]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
removed parse.sff command and made its functionality part of sffinfo command. fixed...
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index 855dad891d3b9b4e3b0422e57a3a5be488aa3c12..edb26d37714cb4702183fc00dc182ba632f15506 100644 (file)
@@ -7,6 +7,12 @@
        objects = {
 
 /* Begin PBXFileReference section */
+               7E13BDD112BE3FEE004B8A53 /* reportfile.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = reportfile.h; sourceTree = "<group>"; };
+               7E13BDD212BE3FEF004B8A53 /* reportfile.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = reportfile.cpp; sourceTree = "<group>"; };
+               7E1CA7D712C2A384003F10B2 /* flowdata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = flowdata.h; sourceTree = "<group>"; };
+               7E1CA7D812C2A384003F10B2 /* flowdata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = flowdata.cpp; sourceTree = "<group>"; };
+               7E1CA7D912C2A425003F10B2 /* trimflowscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = trimflowscommand.h; sourceTree = "<group>"; };
+               7E1CA7DA12C2A425003F10B2 /* trimflowscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = trimflowscommand.cpp; sourceTree = "<group>"; };
                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>"; };
@@ -21,6 +27,8 @@
                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>"; };
+               7E99CA1312C8B0970041246B /* shhhercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shhhercommand.h; sourceTree = "<group>"; };
+               7E99CA1412C8B0970041246B /* shhhercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shhhercommand.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>"; };
@@ -37,6 +45,8 @@
                A71D924511AEB42400D00CBC /* splitabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = splitabundcommand.h; sourceTree = "<group>"; };
                A71D924611AEB42400D00CBC /* splitmatrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = splitmatrix.cpp; sourceTree = "<group>"; };
                A71D924711AEB42400D00CBC /* splitmatrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = splitmatrix.h; sourceTree = "<group>"; };
+               A71FF438129BDC35004397E6 /* consensusseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = consensusseqscommand.h; sourceTree = "<group>"; };
+               A71FF439129BDC35004397E6 /* consensusseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = consensusseqscommand.cpp; sourceTree = "<group>"; };
                A724C2B61254961E006BB1C7 /* parsefastaqcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsefastaqcommand.h; sourceTree = "<group>"; };
                A724C2B71254961E006BB1C7 /* parsefastaqcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsefastaqcommand.cpp; sourceTree = "<group>"; };
                A72B3A62118B37FD004B9F8D /* phylodiversitycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylodiversitycommand.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>"; };
                A73953DB11987ED100B0B160 /* chopseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chopseqscommand.cpp; sourceTree = "<group>"; };
+               A7460A3F12B8EF1C00866BB6 /* structchord.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = structchord.h; sourceTree = "<group>"; };
+               A7460A4012B8EF1C00866BB6 /* structchord.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = structchord.cpp; sourceTree = "<group>"; };
+               A7460A7312B8FCDC00866BB6 /* hellinger.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = hellinger.h; sourceTree = "<group>"; };
+               A7460A7412B8FCDC00866BB6 /* hellinger.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = hellinger.cpp; sourceTree = "<group>"; };
+               A7460A9812B9061B00866BB6 /* manhattan.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = manhattan.h; sourceTree = "<group>"; };
+               A7460A9912B9061B00866BB6 /* manhattan.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = manhattan.cpp; sourceTree = "<group>"; };
+               A7460AC912B90C5600866BB6 /* structpearson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = structpearson.h; sourceTree = "<group>"; };
+               A7460ACA12B90C5600866BB6 /* structpearson.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = structpearson.cpp; sourceTree = "<group>"; };
+               A7460ADB12B914B700866BB6 /* soergel.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = soergel.h; sourceTree = "<group>"; };
+               A7460ADC12B914B700866BB6 /* soergel.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = soergel.cpp; sourceTree = "<group>"; };
+               A7460AF712B9218400866BB6 /* spearman.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = spearman.h; sourceTree = "<group>"; };
+               A7460AF812B9218400866BB6 /* spearman.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = spearman.cpp; sourceTree = "<group>"; };
+               A7460B3612B9377400866BB6 /* structkulczynski.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = structkulczynski.h; sourceTree = "<group>"; };
+               A7460B3712B9377400866BB6 /* structkulczynski.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = structkulczynski.cpp; sourceTree = "<group>"; };
+               A7460B5912B93F1F00866BB6 /* speciesprofile.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = speciesprofile.h; sourceTree = "<group>"; };
+               A7460B5A12B93F1F00866BB6 /* speciesprofile.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = speciesprofile.cpp; sourceTree = "<group>"; };
+               A7460B7812B9444800866BB6 /* hamming.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = hamming.h; sourceTree = "<group>"; };
+               A7460B7912B9444800866BB6 /* hamming.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = hamming.cpp; sourceTree = "<group>"; };
                A747E79B1163442A00FB9042 /* chimeracheckcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeracheckcommand.h; 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>"; };
+               A751032A128AC93F00ABB831 /* removegroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removegroupscommand.h; sourceTree = "<group>"; };
+               A751032B128AC93F00ABB831 /* removegroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removegroupscommand.cpp; sourceTree = "<group>"; };
+               A75103D6128AE34100ABB831 /* getgroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getgroupscommand.h; sourceTree = "<group>"; };
+               A75103D7128AE34100ABB831 /* getgroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getgroupscommand.cpp; sourceTree = "<group>"; };
+               A7510407128AFCC100ABB831 /* getotuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getotuscommand.h; sourceTree = "<group>"; };
+               A7510408128AFCC100ABB831 /* getotuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getotuscommand.cpp; sourceTree = "<group>"; };
                A7639F8D1175DF35008F5578 /* makefile */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.make; path = makefile; sourceTree = "<group>"; };
                A7653CB112789EFD009D6C09 /* subsamplecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = subsamplecommand.h; sourceTree = "<group>"; };
                A7653CB212789EFD009D6C09 /* subsamplecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = subsamplecommand.cpp; 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; };
                A76C4A1111876BAF0009460B /* setlogfilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = setlogfilecommand.cpp; sourceTree = SOURCE_ROOT; };
+               A76D1451128D6A03005D4DFE /* removeotuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removeotuscommand.h; sourceTree = "<group>"; };
+               A76D1452128D6A03005D4DFE /* removeotuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removeotuscommand.cpp; sourceTree = "<group>"; };
+               A76D1473128D9DA2005D4DFE /* indicatorcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = indicatorcommand.h; sourceTree = "<group>"; };
+               A76D1474128D9DA2005D4DFE /* indicatorcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = indicatorcommand.cpp; sourceTree = "<group>"; };
                A77D787B126F387700F351BD /* pairwiseseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pairwiseseqscommand.h; sourceTree = "<group>"; };
                A77D787C126F387700F351BD /* pairwiseseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pairwiseseqscommand.cpp; sourceTree = "<group>"; };
                A780E6CB11E7745D00BB5718 /* endiannessmacros.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = endiannessmacros.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>"; };
+               A7BB555212BB87F30041F26F /* structchi2.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = structchi2.h; sourceTree = "<group>"; };
+               A7BB555312BB87F30041F26F /* structchi2.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = structchi2.cpp; sourceTree = "<group>"; };
+               A7BB565F12BBB0480041F26F /* gower.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = gower.h; sourceTree = "<group>"; };
+               A7BB566012BBB0480041F26F /* gower.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = gower.cpp; sourceTree = "<group>"; };
+               A7BB56B812BBB5690041F26F /* memchi2.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = memchi2.h; sourceTree = "<group>"; };
+               A7BB56B912BBB5690041F26F /* memchi2.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = memchi2.cpp; sourceTree = "<group>"; };
+               A7BB56EB12BBBFDF0041F26F /* memchord.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = memchord.h; sourceTree = "<group>"; };
+               A7BB56EC12BBBFDF0041F26F /* memchord.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = memchord.cpp; sourceTree = "<group>"; };
+               A7BB570B12BBC2880041F26F /* memeuclidean.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = memeuclidean.h; sourceTree = "<group>"; };
+               A7BB570C12BBC2880041F26F /* memeuclidean.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = memeuclidean.cpp; sourceTree = "<group>"; };
+               A7BB573712BBC43B0041F26F /* mempearson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mempearson.h; sourceTree = "<group>"; };
+               A7BB573812BBC43B0041F26F /* mempearson.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mempearson.cpp; sourceTree = "<group>"; };
                A7BBDA7B11B5694E006E6551 /* classifyotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = classifyotucommand.h; sourceTree = "<group>"; };
                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>"; };
                A7D215C911996C6E00F13F13 /* clearcutcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clearcutcommand.cpp; sourceTree = "<group>"; };
                A7D216061199C47F00F13F13 /* catchallcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = catchallcommand.h; sourceTree = "<group>"; };
                A7D216071199C47F00F13F13 /* catchallcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = catchallcommand.cpp; sourceTree = "<group>"; };
+               A7D9006D12C2544A00D8F543 /* corraxescommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = corraxescommand.h; sourceTree = "<group>"; };
+               A7D9006E12C2544A00D8F543 /* corraxescommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = corraxescommand.cpp; sourceTree = "<group>"; };
                A7DA1FEC113FECD400BF472F /* ace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ace.cpp; sourceTree = "<group>"; };
                A7DA1FED113FECD400BF472F /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = "<group>"; };
                A7DA1FEE113FECD400BF472F /* aligncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = aligncommand.cpp; sourceTree = "<group>"; };
                A7DF0AE0121EBB14004A03EA /* getopt_long.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getopt_long.h; 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>"; };
+               A7F0C06412B7D64F0048BC64 /* odum.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = odum.h; sourceTree = "<group>"; };
+               A7F0C06512B7D64F0048BC64 /* odum.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = odum.cpp; sourceTree = "<group>"; };
+               A7F0C08A12B7EAE80048BC64 /* canberra.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = canberra.h; sourceTree = "<group>"; };
+               A7F0C08B12B7EAE80048BC64 /* canberra.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = canberra.cpp; sourceTree = "<group>"; };
+               A7F0C10112B80EEC0048BC64 /* structeuclidean.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = structeuclidean.h; sourceTree = "<group>"; };
+               A7F0C10212B80EEC0048BC64 /* structeuclidean.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = structeuclidean.cpp; 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>"; };
                                A7DA2174113FECD400BF472F /* validparameter.h */,
                                A7DA2175113FECD400BF472F /* venn.cpp */,
                                A7DA2176113FECD400BF472F /* venn.h */,
+                               7E13BDD112BE3FEE004B8A53 /* reportfile.h */,
+                               7E13BDD212BE3FEF004B8A53 /* reportfile.cpp */,
+                               7E1CA7D712C2A384003F10B2 /* flowdata.h */,
+                               7E1CA7D812C2A384003F10B2 /* flowdata.cpp */,
                        );
                        name = mothur;
                        sourceTree = "<group>";
                A7CB593B11402EF90010EB83 /* calculators */ = {
                        isa = PBXGroup;
                        children = (
+                               7E99CA1312C8B0970041246B /* shhhercommand.h */,
+                               7E99CA1412C8B0970041246B /* shhhercommand.cpp */,
                                A7DA200B113FECD400BF472F /* calculator.cpp */,
                                A7DA200C113FECD400BF472F /* calculator.h */,
                                A7DA1FED113FECD400BF472F /* ace.h */,
                                A7DA2006113FECD400BF472F /* bootstrap.h */,
                                A7DA2009113FECD400BF472F /* bstick.cpp */,
                                A7DA200A113FECD400BF472F /* bstick.h */,
+                               A7F0C08A12B7EAE80048BC64 /* canberra.h */,
+                               A7F0C08B12B7EAE80048BC64 /* canberra.cpp */,
                                A7DA200F113FECD400BF472F /* chao1.cpp */,
                                A7DA2010113FECD400BF472F /* chao1.h */,
                                A7DA2033113FECD400BF472F /* coverage.cpp */,
                                A7DA2059113FECD400BF472F /* geom.h */,
                                A7DA206C113FECD400BF472F /* goodscoverage.cpp */,
                                A7DA206D113FECD400BF472F /* goodscoverage.h */,
+                               A7BB565F12BBB0480041F26F /* gower.h */,
+                               A7BB566012BBB0480041F26F /* gower.cpp */,
+                               A7460B7812B9444800866BB6 /* hamming.h */,
+                               A7460B7912B9444800866BB6 /* hamming.cpp */,
                                7E5B2917121FF53C0005339C /* heip.h */,
                                7E5B2918121FF53C0005339C /* heip.cpp */,
+                               A7460A7312B8FCDC00866BB6 /* hellinger.h */,
+                               A7460A7412B8FCDC00866BB6 /* hellinger.cpp */,
                                A7DA2080113FECD400BF472F /* ignoregaps.h */,
                                7E962A40121F76B1007464B5 /* invsimpson.h */,
                                7E962A41121F76B1007464B5 /* invsimpson.cpp */,
                                A7DA2084113FECD400BF472F /* jackknife.h */,
                                A7DA2093113FECD400BF472F /* logsd.cpp */,
                                A7DA2094113FECD400BF472F /* logsd.h */,
+                               A7460A9812B9061B00866BB6 /* manhattan.h */,
+                               A7460A9912B9061B00866BB6 /* manhattan.cpp */,
+                               A7BB56B812BBB5690041F26F /* memchi2.h */,
+                               A7BB56B912BBB5690041F26F /* memchi2.cpp */,
+                               A7BB56EB12BBBFDF0041F26F /* memchord.h */,
+                               A7BB56EC12BBBFDF0041F26F /* memchord.cpp */,
+                               A7BB570B12BBC2880041F26F /* memeuclidean.h */,
+                               A7BB570C12BBC2880041F26F /* memeuclidean.cpp */,
+                               A7BB573712BBC43B0041F26F /* mempearson.h */,
+                               A7BB573812BBC43B0041F26F /* mempearson.cpp */,
                                A7DA20AE113FECD400BF472F /* npshannon.cpp */,
                                A7DA20AF113FECD400BF472F /* npshannon.h */,
                                A7DA20B0113FECD400BF472F /* nseqs.h */,
+                               A7F0C06412B7D64F0048BC64 /* odum.h */,
+                               A7F0C06512B7D64F0048BC64 /* odum.cpp */,
                                A7DA20B2113FECD400BF472F /* onegapdist.h */,
                                A7DA20B3113FECD400BF472F /* onegapignore.h */,
                                A72B3A7B118B4D1B004B9F8D /* phylodiversity.h */,
                                7E4EBD44122018FB00D85E7B /* simpsoneven.cpp */,
                                7E5B294A121FFADC0005339C /* smithwilson.h */,
                                7E5B294B121FFADC0005339C /* smithwilson.cpp */,
-                               A7DA2142113FECD400BF472F /* simpson.cpp */,
                                A7DA2143113FECD400BF472F /* simpson.h */,
+                               A7DA2142113FECD400BF472F /* simpson.cpp */,
                                A7DA2149113FECD400BF472F /* sobs.h */,
+                               A7460ADB12B914B700866BB6 /* soergel.h */,
+                               A7460ADC12B914B700866BB6 /* soergel.cpp */,
                                A7DA214A113FECD400BF472F /* solow.cpp */,
                                A7DA214B113FECD400BF472F /* solow.h */,
+                               A7460B5912B93F1F00866BB6 /* speciesprofile.h */,
+                               A7460B5A12B93F1F00866BB6 /* speciesprofile.cpp */,
+                               A7460AF712B9218400866BB6 /* spearman.h */,
+                               A7460AF812B9218400866BB6 /* spearman.cpp */,
+                               A7BB555212BB87F30041F26F /* structchi2.h */,
+                               A7BB555312BB87F30041F26F /* structchi2.cpp */,
+                               A7460A3F12B8EF1C00866BB6 /* structchord.h */,
+                               A7460A4012B8EF1C00866BB6 /* structchord.cpp */,
+                               A7F0C10112B80EEC0048BC64 /* structeuclidean.h */,
+                               A7F0C10212B80EEC0048BC64 /* structeuclidean.cpp */,
+                               A7460B3612B9377400866BB6 /* structkulczynski.h */,
+                               A7460B3712B9377400866BB6 /* structkulczynski.cpp */,
+                               A7460AC912B90C5600866BB6 /* structpearson.h */,
+                               A7460ACA12B90C5600866BB6 /* structpearson.cpp */,
                                A7DA2160113FECD400BF472F /* treecalculator.h */,
                                A7DA216D113FECD400BF472F /* unweighted.cpp */,
                                A7DA216E113FECD400BF472F /* unweighted.h */,
                A7CB593E11402F110010EB83 /* commands */ = {
                        isa = PBXGroup;
                        children = (
+                               7E1CA7D912C2A425003F10B2 /* trimflowscommand.h */,
+                               7E1CA7DA12C2A425003F10B2 /* trimflowscommand.cpp */,
                                A7DA202B113FECD400BF472F /* command.hpp */,
                                A7DA1FEF113FECD400BF472F /* aligncommand.h */,
                                A7DA1FEE113FECD400BF472F /* aligncommand.cpp */,
                                A7DA2029113FECD400BF472F /* collectsharedcommand.cpp */,
                                A7DA2032113FECD400BF472F /* consensuscommand.h */,
                                A7DA2031113FECD400BF472F /* consensuscommand.cpp */,
+                               A71FF438129BDC35004397E6 /* consensusseqscommand.h */,
+                               A71FF439129BDC35004397E6 /* consensusseqscommand.cpp */,
+                               A7D9006D12C2544A00D8F543 /* corraxescommand.h */,
+                               A7D9006E12C2544A00D8F543 /* corraxescommand.cpp */,
                                A7118EE511CFCAC000CFDE03 /* degapseqscommand.h */,
                                A7118EE611CFCAC000CFDE03 /* degapseqscommand.cpp */,
                                A7DA203B113FECD400BF472F /* deconvolutecommand.h */,
                                A7DA204F113FECD400BF472F /* filterseqscommand.cpp */,
                                A7DA205B113FECD400BF472F /* getgroupcommand.h */,
                                A7DA205A113FECD400BF472F /* getgroupcommand.cpp */,
+                               A75103D6128AE34100ABB831 /* getgroupscommand.h */,
+                               A75103D7128AE34100ABB831 /* getgroupscommand.cpp */,
                                A7DA205D113FECD400BF472F /* getlabelcommand.h */,
                                A7DA205C113FECD400BF472F /* getlabelcommand.cpp */,
                                A787A24F124CB46C0076EB84 /* getlineagecommand.h */,
                                A787A250124CB46C0076EB84 /* getlineagecommand.cpp */,
                                A7DA205F113FECD400BF472F /* getlistcountcommand.h */,
                                A7DA205E113FECD400BF472F /* getlistcountcommand.cpp */,
+                               A7510407128AFCC100ABB831 /* getotuscommand.h */,
+                               A7510408128AFCC100ABB831 /* getotuscommand.cpp */,
                                A7DA2061113FECD400BF472F /* getoturepcommand.h */,
                                A7DA2060113FECD400BF472F /* getoturepcommand.cpp */,
                                A7DA2063113FECD400BF472F /* getrabundcommand.h */,
                                A7DA207C113FECD400BF472F /* heatmapsimcommand.cpp */,
                                A7DA207F113FECD400BF472F /* helpcommand.h */,
                                A7DA207E113FECD400BF472F /* helpcommand.cpp */,
+                               A76D1473128D9DA2005D4DFE /* indicatorcommand.h */,
+                               A76D1474128D9DA2005D4DFE /* indicatorcommand.cpp */,
                                A7DA208E113FECD400BF472F /* libshuffcommand.h */,
                                A7DA208D113FECD400BF472F /* libshuffcommand.cpp */,
                                A7DA2090113FECD400BF472F /* listseqscommand.h */,
                                A724C2B71254961E006BB1C7 /* parsefastaqcommand.cpp */,
                                A7DA20BD113FECD400BF472F /* parselistscommand.h */,
                                A7DA20BC113FECD400BF472F /* parselistscommand.cpp */,
-                               A7E8338C115BBDAA00739EC4 /* parsesffcommand.h */,
-                               A7E8338B115BBDAA00739EC4 /* parsesffcommand.cpp */,
                                A7DA20C1113FECD400BF472F /* parsimonycommand.h */,
                                A7DA20C0113FECD400BF472F /* parsimonycommand.cpp */,
                                A7DA20C3113FECD400BF472F /* pcacommand.h */,
                                A7DA20EA113FECD400BF472F /* readotucommand.cpp */,
                                A7DA20F1113FECD400BF472F /* readtreecommand.h */,
                                A7DA20F0113FECD400BF472F /* readtreecommand.cpp */,
+                               A751032A128AC93F00ABB831 /* removegroupscommand.h */,
+                               A751032B128AC93F00ABB831 /* removegroupscommand.cpp */,
                                A787A28E124CE1470076EB84 /* removelineagecommand.h */,
                                A787A28F124CE1470076EB84 /* removelineagecommand.cpp */,
+                               A76D1451128D6A03005D4DFE /* removeotuscommand.h */,
+                               A76D1452128D6A03005D4DFE /* removeotuscommand.cpp */,
                                A7DA20F3113FECD400BF472F /* removeseqscommand.h */,
                                A7DA20F2113FECD400BF472F /* removeseqscommand.cpp */,
                                A7DA20F5113FECD400BF472F /* reversecommand.h */,
                        };
                        buildConfigurationList = 1DEB919308733D9F0010E9CD /* Build configuration list for PBXProject "Mothur" */;
                        compatibilityVersion = "Xcode 3.0";
+                       developmentRegion = English;
                        hasScannedForEncodings = 1;
                        knownRegions = (
                                English,