpp */,
 				A7DA2069113FECD400BF472F /* getsharedotucommand.h */,
-				A7DA2074113FECD400BF472F /* hclustercommand.cpp */,
+				A7DA2068113FECD400BF472F /* getsharedotucommand.cpp */,
 				A7DA2075113FECD400BF472F /* hclustercommand.h */,
-				A7DA2078113FECD400BF472F /* heatmapcommand.cpp */,
+				A7DA2074113FECD400BF472F /* hclustercommand.cpp */,
 				A7DA2079113FECD400BF472F /* heatmapcommand.h */,
-				A7DA207C113FECD400BF472F /* heatmapsimcommand.cpp */,
+				A7DA2078113FECD400BF472F /* heatmapcommand.cpp */,
 				A7DA207D113FECD400BF472F /* heatmapsimcommand.h */,
-				A7DA207E113FECD400BF472F /* helpcommand.cpp */,
+				A7DA207C113FECD400BF472F /* heatmapsimcommand.cpp */,
 				A7DA207F113FECD400BF472F /* helpcommand.h */,
-				A7DA208D113FECD400BF472F /* libshuffcommand.cpp */,
+				A7DA207E113FECD400BF472F /* helpcommand.cpp */,
 				A7DA208E113FECD400BF472F /* libshuffcommand.h */,
+				A7DA208D113FECD400BF472F /* libshuffcommand.cpp */,
 				A7DA2090113FECD400BF472F /* listseqscommand.h */,
 				A7DA208F113FECD400BF472F /* listseqscommand.cpp */,
 				A703FE931194645F002C397E /* makegroupcommand.h */,
 				A703FE941194645F002C397E /* makegroupcommand.cpp */,
-				A7DA2098113FECD400BF472F /* matrixoutputcommand.cpp */,
 				A7DA2099113FECD400BF472F /* matrixoutputcommand.h */,
-				A7DA209A113FECD400BF472F /* mergefilecommand.cpp */,
+				A7DA2098113FECD400BF472F /* matrixoutputcommand.cpp */,
 				A7DA209B113FECD400BF472F /* mergefilecommand.h */,
-				A7DA209C113FECD400BF472F /* mgclustercommand.cpp */,
+				A7DA209A113FECD400BF472F /* mergefilecommand.cpp */,
+				A7F6C8EA12423C0300299875 /* metastatscommand.h */,
+				A7F6C8EB12423C0300299875 /* metastatscommand.cpp */,
 				A7DA209D113FECD400BF472F /* mgclustercommand.h */,
-				A7DA20AC113FECD400BF472F /* nocommands.cpp */,
+				A7DA209C113FECD400BF472F /* mgclustercommand.cpp */,
 				A7DA20AD113FECD400BF472F /* nocommands.h */,
-				A7DA20B8113FECD400BF472F /* otuhierarchycommand.cpp */,
+				A7DA20AC113FECD400BF472F /* nocommands.cpp */,
+				A798626D1240D91B005FC847 /* normalizesharedcommand.h */,
+				A798626E1240D91B005FC847 /* normalizesharedcommand.cpp */,
 				A7DA20B9113FECD400BF472F /* otuhierarchycommand.h */,
-				A7DA20BC113FECD400BF472F /* parselistscommand.cpp */,
+				A7DA20B8113FECD400BF472F /* otuhierarchycommand.cpp */,
+				A77D787B126F387700F351BD /* pairwiseseqscommand.h */,
+				A77D787C126F387700F351BD /* pairwiseseqscommand.cpp */,
+				A724C2B61254961E006BB1C7 /* parsefastaqcommand.h */,
+				A724C2B71254961E006BB1C7 /* parsefastaqcommand.cpp */,
 				A7DA20BD113FECD400BF472F /* parselistscommand.h */,
-				A7E8338B115BBDAA00739EC4 /* parsesffcommand.cpp */,
+				A7DA20BC113FECD400BF472F /* parselistscommand.cpp */,
 				A7E8338C115BBDAA00739EC4 /* parsesffcommand.h */,
-				A7DA20C0113FECD400BF472F /* parsimonycommand.cpp */,
+				A7E8338B115BBDAA00739EC4 /* parsesffcommand.cpp */,
 				A7DA20C1113FECD400BF472F /* parsimonycommand.h */,
+				A7DA20C0113FECD400BF472F /* parsimonycommand.cpp */,
 				A7DA20C3113FECD400BF472F /* pcacommand.h */,
 				A7DA20C2113FECD400BF472F /* pcacommand.cpp */,
 				A72B3A62118B37FD004B9F8D /* phylodiversitycommand.h */,
 				A72B3A63118B37FD004B9F8D /* phylodiversitycommand.cpp */,
 				A7DA20C7113FECD400BF472F /* phylotypecommand.h */,
 				A7DA20C6113FECD400BF472F /* phylotypecommand.cpp */,
+				A72C66A1125B356F0058C2F9 /* pipelinepdscommand.h */,
+				A72C66A2125B356F0058C2F9 /* pipelinepdscommand.cpp */,
 				A7DA20CB113FECD400BF472F /* preclustercommand.h */,
 				A7DA20CA113FECD400BF472F /* preclustercommand.cpp */,
 				A7DA20D1113FECD400BF472F /* quitcommand.h */,
@@ -819,6 +872,8 @@
 				A7DA20EA113FECD400BF472F /* readotucommand.cpp */,
 				A7DA20F1113FECD400BF472F /* readtreecommand.h */,
 				A7DA20F0113FECD400BF472F /* readtreecommand.cpp */,
+				A787A28E124CE1470076EB84 /* removelineagecommand.h */,
+				A787A28F124CE1470076EB84 /* removelineagecommand.cpp */,
 				A7DA20F3113FECD400BF472F /* removeseqscommand.h */,
 				A7DA20F2113FECD400BF472F /* removeseqscommand.cpp */,
 				A7DA20F5113FECD400BF472F /* reversecommand.h */,
@@ -843,6 +898,10 @@
 				A7DA210F113FECD400BF472F /* sharedcommand.cpp */,
 				A71D924511AEB42400D00CBC /* splitabundcommand.h */,
 				A71D924411AEB42400D00CBC /* splitabundcommand.cpp */,
+				A7F139481247C3CB0033324C /* splitgroupscommand.h */,
+				A7F139491247C3CB0033324C /* splitgroupscommand.cpp */,
+				A7653CB112789EFD009D6C09 /* subsamplecommand.h */,
+				A7653CB212789EFD009D6C09 /* subsamplecommand.cpp */,
 				A7DA2155113FECD400BF472F /* summarycommand.h */,
 				A7DA2154113FECD400BF472F /* summarycommand.cpp */,
 				A7DA2159113FECD400BF472F /* summarysharedcommand.h */,
@@ -1008,25 +1067,36 @@
 			isa = PBXGroup;
 			children = (
 				A7DF0AD4121EBB14004A03EA /* clearcut.h */,
-				A7DF0AD3121EBB14004A03EA /* clearcut.c */,
-				A7DF0AD6121EBB14004A03EA /* cmdargs.h */,
+				A71BA75F1225694E00C57506 /* clearcut.cpp */,
 				A7DF0AD7121EBB14004A03EA /* common.h */,
 				A7DF0AD8121EBB14004A03EA /* dayhoff.h */,
-				A7DF0AD5121EBB14004A03EA /* cmdargs.c */,
-				A7DF0AD9121EBB14004A03EA /* distclearcut.c */,
+				A7DF0AD6121EBB14004A03EA /* cmdargs.h */,
+				A7DF0AD5121EBB14004A03EA /* cmdargs.cpp */,
+				A7DF0AD9121EBB14004A03EA /* distclearcut.cpp */,
 				A7DF0ADA121EBB14004A03EA /* distclearcut.h */,
-				A7DF0ADB121EBB14004A03EA /* dmat.c */,
+				A7DF0ADB121EBB14004A03EA /* dmat.cpp */,
 				A7DF0ADC121EBB14004A03EA /* dmat.h */,
-				A7DF0ADD121EBB14004A03EA /* fasta.c */,
+				A7DF0ADD121EBB14004A03EA /* fasta.cpp */,
 				A7DF0ADE121EBB14004A03EA /* fasta.h */,
-				A7DF0ADF121EBB14004A03EA /* getopt_long.c */,
+				A7DF0ADF121EBB14004A03EA /* getopt_long.cpp */,
 				A7DF0AE0121EBB14004A03EA /* getopt_long.h */,
 				A7DF0AE2121EBB14004A03EA /* prng.h */,
-				A7DF0AE1121EBB14004A03EA /* prng.c */,
+				A7DF0AE1121EBB14004A03EA /* prng.cpp */,
 			);
 			name = clearcutsource;
 			sourceTree = "<group>";
 		};
+		A7F6C8DC1242299300299875 /* metastatsource */ = {
+			isa = PBXGroup;
+			children = (
+				A7F6C8E2124229F900299875 /* fisher2.h */,
+				A7F6C8E1124229F900299875 /* fisher2.c */,
+				A7F6C9D512425D4600299875 /* metastats.h */,
+				A7F6C8E3124229F900299875 /* metastats2.c */,
+			);
+			name = metastatsource;
+			sourceTree = "<group>";
+		};
 /* End PBXGroup section */
 
 /* Begin PBXLegacyTarget section */
@@ -1055,6 +1125,12 @@
 			buildConfigurationList = 1DEB919308733D9F0010E9CD /* Build configuration list for PBXProject "Mothur" */;
 			compatibilityVersion = "Xcode 3.0";
 			hasScannedForEncodings = 1;
+			knownRegions = (
+				English,
+				Japanese,
+				French,
+				German,
+			);
 			mainGroup = 08FB7794FE84155DC02AAC07 /* mothur */;
 			projectDirPath = "";
 			projectRoot = "";