added pipeline commands which involved change to command factory and command class...

[mothur.git] / Mothur.xcodeproj / project.pbxproj

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index e2673fc9331524944d0b8b3553e00c42a1f34766..5e84c7eabc213ba337255d55f61034df9e7384fa 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -43,6 +43,8 @@
                A72B3A63118B37FD004B9F8D /* phylodiversitycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversitycommand.cpp; sourceTree = "<group>"; };
                A72B3A7B118B4D1B004B9F8D /* phylodiversity.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylodiversity.h; sourceTree = "<group>"; };
                A72B3A7C118B4D1B004B9F8D /* phylodiversity.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversity.cpp; sourceTree = "<group>"; };
+               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>"; };
                A732505E11E49EF100484B90 /* sffinfocommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sffinfocommand.h; sourceTree = "<group>"; };
                A732505F11E49EF100484B90 /* sffinfocommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sffinfocommand.cpp; sourceTree = "<group>"; };
                A73953DA11987ED100B0B160 /* chopseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chopseqscommand.h; sourceTree = "<group>"; };
@@ -730,12 +732,12 @@
                                A7DA1FEE113FECD400BF472F /* aligncommand.cpp */,
                                A7DA1FFE113FECD400BF472F /* binsequencecommand.h */,
                                A7DA1FFD113FECD400BF472F /* binsequencecommand.cpp */,
-                               A7DA2007113FECD400BF472F /* bootstrapsharedcommand.cpp */,
                                A7DA2008113FECD400BF472F /* bootstrapsharedcommand.h */,
+                               A7DA2007113FECD400BF472F /* bootstrapsharedcommand.cpp */,
                                A7D216061199C47F00F13F13 /* catchallcommand.h */,
                                A7D216071199C47F00F13F13 /* catchallcommand.cpp */,
-                               A7DA2017113FECD400BF472F /* chimeraseqscommand.cpp */,
                                A7DA2018113FECD400BF472F /* chimeraseqscommand.h */,
+                               A7DA2017113FECD400BF472F /* chimeraseqscommand.cpp */,
                                A7825502116519F70002E2DD /* chimerabellerophoncommand.h */,
                                A7825503116519F70002E2DD /* chimerabellerophoncommand.cpp */,
                                A747E79B1163442A00FB9042 /* chimeracheckcommand.h */,
@@ -754,88 +756,90 @@
                                A7BBDA7C11B5694E006E6551 /* classifyotucommand.cpp */,
                                A7D215C811996C6E00F13F13 /* clearcutcommand.h */,
                                A7D215C911996C6E00F13F13 /* clearcutcommand.cpp */,
-                               A7DA2021113FECD400BF472F /* clustercommand.cpp */,
                                A7DA2022113FECD400BF472F /* clustercommand.h */,
+                               A7DA2021113FECD400BF472F /* clustercommand.cpp */,
                                A74A9C03124B72DB000D5D25 /* clusterfragmentscommand.h */,
                                A74A9C04124B72DB000D5D25 /* clusterfragmentscommand.cpp */,
                                A71D924311AEB42400D00CBC /* clustersplitcommand.h */,
                                A71D924211AEB42400D00CBC /* clustersplitcommand.cpp */,
                                A7DA2026113FECD400BF472F /* collectcommand.h */,
                                A7DA2025113FECD400BF472F /* collectcommand.cpp */,
-                               A7DA2029113FECD400BF472F /* collectsharedcommand.cpp */,
                                A7DA202A113FECD400BF472F /* collectsharedcommand.h */,
-                               A7DA2031113FECD400BF472F /* consensuscommand.cpp */,
+                               A7DA2029113FECD400BF472F /* collectsharedcommand.cpp */,
                                A7DA2032113FECD400BF472F /* consensuscommand.h */,
+                               A7DA2031113FECD400BF472F /* consensuscommand.cpp */,
                                A7118EE511CFCAC000CFDE03 /* degapseqscommand.h */,
                                A7118EE611CFCAC000CFDE03 /* degapseqscommand.cpp */,
-                               A7DA203A113FECD400BF472F /* deconvolutecommand.cpp */,
                                A7DA203B113FECD400BF472F /* deconvolutecommand.h */,
-                               A7DA203E113FECD400BF472F /* distancecommand.cpp */,
+                               A7DA203A113FECD400BF472F /* deconvolutecommand.cpp */,
                                A7DA203F113FECD400BF472F /* distancecommand.h */,
-                               A7DA204F113FECD400BF472F /* filterseqscommand.cpp */,
+                               A7DA203E113FECD400BF472F /* distancecommand.cpp */,
                                A7DA2050113FECD400BF472F /* filterseqscommand.h */,
-                               A7DA205A113FECD400BF472F /* getgroupcommand.cpp */,
+                               A7DA204F113FECD400BF472F /* filterseqscommand.cpp */,
                                A7DA205B113FECD400BF472F /* getgroupcommand.h */,
-                               A7DA205C113FECD400BF472F /* getlabelcommand.cpp */,
+                               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 */,
+                               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 */,
+                               A7DA209A113FECD400BF472F /* mergefilecommand.cpp */,
                                A7F6C8EA12423C0300299875 /* metastatscommand.h */,
                                A7F6C8EB12423C0300299875 /* metastatscommand.cpp */,
-                               A7DA209C113FECD400BF472F /* mgclustercommand.cpp */,
                                A7DA209D113FECD400BF472F /* mgclustercommand.h */,
-                               A7DA20AC113FECD400BF472F /* nocommands.cpp */,
+                               A7DA209C113FECD400BF472F /* mgclustercommand.cpp */,
                                A7DA20AD113FECD400BF472F /* nocommands.h */,
+                               A7DA20AC113FECD400BF472F /* nocommands.cpp */,
                                A798626D1240D91B005FC847 /* normalizesharedcommand.h */,
                                A798626E1240D91B005FC847 /* normalizesharedcommand.cpp */,
-                               A7DA20B8113FECD400BF472F /* otuhierarchycommand.cpp */,
                                A7DA20B9113FECD400BF472F /* otuhierarchycommand.h */,
+                               A7DA20B8113FECD400BF472F /* otuhierarchycommand.cpp */,
                                A724C2B61254961E006BB1C7 /* parsefastaqcommand.h */,
                                A724C2B71254961E006BB1C7 /* parsefastaqcommand.cpp */,
-                               A7DA20BC113FECD400BF472F /* parselistscommand.cpp */,
                                A7DA20BD113FECD400BF472F /* parselistscommand.h */,
+                               A7DA20BC113FECD400BF472F /* parselistscommand.cpp */,
                                A7E8338C115BBDAA00739EC4 /* parsesffcommand.h */,
                                A7E8338B115BBDAA00739EC4 /* parsesffcommand.cpp */,
-                               A7DA20C0113FECD400BF472F /* parsimonycommand.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 */,