added oligos class. added check orient parameter to trim.flows, sffinfo, fastq.info...

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

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 26456a3ee2c230477db7c945e2b9586dc45aea8d..57b6624d0e7ecf0f95f4a74d74fb58b93577435b 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -9,6 +9,10 @@
 /* Begin PBXBuildFile section */
                219C1DE01552C4BD004209F9 /* newcommandtemplate.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 219C1DDF1552C4BD004209F9 /* newcommandtemplate.cpp */; };
                219C1DE41559BCCF004209F9 /* getcoremicrobiomecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 219C1DE31559BCCD004209F9 /* getcoremicrobiomecommand.cpp */; };
+               483C952E188F0CAD0035E7B7 /* sharedrjsd.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 483C952D188F0CAD0035E7B7 /* sharedrjsd.cpp */; };
+               4893DE2918EEF28100C615DF /* oligos.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 4893DE2818EEF28100C615DF /* oligos.cpp */; };
+               48A85BAD18E1AF2000199B6F /* getmimarkspackagecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48A85BAC18E1AF2000199B6F /* getmimarkspackagecommand.cpp */; };
+               48E981CF189C38FB0042BE9D /* mergesfffilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48E981CE189C38FB0042BE9D /* mergesfffilecommand.cpp */; };
                7E6BE10A12F710D8007ADDBE /* refchimeratest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */; };
                834D9D581656D7C400E7FAB9 /* regularizedrandomforest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 834D9D561656D7C400E7FAB9 /* regularizedrandomforest.cpp */; };
                834D9D5C1656DEC800E7FAB9 /* regularizeddecisiontree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 834D9D5A1656DEC700E7FAB9 /* regularizeddecisiontree.cpp */; };
@@ -406,6 +410,14 @@
                219C1DE11552C508004209F9 /* newcommandtemplate.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = newcommandtemplate.h; sourceTree = "<group>"; };
                219C1DE31559BCCD004209F9 /* getcoremicrobiomecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getcoremicrobiomecommand.cpp; sourceTree = "<group>"; };
                219C1DE51559BCF2004209F9 /* getcoremicrobiomecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getcoremicrobiomecommand.h; sourceTree = "<group>"; };
+               483C952C188F0C960035E7B7 /* sharedrjsd.h */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.c.h; path = sharedrjsd.h; sourceTree = "<group>"; };
+               483C952D188F0CAD0035E7B7 /* sharedrjsd.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedrjsd.cpp; sourceTree = "<group>"; };
+               4893DE2718EEF27300C615DF /* oligos.h */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.c.h; path = oligos.h; sourceTree = "<group>"; };
+               4893DE2818EEF28100C615DF /* oligos.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = oligos.cpp; sourceTree = "<group>"; };
+               48A85BAB18E1AF0600199B6F /* getmimarkspackagecommand.h */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.c.h; path = getmimarkspackagecommand.h; sourceTree = "<group>"; };
+               48A85BAC18E1AF2000199B6F /* getmimarkspackagecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getmimarkspackagecommand.cpp; sourceTree = "<group>"; };
+               48E981CD189C38E60042BE9D /* mergesfffilecommand.h */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.c.h; path = mergesfffilecommand.h; sourceTree = "<group>"; };
+               48E981CE189C38FB0042BE9D /* mergesfffilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mergesfffilecommand.cpp; sourceTree = "<group>"; };
                7E6BE10812F710D8007ADDBE /* refchimeratest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = refchimeratest.h; sourceTree = "<group>"; };
                7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = refchimeratest.cpp; sourceTree = "<group>"; };
                7E78911B135F3E8600E725D2 /* eachgapdistignorens.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = eachgapdistignorens.h; sourceTree = "<group>"; };
@@ -1449,6 +1461,8 @@
                                A7E9B6F812D37EC400DA6239 /* getlineagecommand.cpp */,
                                A7E9B6FB12D37EC400DA6239 /* getlistcountcommand.h */,
                                A7E9B6FA12D37EC400DA6239 /* getlistcountcommand.cpp */,
+                               48A85BAB18E1AF0600199B6F /* getmimarkspackagecommand.h */,
+                               48A85BAC18E1AF2000199B6F /* getmimarkspackagecommand.cpp */,
                                A7E9B6FF12D37EC400DA6239 /* getoturepcommand.h */,
                                A7E9B6FE12D37EC400DA6239 /* getoturepcommand.cpp */,
                                A7E9B70112D37EC400DA6239 /* getotuscommand.h */,
@@ -1509,6 +1523,8 @@
                                A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */,
                                A71FE12A12EDF72400963CA7 /* mergegroupscommand.h */,
                                A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */,
+                               48E981CD189C38E60042BE9D /* mergesfffilecommand.h */,
+                               48E981CE189C38FB0042BE9D /* mergesfffilecommand.cpp */,
                                A799314816CBD0BC0017E888 /* mergetaxsummarycommand.h */,
                                A799314A16CBD0CD0017E888 /* mergetaxsummarycommand.cpp */,
                                A7E9B75812D37EC400DA6239 /* metastatscommand.h */,
@@ -1715,6 +1731,7 @@
                                A7A09B0E18773BF700FAA081 /* shannonrange.h */,
                                A7A09B0F18773C0E00FAA081 /* shannonrange.cpp */,
                                A7E9B7E912D37EC400DA6239 /* sharedace.cpp */,
+                               A7E9B7F412D37EC400DA6239 /* sharedjabund.cpp */,
                                A7E9B7EA12D37EC400DA6239 /* sharedace.h */,
                                A7E9B7EC12D37EC400DA6239 /* sharedanderbergs.cpp */,
                                A7E9B7ED12D37EC400DA6239 /* sharedanderbergs.h */,
@@ -1722,7 +1739,6 @@
                                A7E9B7EF12D37EC400DA6239 /* sharedbraycurtis.h */,
                                A7E9B7F012D37EC400DA6239 /* sharedchao1.cpp */,
                                A7E9B7F112D37EC400DA6239 /* sharedchao1.h */,
-                               A7E9B7F412D37EC400DA6239 /* sharedjabund.cpp */,
                                A7E9B7F512D37EC400DA6239 /* sharedjabund.h */,
                                A7E9B7F612D37EC400DA6239 /* sharedjackknife.cpp */,
                                A7E9B7F712D37EC400DA6239 /* sharedjackknife.h */,
@@ -1732,6 +1748,8 @@
                                A7E9B7FB12D37EC400DA6239 /* sharedjest.h */,
                                A7222D711856276C0055A993 /* sharedjsd.h */,
                                A7222D721856277C0055A993 /* sharedjsd.cpp */,
+                               483C952C188F0C960035E7B7 /* sharedrjsd.h */,
+                               483C952D188F0CAD0035E7B7 /* sharedrjsd.cpp */,
                                A7E9B7FC12D37EC400DA6239 /* sharedkstest.cpp */,
                                A7E9B7FD12D37EC400DA6239 /* sharedkstest.h */,
                                A7E9B7FE12D37EC400DA6239 /* sharedkulczynski.cpp */,
@@ -1839,6 +1857,8 @@
                                A7E9B74012D37EC400DA6239 /* listvector.hpp */,
                                A7E9B75F12D37EC400DA6239 /* nameassignment.cpp */,
                                A7E9B76012D37EC400DA6239 /* nameassignment.hpp */,
+                               4893DE2718EEF27300C615DF /* oligos.h */,
+                               4893DE2818EEF28100C615DF /* oligos.cpp */,
                                A7E9B77712D37EC400DA6239 /* ordervector.cpp */,
                                A7E9B77812D37EC400DA6239 /* ordervector.hpp */,
                                A7E9B79F12D37EC400DA6239 /* qualityscores.cpp */,
@@ -2097,6 +2117,7 @@
                                A7E9B89712D37EC400DA6239 /* chimerabellerophoncommand.cpp in Sources */,
                                A7E9B89812D37EC400DA6239 /* chimeraccodecommand.cpp in Sources */,
                                A7E9B89912D37EC400DA6239 /* chimeracheckcommand.cpp in Sources */,
+                               48E981CF189C38FB0042BE9D /* mergesfffilecommand.cpp in Sources */,
                                A7E9B89A12D37EC400DA6239 /* chimeracheckrdp.cpp in Sources */,
                                A7E9B89B12D37EC400DA6239 /* chimerapintailcommand.cpp in Sources */,
                                A7E9B89C12D37EC400DA6239 /* chimerarealigner.cpp in Sources */,
@@ -2163,6 +2184,7 @@
                                A7E9B8DC12D37EC400DA6239 /* gotohoverlap.cpp in Sources */,
                                A7E9B8DD12D37EC400DA6239 /* gower.cpp in Sources */,
                                A7E9B8DE12D37EC400DA6239 /* groupmap.cpp in Sources */,
+                               4893DE2918EEF28100C615DF /* oligos.cpp in Sources */,
                                A7E9B8DF12D37EC400DA6239 /* hamming.cpp in Sources */,
                                A7E9B8E012D37EC400DA6239 /* hcluster.cpp in Sources */,
                                A7E9B8E112D37EC400DA6239 /* hclustercommand.cpp in Sources */,
@@ -2180,6 +2202,7 @@
                                A7E9B8ED12D37EC400DA6239 /* kmer.cpp in Sources */,
                                A7E9B8EE12D37EC400DA6239 /* kmerdb.cpp in Sources */,
                                A7E9B8EF12D37EC400DA6239 /* knn.cpp in Sources */,
+                               48A85BAD18E1AF2000199B6F /* getmimarkspackagecommand.cpp in Sources */,
                                A7E9B8F012D37EC400DA6239 /* libshuff.cpp in Sources */,
                                A7E9B8F112D37EC400DA6239 /* libshuffcommand.cpp in Sources */,
                                A7E9B8F212D37EC400DA6239 /* listseqscommand.cpp in Sources */,
@@ -2258,6 +2281,7 @@
                                A7E9B94112D37EC400DA6239 /* setlogfilecommand.cpp in Sources */,
                                A7E9B94212D37EC400DA6239 /* sffinfocommand.cpp in Sources */,
                                A7E9B94312D37EC400DA6239 /* shannon.cpp in Sources */,
+                               483C952E188F0CAD0035E7B7 /* sharedrjsd.cpp in Sources */,
                                A7E9B94412D37EC400DA6239 /* shannoneven.cpp in Sources */,
                                A7E9B94512D37EC400DA6239 /* sharedace.cpp in Sources */,
                                A7E9B94612D37EC400DA6239 /* sharedanderbergs.cpp in Sources */,
@@ -2489,9 +2513,9 @@
                                GCC_ENABLE_SSE42_EXTENSIONS = NO;
                                GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_PREPROCESSOR_DEFINITIONS = (
-                                       "MOTHUR_FILES=\"\\\"../../release\\\"\"",
-                                       "VERSION=\"\\\"1.32.0\\\"\"",
-                                       "RELEASE_DATE=\"\\\"10/31/2013\\\"\"",
+                                       "MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
+                                       "VERSION=\"\\\"1.33.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"2/7/2014\\\"\"",
                                );
                                GCC_VERSION = "";
                                "GCC_VERSION[arch=*]" = "";