]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
added shannonrange calc.
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index 096a09b7287bb0ef159a28ae3d13915073e18053..80b05db9c02288a1c91fb0085c13426774d06fc7 100644 (file)
@@ -9,6 +9,8 @@
 /* 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 */; };
+               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 */; };
@@ -18,6 +20,7 @@
                A70056EB156AB6E500924A2D /* removeotulabelscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70056EA156AB6E500924A2D /* removeotulabelscommand.cpp */; };
                A70332B712D3A13400761E33 /* makefile in Sources */ = {isa = PBXBuildFile; fileRef = A70332B512D3A13400761E33 /* makefile */; };
                A7128B1D16B7002A00723BE4 /* getdistscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7128B1C16B7002600723BE4 /* getdistscommand.cpp */; };
+               A7132EB3184E792700AAA402 /* communitytype.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7132EB2184E792700AAA402 /* communitytype.cpp */; };
                A713EBAC12DC7613000092AC /* readphylipvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A713EBAB12DC7613000092AC /* readphylipvector.cpp */; };
                A713EBED12DC7C5E000092AC /* nmdscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */; };
                A7190B221768E0DF00A9AFA6 /* lefsecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7190B201768E0DF00A9AFA6 /* lefsecommand.cpp */; };
@@ -29,9 +32,9 @@
                A721AB71161C572A009860A1 /* kmernode.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A721AB6D161C572A009860A1 /* kmernode.cpp */; };
                A721AB72161C572A009860A1 /* kmertree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A721AB6F161C572A009860A1 /* kmertree.cpp */; };
                A721AB77161C573B009860A1 /* taxonomynode.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A721AB73161C573B009860A1 /* taxonomynode.cpp */; };
+               A7222D731856277C0055A993 /* sharedjsd.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7222D721856277C0055A993 /* sharedjsd.cpp */; };
                A724D2B7153C8628000A826F /* makebiomcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A724D2B6153C8628000A826F /* makebiomcommand.cpp */; };
                A727864412E9E28C00F86ABA /* removerarecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A727864312E9E28C00F86ABA /* removerarecommand.cpp */; };
-               A7386C231619CCE600651424 /* classifysharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7386C211619CCE600651424 /* classifysharedcommand.cpp */; };
                A7386C251619E52300651424 /* abstractdecisiontree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7386C241619E52200651424 /* abstractdecisiontree.cpp */; };
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                A73901081588C40900ED2ED6 /* loadlogfilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A73901071588C40900ED2ED6 /* loadlogfilecommand.cpp */; };
@@ -39,6 +42,7 @@
                A73DDC3813C4BF64006AAE38 /* mothurmetastats.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A73DDC3713C4BF64006AAE38 /* mothurmetastats.cpp */; };
                A741744C175CD9B1007DF49B /* makelefsecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A741744A175CD9B1007DF49B /* makelefsecommand.cpp */; };
                A741FAD215D1688E0067BCC5 /* sequencecountparser.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A741FAD115D1688E0067BCC5 /* sequencecountparser.cpp */; };
+               A747EC71181EA0F900345732 /* sracommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A747EC70181EA0F900345732 /* sracommand.cpp */; };
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                A74A9A9F148E881E00AB5E3E /* spline.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74A9A9E148E881E00AB5E3E /* spline.cpp */; };
                A74C06E916A9C0A9008390A3 /* primerdesigncommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74C06E816A9C0A8008390A3 /* primerdesigncommand.cpp */; };
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                A7A0671A1562946F0095C8C5 /* listotulabelscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7A067191562946F0095C8C5 /* listotulabelscommand.cpp */; };
                A7A0671F1562AC3E0095C8C5 /* makecontigscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7A0671E1562AC3E0095C8C5 /* makecontigscommand.cpp */; };
+               A7A09B1018773C0E00FAA081 /* shannonrange.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7A09B0F18773C0E00FAA081 /* shannonrange.cpp */; };
                A7A32DAA14DC43B00001D2E5 /* sortseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7A32DA914DC43B00001D2E5 /* sortseqscommand.cpp */; };
                A7A3C8C914D041AD00B1BFBE /* otuassociationcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7A3C8C714D041AD00B1BFBE /* otuassociationcommand.cpp */; };
                A7A61F2D130062E000E05B6B /* amovacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7A61F2C130062E000E05B6B /* amovacommand.cpp */; };
                A7B0231516B8244C006BA09E /* removedistscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7B0231416B8244B006BA09E /* removedistscommand.cpp */; };
+               A7B093C018579F0400843CD1 /* pam.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7B093BF18579F0400843CD1 /* pam.cpp */; };
                A7BF221414587886000AD524 /* myPerseus.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7BF221214587886000AD524 /* myPerseus.cpp */; };
                A7BF2232145879B2000AD524 /* chimeraperseuscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7BF2231145879B2000AD524 /* chimeraperseuscommand.cpp */; };
                A7C3DC0B14FE457500FE1924 /* cooccurrencecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7C3DC0914FE457500FE1924 /* cooccurrencecommand.cpp */; };
                A7C3DC0F14FE469500FE1924 /* trialSwap2.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7C3DC0D14FE469500FE1924 /* trialSwap2.cpp */; };
                A7C7DAB915DA758B0059B0CF /* sffmultiplecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7C7DAB815DA758B0059B0CF /* sffmultiplecommand.cpp */; };
                A7CFA4311755401800D9ED4D /* renameseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7CFA4301755401800D9ED4D /* renameseqscommand.cpp */; };
+               A7D395C4184FA3A200A350D7 /* kmeans.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7D395C3184FA3A200A350D7 /* kmeans.cpp */; };
                A7D755DA1535F679009BF21A /* treereader.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7D755D91535F679009BF21A /* treereader.cpp */; };
+               A7D9378A17B146B5001E90B0 /* wilcox.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7D9378917B146B5001E90B0 /* wilcox.cpp */; };
                A7E0243D15B4520A00A5F046 /* sparsedistancematrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E0243C15B4520A00A5F046 /* sparsedistancematrix.cpp */; };
                A7E6F69E17427D06006775E2 /* makelookupcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E6F69D17427D06006775E2 /* makelookupcommand.cpp */; };
                A7E9B88112D37EC400DA6239 /* ace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B64F12D37EC300DA6239 /* ace.cpp */; };
                A7E9B98E12D37EC400DA6239 /* weightedlinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87E12D37EC400DA6239 /* weightedlinkage.cpp */; };
                A7E9B98F12D37EC400DA6239 /* whittaker.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87F12D37EC400DA6239 /* whittaker.cpp */; };
                A7EEB0F514F29BFE00344B83 /* classifytreecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7EEB0F414F29BFD00344B83 /* classifytreecommand.cpp */; };
+               A7F24FC317EA36600021DC9A /* classifyrfsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7F24FC117EA365F0021DC9A /* classifyrfsharedcommand.cpp */; };
                A7F9F5CF141A5E500032F693 /* sequenceparser.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7F9F5CE141A5E500032F693 /* sequenceparser.cpp */; };
                A7FA10021302E097003860FE /* mantelcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FA10011302E096003860FE /* mantelcommand.cpp */; };
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                        outputFiles = (
                                "$(TARGET_BUILD_DIR)/$(INPUT_FILE_BASE).o",
                        );
-                       script = "/usr/local/bin/gfortran -g -m64 -c ${PROJECT_DIR}/${INPUT_FILE_NAME} -o ${TARGET_BUILD_DIR}/${INPUT_FILE_BASE}.o";
+                       script = "/usr/local/gfortran/bin/gfortran -g -m64 -c ${PROJECT_DIR}/${INPUT_FILE_NAME} -o ${TARGET_BUILD_DIR}/${INPUT_FILE_BASE}.o";
                };
 /* End PBXBuildRule section */
 
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+               483C952D188F0CAD0035E7B7 /* sharedrjsd.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedrjsd.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>"; };
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+               A7132EAE184E76EB00AAA402 /* communitytype.h */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.c.h; path = communitytype.h; sourceTree = "<group>"; };
+               A7132EB2184E792700AAA402 /* communitytype.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = communitytype.cpp; sourceTree = "<group>"; };
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-               A7386C211619CCE600651424 /* classifysharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = classifysharedcommand.cpp; sourceTree = "<group>"; };
-               A7386C221619CCE600651424 /* classifysharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = classifysharedcommand.h; sourceTree = "<group>"; };
                A7386C241619E52200651424 /* abstractdecisiontree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = abstractdecisiontree.cpp; sourceTree = "<group>"; };
                A7386C28161A110700651424 /* decisiontree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = decisiontree.cpp; sourceTree = "<group>"; };
                A73901051588C3EF00ED2ED6 /* loadlogfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = loadlogfilecommand.h; sourceTree = "<group>"; };
                A741744B175CD9B1007DF49B /* makelefsecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = makelefsecommand.h; sourceTree = "<group>"; };
                A741FAD115D1688E0067BCC5 /* sequencecountparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequencecountparser.cpp; sourceTree = "<group>"; };
                A741FAD415D168A00067BCC5 /* sequencecountparser.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sequencecountparser.h; sourceTree = "<group>"; };
+               A747EC6F181EA0E500345732 /* sracommand.h */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.c.h; path = sracommand.h; sourceTree = "<group>"; };
+               A747EC70181EA0F900345732 /* sracommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sracommand.cpp; sourceTree = "<group>"; };
                A7496D2C167B531B00CC7D7C /* kruskalwalliscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = kruskalwalliscommand.cpp; sourceTree = "<group>"; };
                A7496D2D167B531B00CC7D7C /* kruskalwalliscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = kruskalwalliscommand.h; sourceTree = "<group>"; };
                A74A9A9D148E881E00AB5E3E /* spline.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = spline.h; sourceTree = "<group>"; };
                A7A0671C156294810095C8C5 /* listotulabelscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = listotulabelscommand.h; sourceTree = "<group>"; };
                A7A0671D1562AC230095C8C5 /* makecontigscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = makecontigscommand.h; sourceTree = "<group>"; };
                A7A0671E1562AC3E0095C8C5 /* makecontigscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = makecontigscommand.cpp; sourceTree = "<group>"; };
+               A7A09B0E18773BF700FAA081 /* shannonrange.h */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.c.h; path = shannonrange.h; sourceTree = "<group>"; };
+               A7A09B0F18773C0E00FAA081 /* shannonrange.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shannonrange.cpp; sourceTree = "<group>"; };
                A7A32DA914DC43B00001D2E5 /* sortseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sortseqscommand.cpp; sourceTree = "<group>"; };
                A7A32DAC14DC43D10001D2E5 /* sortseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sortseqscommand.h; sourceTree = "<group>"; };
                A7A3C8C714D041AD00B1BFBE /* otuassociationcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = otuassociationcommand.cpp; sourceTree = "<group>"; };
                A7AACFBA132FE008003D6C4D /* currentfile.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = currentfile.h; sourceTree = "<group>"; };
                A7B0231416B8244B006BA09E /* removedistscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removedistscommand.cpp; sourceTree = "<group>"; };
                A7B0231716B8245D006BA09E /* removedistscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removedistscommand.h; sourceTree = "<group>"; };
+               A7B093BE18579EF600843CD1 /* pam.h */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.c.h; path = pam.h; sourceTree = "<group>"; };
+               A7B093BF18579F0400843CD1 /* pam.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pam.cpp; sourceTree = "<group>"; };
                A7BF221214587886000AD524 /* myPerseus.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = myPerseus.cpp; sourceTree = "<group>"; };
                A7BF221314587886000AD524 /* myPerseus.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = myPerseus.h; sourceTree = "<group>"; };
                A7BF2230145879B2000AD524 /* chimeraperseuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraperseuscommand.h; sourceTree = "<group>"; };
                A7C7DAB815DA758B0059B0CF /* sffmultiplecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sffmultiplecommand.cpp; sourceTree = "<group>"; };
                A7CFA42F1755400500D9ED4D /* renameseqscommand.h */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.c.h; path = renameseqscommand.h; sourceTree = "<group>"; };
                A7CFA4301755401800D9ED4D /* renameseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = renameseqscommand.cpp; sourceTree = "<group>"; };
+               A7D395C2184FA39300A350D7 /* kmeans.h */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.c.h; path = kmeans.h; sourceTree = "<group>"; };
+               A7D395C3184FA3A200A350D7 /* kmeans.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = kmeans.cpp; sourceTree = "<group>"; };
                A7D755D71535F665009BF21A /* treereader.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treereader.h; sourceTree = "<group>"; };
                A7D755D91535F679009BF21A /* treereader.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treereader.cpp; sourceTree = "<group>"; };
+               A7D9378917B146B5001E90B0 /* wilcox.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = wilcox.cpp; sourceTree = "<group>"; };
+               A7D9378B17B15215001E90B0 /* wilcox.h */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.c.h; path = wilcox.h; sourceTree = "<group>"; };
                A7DAAFA3133A254E003956EB /* commandparameter.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = commandparameter.h; sourceTree = "<group>"; };
                A7E0243C15B4520A00A5F046 /* sparsedistancematrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sparsedistancematrix.cpp; sourceTree = "<group>"; };
                A7E0243F15B4522000A5F046 /* sparsedistancematrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sparsedistancematrix.h; sourceTree = "<group>"; };
                A7E9B88012D37EC400DA6239 /* whittaker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = whittaker.h; sourceTree = "<group>"; };
                A7EEB0F414F29BFD00344B83 /* classifytreecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = classifytreecommand.cpp; sourceTree = "<group>"; };
                A7EEB0F714F29C1B00344B83 /* classifytreecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = classifytreecommand.h; sourceTree = "<group>"; };
+               A7F24FC117EA365F0021DC9A /* classifyrfsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = classifyrfsharedcommand.cpp; sourceTree = "<group>"; };
+               A7F24FC217EA365F0021DC9A /* classifyrfsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = classifyrfsharedcommand.h; sourceTree = "<group>"; };
                A7F9F5CD141A5E500032F693 /* sequenceparser.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sequenceparser.h; sourceTree = "<group>"; };
                A7F9F5CE141A5E500032F693 /* sequenceparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequenceparser.cpp; sourceTree = "<group>"; };
                A7FA10001302E096003860FE /* mantelcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mantelcommand.h; sourceTree = "<group>"; };
                                A7E9B6B112D37EC400DA6239 /* commandoptionparser.cpp */,
                                A7E9B6B212D37EC400DA6239 /* commandoptionparser.hpp */,
                                A7DAAFA3133A254E003956EB /* commandparameter.h */,
+                               A7D395C1184FA34300A350D7 /* communitytype */,
                                A7E9B6B412D37EC400DA6239 /* completelinkage.cpp */,
                                A7E9BA4212D3960D00DA6239 /* containers */,
                                A7E9B6B612D37EC400DA6239 /* consensus.h */,
                                A7E9B73A12D37EC400DA6239 /* libshuff.h */,
                                A7FC480C12D788F20055BC5C /* linearalgebra.h */,
                                A7FC480D12D788F20055BC5C /* linearalgebra.cpp */,
+                               A7D9378B17B15215001E90B0 /* wilcox.h */,
+                               A7D9378917B146B5001E90B0 /* wilcox.cpp */,
                                A7E9BA5612D39BD800DA6239 /* metastats */,
                                A7E9B75B12D37EC400DA6239 /* mothur.cpp */,
                                A7E9B75C12D37EC400DA6239 /* mothur.h */,
                                A7E9B77C12D37EC400DA6239 /* overlap.hpp */,
                                A7E9B79B12D37EC400DA6239 /* progress.cpp */,
                                A7E9B79C12D37EC400DA6239 /* progress.hpp */,
-                               A7548FAF171440ED00B1F05A /* qFinderDMM.h */,
-                               A7548FAE171440EC00B1F05A /* qFinderDMM.cpp */,
                                A77B7187173D4041002163C2 /* randomnumber.h */,
                                A77B7186173D4041002163C2 /* randomnumber.cpp */,
                                A7E9B7A512D37EC400DA6239 /* rarecalc.cpp */,
                        name = fortran;
                        sourceTree = "<group>";
                };
+               A7D395C1184FA34300A350D7 /* communitytype */ = {
+                       isa = PBXGroup;
+                       children = (
+                               A7132EAE184E76EB00AAA402 /* communitytype.h */,
+                               A7132EB2184E792700AAA402 /* communitytype.cpp */,
+                               A7D395C2184FA39300A350D7 /* kmeans.h */,
+                               A7D395C3184FA3A200A350D7 /* kmeans.cpp */,
+                               A7B093BE18579EF600843CD1 /* pam.h */,
+                               A7B093BF18579F0400843CD1 /* pam.cpp */,
+                               A7548FAF171440ED00B1F05A /* qFinderDMM.h */,
+                               A7548FAE171440EC00B1F05A /* qFinderDMM.cpp */,
+                       );
+                       name = communitytype;
+                       sourceTree = "<group>";
+               };
                A7E9BA3812D3956100DA6239 /* commands */ = {
                        isa = PBXGroup;
                        children = (
                                A7E9B69012D37EC400DA6239 /* classifyotucommand.cpp */,
                                A7E9B69312D37EC400DA6239 /* classifyseqscommand.h */,
                                A7E9B69212D37EC400DA6239 /* classifyseqscommand.cpp */,
-                               A7386C221619CCE600651424 /* classifysharedcommand.h */,
-                               A7386C211619CCE600651424 /* classifysharedcommand.cpp */,
+                               A7F24FC217EA365F0021DC9A /* classifyrfsharedcommand.h */,
+                               A7F24FC117EA365F0021DC9A /* classifyrfsharedcommand.cpp */,
                                A7EEB0F714F29C1B00344B83 /* classifytreecommand.h */,
                                A7EEB0F414F29BFD00344B83 /* classifytreecommand.cpp */,
                                A7E9B69712D37EC400DA6239 /* clearcutcommand.h */,
                                A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */,
                                A71FE12A12EDF72400963CA7 /* mergegroupscommand.h */,
                                A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */,
+                               48E981CD189C38E60042BE9D /* mergesfffilecommand.h */,
+                               48E981CE189C38FB0042BE9D /* mergesfffilecommand.cpp */,
                                A799314816CBD0BC0017E888 /* mergetaxsummarycommand.h */,
                                A799314A16CBD0CD0017E888 /* mergetaxsummarycommand.cpp */,
                                A7E9B75812D37EC400DA6239 /* metastatscommand.h */,
                                A7E9B83F12D37EC400DA6239 /* splitabundcommand.cpp */,
                                A7E9B84212D37EC400DA6239 /* splitgroupscommand.h */,
                                A7E9B84112D37EC400DA6239 /* splitgroupscommand.cpp */,
+                               A747EC6F181EA0E500345732 /* sracommand.h */,
+                               A747EC70181EA0F900345732 /* sracommand.cpp */,
                                A7E9B85012D37EC400DA6239 /* subsamplecommand.h */,
                                A7E9B84F12D37EC400DA6239 /* subsamplecommand.cpp */,
                                A7E9B85812D37EC400DA6239 /* summarycommand.h */,
                                A7E9B7E612D37EC400DA6239 /* shannon.h */,
                                A7E9B7E712D37EC400DA6239 /* shannoneven.cpp */,
                                A7E9B7E812D37EC400DA6239 /* shannoneven.h */,
+                               A7A09B0E18773BF700FAA081 /* shannonrange.h */,
+                               A7A09B0F18773C0E00FAA081 /* shannonrange.cpp */,
                                A7E9B7E912D37EC400DA6239 /* sharedace.cpp */,
+                               A7E9B7F412D37EC400DA6239 /* sharedjabund.cpp */,
                                A7E9B7EA12D37EC400DA6239 /* sharedace.h */,
                                A7E9B7EC12D37EC400DA6239 /* sharedanderbergs.cpp */,
                                A7E9B7ED12D37EC400DA6239 /* sharedanderbergs.h */,
                                A7E9B7EF12D37EC400DA6239 /* sharedbraycurtis.h */,
                                A7E9B7F012D37EC400DA6239 /* sharedchao1.cpp */,
                                A7E9B7F112D37EC400DA6239 /* sharedchao1.h */,
-                               A7E9B7F412D37EC400DA6239 /* sharedjabund.cpp */,
                                A7E9B7F512D37EC400DA6239 /* sharedjabund.h */,
                                A7E9B7F612D37EC400DA6239 /* sharedjackknife.cpp */,
                                A7E9B7F712D37EC400DA6239 /* sharedjackknife.h */,
                                A7E9B7F912D37EC400DA6239 /* sharedjclass.h */,
                                A7E9B7FA12D37EC400DA6239 /* sharedjest.cpp */,
                                A7E9B7FB12D37EC400DA6239 /* sharedjest.h */,
+                               A7222D711856276C0055A993 /* sharedjsd.h */,
+                               A7222D721856277C0055A993 /* sharedjsd.cpp */,
+                               483C952C188F0C960035E7B7 /* sharedrjsd.h */,
+                               483C952D188F0CAD0035E7B7 /* sharedrjsd.cpp */,
                                A7E9B7FC12D37EC400DA6239 /* sharedkstest.cpp */,
                                A7E9B7FD12D37EC400DA6239 /* sharedkstest.h */,
                                A7E9B7FE12D37EC400DA6239 /* sharedkulczynski.cpp */,
                                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 */,
                                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 */,
                                A7E0243D15B4520A00A5F046 /* sparsedistancematrix.cpp in Sources */,
                                A741FAD215D1688E0067BCC5 /* sequencecountparser.cpp in Sources */,
                                A7C7DAB915DA758B0059B0CF /* sffmultiplecommand.cpp in Sources */,
-                               A7386C231619CCE600651424 /* classifysharedcommand.cpp in Sources */,
                                A7386C251619E52300651424 /* abstractdecisiontree.cpp in Sources */,
                                A7386C29161A110800651424 /* decisiontree.cpp in Sources */,
                                A77E1938161B201E00DB1A2A /* randomforest.cpp in Sources */,
                                A741744C175CD9B1007DF49B /* makelefsecommand.cpp in Sources */,
                                A7190B221768E0DF00A9AFA6 /* lefsecommand.cpp in Sources */,
                                A77916E8176F7F7600EEFE18 /* designmap.cpp in Sources */,
+                               A7D9378A17B146B5001E90B0 /* wilcox.cpp in Sources */,
+                               A7F24FC317EA36600021DC9A /* classifyrfsharedcommand.cpp in Sources */,
+                               A747EC71181EA0F900345732 /* sracommand.cpp in Sources */,
+                               A7132EB3184E792700AAA402 /* communitytype.cpp in Sources */,
+                               A7D395C4184FA3A200A350D7 /* kmeans.cpp in Sources */,
+                               A7222D731856277C0055A993 /* sharedjsd.cpp in Sources */,
+                               A7B093C018579F0400843CD1 /* pam.cpp in Sources */,
+                               A7A09B1018773C0E00FAA081 /* shannonrange.cpp in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
                                "DSTROOT[sdk=*]" = TARGET_BUILD_DIR;
                                GCC_DYNAMIC_NO_PIC = NO;
                                GCC_MODEL_TUNING = G5;
-                               GCC_OPTIMIZATION_LEVEL = 3;
+                               GCC_OPTIMIZATION_LEVEL = 0;
                                "INSTALL_PATH[sdk=*]" = TARGET_BUILD_DIR;
                                PRODUCT_NAME = mothur;
-                               SDKROOT = macosx10.8;
+                               SDKROOT = macosx;
                                SKIP_INSTALL = NO;
                        };
                        name = Debug;
                                DEPLOYMENT_LOCATION = YES;
                                DSTROOT = TARGET_BUILD_DIR;
                                GCC_MODEL_TUNING = G5;
-                               GCC_OPTIMIZATION_LEVEL = 3;
+                               GCC_OPTIMIZATION_LEVEL = 0;
                                GCC_WARN_UNUSED_VALUE = YES;
                                PRODUCT_NAME = mothur;
                                SDKROOT = macosx;
                                GCC_ENABLE_SSE3_EXTENSIONS = NO;
                                GCC_ENABLE_SSE41_EXTENSIONS = NO;
                                GCC_ENABLE_SSE42_EXTENSIONS = NO;
-                               GCC_OPTIMIZATION_LEVEL = s;
+                               GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_PREPROCESSOR_DEFINITIONS = (
-                                       "MOTHUR_FILES=\"\\\"../../release\\\"\"",
-                                       "VERSION=\"\\\"1.31.0\\\"\"",
-                                       "RELEASE_DATE=\"\\\"5/24/2013\\\"\"",
+                                       "MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
+                                       "VERSION=\"\\\"1.33.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"2/7/2014\\\"\"",
                                );
+                               GCC_VERSION = "";
                                "GCC_VERSION[arch=*]" = "";
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                        "-lncurses",
                                        "-lreadline",
                                );
-                               SDKROOT = macosx;
+                               SDKROOT = macosx10.8;
                                SKIP_INSTALL = NO;
                                USER_HEADER_SEARCH_PATHS = "";
                        };
                                GCC_C_LANGUAGE_STANDARD = gnu99;
                                GCC_GENERATE_DEBUGGING_SYMBOLS = NO;
                                GCC_MODEL_TUNING = "";
-                               GCC_OPTIMIZATION_LEVEL = s;
+                               GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_PREPROCESSOR_DEFINITIONS = (
-                                       "VERSION=\"\\\"1.31.0\\\"\"",
-                                       "RELEASE_DATE=\"\\\"5/24/2013\\\"\"",
+                                       "VERSION=\"\\\"1.32.1\\\"\"",
+                                       "RELEASE_DATE=\"\\\"10/16/2013\\\"\"",
                                );
+                               GCC_VERSION = "";
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                GCC_WARN_MISSING_PARENTHESES = YES;
                                        "-lncurses",
                                        "-lreadline",
                                );
-                               SDKROOT = macosx;
+                               SDKROOT = macosx10.8;
                                SKIP_INSTALL = NO;
                        };
                        name = Release;