added sharedRabundFloatVector class to represent the relabund file. modified read...

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

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 919bc12b5d6348c292505ff53545033ea77029ae..ebe8a90115bbc86641664e6922ba39a23e92de25 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -7,10 +7,20 @@
        objects = {
 
 /* Begin PBXFileReference section */
+               7E4EBD43122018FB00D85E7B /* simpsoneven.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = simpsoneven.h; sourceTree = "<group>"; };
+               7E4EBD44122018FB00D85E7B /* simpsoneven.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = simpsoneven.cpp; sourceTree = "<group>"; };
+               7E5B28DC121FEFCC0005339C /* shannoneven.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shannoneven.h; sourceTree = "<group>"; };
+               7E5B28DD121FEFCC0005339C /* shannoneven.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shannoneven.cpp; sourceTree = "<group>"; };
+               7E5B2917121FF53C0005339C /* heip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heip.h; sourceTree = "<group>"; };
+               7E5B2918121FF53C0005339C /* heip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heip.cpp; sourceTree = "<group>"; };
+               7E5B294A121FFADC0005339C /* smithwilson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = smithwilson.h; sourceTree = "<group>"; };
+               7E5B294B121FFADC0005339C /* smithwilson.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = smithwilson.cpp; sourceTree = "<group>"; };
                7E84528511EF4BEB00564975 /* seqerrorcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = seqerrorcommand.h; sourceTree = "<group>"; };
                7E84528611EF4BEB00564975 /* seqerrorcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = seqerrorcommand.cpp; sourceTree = "<group>"; };
                7E85BD1C11EB5E9B00FD37C0 /* qualityscores.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = qualityscores.h; sourceTree = "<group>"; };
                7E85BD1D11EB5E9B00FD37C0 /* qualityscores.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = qualityscores.cpp; sourceTree = "<group>"; };
+               7E962A40121F76B1007464B5 /* invsimpson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = invsimpson.h; sourceTree = "<group>"; };
+               7E962A41121F76B1007464B5 /* invsimpson.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = invsimpson.cpp; sourceTree = "<group>"; };
                7EA299BA11E384940022D8D3 /* sensspeccommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sensspeccommand.h; sourceTree = "<group>"; };
                7EA299BB11E384940022D8D3 /* sensspeccommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sensspeccommand.cpp; sourceTree = "<group>"; };
                7EC61A0911BEA6AF00F668D9 /* weightedlinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = weightedlinkage.cpp; sourceTree = "<group>"; };
@@ -50,6 +60,8 @@
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                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>"; };
+               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>"; };
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                A7BBDA7C11B5694E006E6551 /* classifyotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = classifyotucommand.cpp; sourceTree = "<group>"; };
                A7D215C811996C6E00F13F13 /* clearcutcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clearcutcommand.h; sourceTree = "<group>"; };
@@ -454,6 +466,22 @@
                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>"; };
+               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>"; };
+               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>"; };
+               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>"; };
+               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>"; };
+               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>"; };
+               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>"; };
 /* End PBXFileReference section */
@@ -473,6 +501,7 @@
                                A7CB593B11402EF90010EB83 /* calculators */,
                                A7CB594A11402FB40010EB83 /* chimeras */,
                                A7CB594511402F6E0010EB83 /* classifers */,
+                               A7DF0AE5121EBC26004A03EA /* clearcutsource */,
                                A7CB593E11402F110010EB83 /* commands */,
                                A7CB594211402F430010EB83 /* containers */,
                                A7DA2023113FECD400BF472F /* collect.cpp */,
@@ -577,7 +606,11 @@
                                A7DA2059113FECD400BF472F /* geom.h */,
                                A7DA206C113FECD400BF472F /* goodscoverage.cpp */,
                                A7DA206D113FECD400BF472F /* goodscoverage.h */,
+                               7E5B2917121FF53C0005339C /* heip.h */,
+                               7E5B2918121FF53C0005339C /* heip.cpp */,
                                A7DA2080113FECD400BF472F /* ignoregaps.h */,
+                               7E962A40121F76B1007464B5 /* invsimpson.h */,
+                               7E962A41121F76B1007464B5 /* invsimpson.cpp */,
                                A7DA2083113FECD400BF472F /* jackknife.cpp */,
                                A7DA2084113FECD400BF472F /* jackknife.h */,
                                A7DA2093113FECD400BF472F /* logsd.cpp */,
@@ -595,6 +628,8 @@
                                A7DA20CF113FECD400BF472F /* qstat.h */,
                                A7DA2104113FECD400BF472F /* shannon.cpp */,
                                A7DA2105113FECD400BF472F /* shannon.h */,
+                               7E5B28DC121FEFCC0005339C /* shannoneven.h */,
+                               7E5B28DD121FEFCC0005339C /* shannoneven.cpp */,
                                A7DA2106113FECD400BF472F /* sharedace.cpp */,
                                A7DA2107113FECD400BF472F /* sharedace.h */,
                                A7DA2108113FECD400BF472F /* sharedanderberg.h */,
@@ -643,6 +678,10 @@
                                A7DA213D113FECD400BF472F /* sharedthetayc.h */,
                                A7DA2140113FECD400BF472F /* shen.cpp */,
                                A7DA2141113FECD400BF472F /* shen.h */,
+                               7E4EBD43122018FB00D85E7B /* simpsoneven.h */,
+                               7E4EBD44122018FB00D85E7B /* simpsoneven.cpp */,
+                               7E5B294A121FFADC0005339C /* smithwilson.h */,
+                               7E5B294B121FFADC0005339C /* smithwilson.cpp */,
                                A7DA2142113FECD400BF472F /* simpson.cpp */,
                                A7DA2143113FECD400BF472F /* simpson.h */,
                                A7DA2149113FECD400BF472F /* sobs.h */,
@@ -698,8 +737,8 @@
                                A7DA2022113FECD400BF472F /* clustercommand.h */,
                                A71D924311AEB42400D00CBC /* clustersplitcommand.h */,
                                A71D924211AEB42400D00CBC /* clustersplitcommand.cpp */,
-                               A7DA2025113FECD400BF472F /* collectcommand.cpp */,
                                A7DA2026113FECD400BF472F /* collectcommand.h */,
+                               A7DA2025113FECD400BF472F /* collectcommand.cpp */,
                                A7DA2029113FECD400BF472F /* collectsharedcommand.cpp */,
                                A7DA202A113FECD400BF472F /* collectsharedcommand.h */,
                                A7DA2031113FECD400BF472F /* consensuscommand.cpp */,
@@ -870,8 +909,10 @@
                                A7DA212B113FECD400BF472F /* sharedordervector.h */,
                                A7DA212C113FECD400BF472F /* sharedrabundvector.cpp */,
                                A7DA212D113FECD400BF472F /* sharedrabundvector.h */,
-                               A7DA212E113FECD400BF472F /* sharedsabundvector.cpp */,
+                               A7AE6302121C3408001DE6FC /* sharedrabundfloatvector.h */,
+                               A7AE6303121C3408001DE6FC /* sharedrabundfloatvector.cpp */,
                                A7DA212F113FECD400BF472F /* sharedsabundvector.h */,
+                               A7DA212E113FECD400BF472F /* sharedsabundvector.cpp */,
                                A7DA214C113FECD400BF472F /* sparsematrix.cpp */,
                                A7DA214D113FECD400BF472F /* sparsematrix.hpp */,
                                A7DA214E113FECD400BF472F /* suffixdb.cpp */,
@@ -963,6 +1004,29 @@
                        name = read;
                        sourceTree = "<group>";
                };
+               A7DF0AE5121EBC26004A03EA /* clearcutsource */ = {
+                       isa = PBXGroup;
+                       children = (
+                               A7DF0AD4121EBB14004A03EA /* clearcut.h */,
+                               A7DF0AD3121EBB14004A03EA /* clearcut.c */,
+                               A7DF0AD6121EBB14004A03EA /* cmdargs.h */,
+                               A7DF0AD7121EBB14004A03EA /* common.h */,
+                               A7DF0AD8121EBB14004A03EA /* dayhoff.h */,
+                               A7DF0AD5121EBB14004A03EA /* cmdargs.c */,
+                               A7DF0AD9121EBB14004A03EA /* distclearcut.c */,
+                               A7DF0ADA121EBB14004A03EA /* distclearcut.h */,
+                               A7DF0ADB121EBB14004A03EA /* dmat.c */,
+                               A7DF0ADC121EBB14004A03EA /* dmat.h */,
+                               A7DF0ADD121EBB14004A03EA /* fasta.c */,
+                               A7DF0ADE121EBB14004A03EA /* fasta.h */,
+                               A7DF0ADF121EBB14004A03EA /* getopt_long.c */,
+                               A7DF0AE0121EBB14004A03EA /* getopt_long.h */,
+                               A7DF0AE2121EBB14004A03EA /* prng.h */,
+                               A7DF0AE1121EBB14004A03EA /* prng.c */,
+                       );
+                       name = clearcutsource;
+                       sourceTree = "<group>";
+               };
 /* End PBXGroup section */
 
 /* Begin PBXLegacyTarget section */