]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
added get.lineage and remove.lineage commands
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index 71436b740ed32cdcbb984847f71ca81ea44da0ae..9c147b81cdc3158238e6867d2d28375146f2eb5b 100644 (file)
@@ -30,6 +30,7 @@
                A7118EE611CFCAC000CFDE03 /* degapseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = degapseqscommand.cpp; sourceTree = "<group>"; };
                A7118F0F11CFD5DC00CFDE03 /* getrelabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getrelabundcommand.h; sourceTree = "<group>"; };
                A7118F1011CFD5DC00CFDE03 /* getrelabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getrelabundcommand.cpp; sourceTree = "<group>"; };
+               A71BA75F1225694E00C57506 /* clearcut.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clearcut.cpp; sourceTree = "<group>"; };
                A71D924211AEB42400D00CBC /* clustersplitcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clustersplitcommand.cpp; sourceTree = "<group>"; };
                A71D924311AEB42400D00CBC /* clustersplitcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clustersplitcommand.h; sourceTree = "<group>"; };
                A71D924411AEB42400D00CBC /* splitabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = splitabundcommand.cpp; sourceTree = "<group>"; };
                A747E79C1163442A00FB9042 /* chimeracheckcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeracheckcommand.cpp; sourceTree = "<group>"; };
                A747E81C116365E000FB9042 /* chimeraslayercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraslayercommand.h; sourceTree = "<group>"; };
                A747E81D116365E000FB9042 /* chimeraslayercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraslayercommand.cpp; sourceTree = "<group>"; };
+               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>"; };
                A7639F8D1175DF35008F5578 /* makefile */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.make; path = makefile; sourceTree = "<group>"; };
+               A768D95D1248FEAA008AB1D0 /* mothur */ = {isa = PBXFileReference; lastKnownFileType = "compiled.mach-o.executable"; path = mothur; sourceTree = "<group>"; };
                A76AAD02117F322B003D8DA1 /* phylosummary.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylosummary.h; sourceTree = "<group>"; };
                A76AAD03117F322B003D8DA1 /* phylosummary.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylosummary.cpp; sourceTree = "<group>"; };
                A76C4A1011876BAF0009460B /* setlogfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = setlogfilecommand.h; sourceTree = SOURCE_ROOT; };
                A7825503116519F70002E2DD /* chimerabellerophoncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerabellerophoncommand.cpp; sourceTree = "<group>"; };
                A78434881162224F00100BE0 /* chimeraccodecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraccodecommand.h; sourceTree = "<group>"; };
                A78434891162224F00100BE0 /* chimeraccodecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraccodecommand.cpp; sourceTree = "<group>"; };
+               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>"; };
                A7AE6302121C3408001DE6FC /* sharedrabundfloatvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedrabundfloatvector.h; sourceTree = "<group>"; };
                A7AE6303121C3408001DE6FC /* sharedrabundfloatvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedrabundfloatvector.cpp; sourceTree = "<group>"; };
                A7BBDA7B11B5694E006E6551 /* classifyotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = classifyotucommand.h; sourceTree = "<group>"; };
                A7DA217A113FECD400BF472F /* weighted.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = weighted.h; sourceTree = "<group>"; };
                A7DA217B113FECD400BF472F /* whittaker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = whittaker.cpp; sourceTree = "<group>"; };
                A7DA217C113FECD400BF472F /* whittaker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = whittaker.h; sourceTree = "<group>"; };
-               A7DF0AD3121EBB14004A03EA /* clearcut.c */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.c; path = clearcut.c; sourceTree = "<group>"; };
                A7DF0AD4121EBB14004A03EA /* clearcut.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clearcut.h; sourceTree = "<group>"; };
-               A7DF0AD5121EBB14004A03EA /* cmdargs.c */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.c; path = cmdargs.c; sourceTree = "<group>"; };
+               A7DF0AD5121EBB14004A03EA /* cmdargs.cpp */ = {isa = PBXFileReference; explicitFileType = sourcecode.cpp.cpp; fileEncoding = 4; path = cmdargs.cpp; sourceTree = "<group>"; };
                A7DF0AD6121EBB14004A03EA /* cmdargs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cmdargs.h; sourceTree = "<group>"; };
                A7DF0AD7121EBB14004A03EA /* common.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = common.h; sourceTree = "<group>"; };
                A7DF0AD8121EBB14004A03EA /* dayhoff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dayhoff.h; sourceTree = "<group>"; };
-               A7DF0AD9121EBB14004A03EA /* distclearcut.c */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.c; path = distclearcut.c; sourceTree = "<group>"; };
+               A7DF0AD9121EBB14004A03EA /* distclearcut.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distclearcut.cpp; sourceTree = "<group>"; };
                A7DF0ADA121EBB14004A03EA /* distclearcut.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = distclearcut.h; sourceTree = "<group>"; };
-               A7DF0ADB121EBB14004A03EA /* dmat.c */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.c; path = dmat.c; sourceTree = "<group>"; };
+               A7DF0ADB121EBB14004A03EA /* dmat.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = dmat.cpp; sourceTree = "<group>"; };
                A7DF0ADC121EBB14004A03EA /* dmat.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dmat.h; sourceTree = "<group>"; };
-               A7DF0ADD121EBB14004A03EA /* fasta.c */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.c; path = fasta.c; sourceTree = "<group>"; };
+               A7DF0ADD121EBB14004A03EA /* fasta.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fasta.cpp; sourceTree = "<group>"; };
                A7DF0ADE121EBB14004A03EA /* fasta.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fasta.h; sourceTree = "<group>"; };
-               A7DF0ADF121EBB14004A03EA /* getopt_long.c */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.c; path = getopt_long.c; sourceTree = "<group>"; };
+               A7DF0ADF121EBB14004A03EA /* getopt_long.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getopt_long.cpp; sourceTree = "<group>"; };
                A7DF0AE0121EBB14004A03EA /* getopt_long.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getopt_long.h; sourceTree = "<group>"; };
-               A7DF0AE1121EBB14004A03EA /* prng.c */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.c; path = prng.c; sourceTree = "<group>"; };
+               A7DF0AE1121EBB14004A03EA /* prng.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = prng.cpp; sourceTree = "<group>"; };
                A7DF0AE2121EBB14004A03EA /* prng.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = prng.h; sourceTree = "<group>"; };
                A7E8338B115BBDAA00739EC4 /* parsesffcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsesffcommand.cpp; sourceTree = "<group>"; };
                A7E8338C115BBDAA00739EC4 /* parsesffcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsesffcommand.h; sourceTree = "<group>"; };
+               A7F139481247C3CB0033324C /* splitgroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = splitgroupscommand.h; sourceTree = "<group>"; };
+               A7F139491247C3CB0033324C /* splitgroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = splitgroupscommand.cpp; sourceTree = "<group>"; };
+               A7F6C8E1124229F900299875 /* fisher2.c */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.c; path = fisher2.c; sourceTree = "<group>"; };
+               A7F6C8E2124229F900299875 /* fisher2.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fisher2.h; sourceTree = "<group>"; };
+               A7F6C8E3124229F900299875 /* metastats2.c */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.c; path = metastats2.c; sourceTree = "<group>"; };
+               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 */
                08FB7794FE84155DC02AAC07 /* mothur */ = {
                        isa = PBXGroup;
                        children = (
+                               A768D95D1248FEAA008AB1D0 /* mothur */,
                                A7639F8D1175DF35008F5578 /* makefile */,
                                A7DA1FF0113FECD400BF472F /* alignment.cpp */,
                                A7DA1FF1113FECD400BF472F /* alignment.hpp */,
                                A7DA2082113FECD400BF472F /* inputdata.h */,
                                A7DA208B113FECD400BF472F /* libshuff.cpp */,
                                A7DA208C113FECD400BF472F /* libshuff.h */,
+                               A7F6C8DC1242299300299875 /* metastatsource */,
                                A7DA209E113FECD400BF472F /* mothur.cpp */,
                                A7DA209F113FECD400BF472F /* mothur.h */,
                                A7DA20A0113FECD400BF472F /* mothurout.cpp */,
                                A7D215C911996C6E00F13F13 /* clearcutcommand.cpp */,
                                A7DA2021113FECD400BF472F /* clustercommand.cpp */,
                                A7DA2022113FECD400BF472F /* clustercommand.h */,
+                               A74A9C03124B72DB000D5D25 /* clusterfragmentscommand.h */,
+                               A74A9C04124B72DB000D5D25 /* clusterfragmentscommand.cpp */,
                                A71D924311AEB42400D00CBC /* clustersplitcommand.h */,
                                A71D924211AEB42400D00CBC /* clustersplitcommand.cpp */,
-                               A7DA2025113FECD400BF472F /* collectcommand.cpp */,
                                A7DA2026113FECD400BF472F /* collectcommand.h */,
+                               A7DA2025113FECD400BF472F /* collectcommand.cpp */,
                                A7DA2029113FECD400BF472F /* collectsharedcommand.cpp */,
                                A7DA202A113FECD400BF472F /* collectsharedcommand.h */,
                                A7DA2031113FECD400BF472F /* consensuscommand.cpp */,
                                A7DA205B113FECD400BF472F /* getgroupcommand.h */,
                                A7DA205C113FECD400BF472F /* getlabelcommand.cpp */,
                                A7DA205D113FECD400BF472F /* getlabelcommand.h */,
+                               A787A24F124CB46C0076EB84 /* getlineagecommand.h */,
+                               A787A250124CB46C0076EB84 /* getlineagecommand.cpp */,
                                A7DA205F113FECD400BF472F /* getlistcountcommand.h */,
                                A7DA205E113FECD400BF472F /* getlistcountcommand.cpp */,
                                A7DA2061113FECD400BF472F /* getoturepcommand.h */,
                                A7DA207D113FECD400BF472F /* heatmapsimcommand.h */,
                                A7DA207E113FECD400BF472F /* helpcommand.cpp */,
                                A7DA207F113FECD400BF472F /* helpcommand.h */,
-                               A7DA208D113FECD400BF472F /* libshuffcommand.cpp */,
                                A7DA208E113FECD400BF472F /* libshuffcommand.h */,
+                               A7DA208D113FECD400BF472F /* libshuffcommand.cpp */,
                                A7DA2090113FECD400BF472F /* listseqscommand.h */,
                                A7DA208F113FECD400BF472F /* listseqscommand.cpp */,
                                A703FE931194645F002C397E /* makegroupcommand.h */,
                                A7DA2099113FECD400BF472F /* matrixoutputcommand.h */,
                                A7DA209A113FECD400BF472F /* mergefilecommand.cpp */,
                                A7DA209B113FECD400BF472F /* mergefilecommand.h */,
+                               A7F6C8EA12423C0300299875 /* metastatscommand.h */,
+                               A7F6C8EB12423C0300299875 /* metastatscommand.cpp */,
                                A7DA209C113FECD400BF472F /* mgclustercommand.cpp */,
                                A7DA209D113FECD400BF472F /* mgclustercommand.h */,
                                A7DA20AC113FECD400BF472F /* nocommands.cpp */,
                                A7DA20AD113FECD400BF472F /* nocommands.h */,
+                               A798626D1240D91B005FC847 /* normalizesharedcommand.h */,
+                               A798626E1240D91B005FC847 /* normalizesharedcommand.cpp */,
                                A7DA20B8113FECD400BF472F /* otuhierarchycommand.cpp */,
                                A7DA20B9113FECD400BF472F /* otuhierarchycommand.h */,
                                A7DA20BC113FECD400BF472F /* parselistscommand.cpp */,
                                A7DA20EA113FECD400BF472F /* readotucommand.cpp */,
                                A7DA20F1113FECD400BF472F /* readtreecommand.h */,
                                A7DA20F0113FECD400BF472F /* readtreecommand.cpp */,
+                               A787A28E124CE1470076EB84 /* removelineagecommand.h */,
+                               A787A28F124CE1470076EB84 /* removelineagecommand.cpp */,
                                A7DA20F3113FECD400BF472F /* removeseqscommand.h */,
                                A7DA20F2113FECD400BF472F /* removeseqscommand.cpp */,
                                A7DA20F5113FECD400BF472F /* reversecommand.h */,
                                A7DA210F113FECD400BF472F /* sharedcommand.cpp */,
                                A71D924511AEB42400D00CBC /* splitabundcommand.h */,
                                A71D924411AEB42400D00CBC /* splitabundcommand.cpp */,
+                               A7F139481247C3CB0033324C /* splitgroupscommand.h */,
+                               A7F139491247C3CB0033324C /* splitgroupscommand.cpp */,
                                A7DA2155113FECD400BF472F /* summarycommand.h */,
                                A7DA2154113FECD400BF472F /* summarycommand.cpp */,
                                A7DA2159113FECD400BF472F /* summarysharedcommand.h */,
                        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 */