added make.biom command

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

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 2088e3791a7a7602e0a8015c06606afad8dc5d52..1387399e7be27dcf0f80316478c2519fb5d5daf3 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -3,7 +3,7 @@
        archiveVersion = 1;
        classes = {
        };
-       objectVersion = 45;
+       objectVersion = 46;
        objects = {
 
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@@ -15,6 +15,7 @@
                A71CB160130B04A2001E7287 /* anosimcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A71CB15E130B04A2001E7287 /* anosimcommand.cpp */; };
                A71FE12C12EDF72400963CA7 /* mergegroupscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */; };
                A721765713BB9F7D0014DAAE /* referencedb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A721765613BB9F7D0014DAAE /* referencedb.cpp */; };
+               A724D2B7153C8628000A826F /* makebiomcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A724D2B6153C8628000A826F /* makebiomcommand.cpp */; };
                A727864412E9E28C00F86ABA /* removerarecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A727864312E9E28C00F86ABA /* removerarecommand.cpp */; };
                A73DDBBA13C4A0D1006AAE38 /* clearmemorycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A73DDBB913C4A0D1006AAE38 /* clearmemorycommand.cpp */; };
                A73DDC3813C4BF64006AAE38 /* mothurmetastats.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A73DDC3713C4BF64006AAE38 /* mothurmetastats.cpp */; };
@@ -63,6 +64,7 @@
                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 */; };
+               A7D755DA1535F679009BF21A /* treereader.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7D755D91535F679009BF21A /* treereader.cpp */; };
                A7E9B88112D37EC400DA6239 /* ace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B64F12D37EC300DA6239 /* ace.cpp */; };
                A7E9B88212D37EC400DA6239 /* aligncommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B65112D37EC300DA6239 /* aligncommand.cpp */; };
                A7E9B88312D37EC400DA6239 /* alignment.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B65312D37EC300DA6239 /* alignment.cpp */; };
@@ -77,7 +79,6 @@
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                A7E9B88E12D37EC400DA6239 /* bootstrap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B66812D37EC400DA6239 /* bootstrap.cpp */; };
-               A7E9B88F12D37EC400DA6239 /* bootstrapsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B66A12D37EC400DA6239 /* bootstrapsharedcommand.cpp */; };
                A7E9B89012D37EC400DA6239 /* bstick.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B66C12D37EC400DA6239 /* bstick.cpp */; };
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                A7E9B89212D37EC400DA6239 /* canberra.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B67012D37EC400DA6239 /* canberra.cpp */; };
@@ -112,7 +113,7 @@
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-               A7E9B8B312D37EC400DA6239 /* consensuscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6B512D37EC400DA6239 /* consensuscommand.cpp */; };
+               A7E9B8B312D37EC400DA6239 /* consensus.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6B512D37EC400DA6239 /* consensus.cpp */; };
                A7E9B8B412D37EC400DA6239 /* consensusseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */; };
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                A7E9B8B612D37EC400DA6239 /* coverage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6BB12D37EC400DA6239 /* coverage.cpp */; };
@@ -208,7 +209,6 @@
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-               A7E9B91612D37EC400DA6239 /* phylodiversity.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78912D37EC400DA6239 /* phylodiversity.cpp */; };
                A7E9B91712D37EC400DA6239 /* phylodiversitycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */; };
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                A7E9B91912D37EC400DA6239 /* phylotree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78F12D37EC400DA6239 /* phylotree.cpp */; };
@@ -395,6 +395,8 @@
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                A721765613BB9F7D0014DAAE /* referencedb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = referencedb.cpp; sourceTree = "<group>"; };
+               A724D2B4153C8600000A826F /* makebiomcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = makebiomcommand.h; sourceTree = "<group>"; };
+               A724D2B6153C8628000A826F /* makebiomcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = makebiomcommand.cpp; sourceTree = "<group>"; };
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                A727864312E9E28C00F86ABA /* removerarecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removerarecommand.cpp; sourceTree = "<group>"; };
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@@ -499,6 +501,8 @@
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+               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>"; };
                A7DAAFA3133A254E003956EB /* commandparameter.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = commandparameter.h; sourceTree = "<group>"; };
                A7E9B64F12D37EC300DA6239 /* ace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ace.cpp; sourceTree = "<group>"; };
                A7E9B65012D37EC300DA6239 /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = "<group>"; };
@@ -527,8 +531,6 @@
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                A7E9B66812D37EC400DA6239 /* bootstrap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bootstrap.cpp; sourceTree = "<group>"; };
                A7E9B66912D37EC400DA6239 /* bootstrap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bootstrap.h; sourceTree = "<group>"; };
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                A7E9B66E12D37EC400DA6239 /* calculator.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = calculator.cpp; sourceTree = "<group>"; };
@@ -600,8 +602,8 @@
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-               A7E9B6B512D37EC400DA6239 /* consensuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = consensuscommand.cpp; sourceTree = "<group>"; };
-               A7E9B6B612D37EC400DA6239 /* consensuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = consensuscommand.h; sourceTree = "<group>"; };
+               A7E9B6B512D37EC400DA6239 /* consensus.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = consensus.cpp; sourceTree = "<group>"; };
+               A7E9B6B612D37EC400DA6239 /* consensus.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = consensus.h; sourceTree = "<group>"; };
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                A7E9B6B812D37EC400DA6239 /* consensusseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = consensusseqscommand.h; sourceTree = "<group>"; };
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@@ -806,8 +808,6 @@
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                A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcoacommand.cpp; sourceTree = "<group>"; };
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-               A7E9B78912D37EC400DA6239 /* phylodiversity.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversity.cpp; sourceTree = "<group>"; };
-               A7E9B78A12D37EC400DA6239 /* phylodiversity.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylodiversity.h; sourceTree = "<group>"; };
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                A7E9B78C12D37EC400DA6239 /* phylodiversitycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylodiversitycommand.h; sourceTree = "<group>"; };
                A7E9B78D12D37EC400DA6239 /* phylosummary.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylosummary.cpp; sourceTree = "<group>"; };
@@ -1132,6 +1132,8 @@
                                A7DAAFA3133A254E003956EB /* commandparameter.h */,
                                A7E9B6B412D37EC400DA6239 /* completelinkage.cpp */,
                                A7E9BA4212D3960D00DA6239 /* containers */,
+                               A7E9B6B612D37EC400DA6239 /* consensus.h */,
+                               A7E9B6B512D37EC400DA6239 /* consensus.cpp */,
                                A7AACFBA132FE008003D6C4D /* currentfile.h */,
                                A7E9B6C912D37EC400DA6239 /* display.h */,
                                A7E9B6D112D37EC400DA6239 /* dlibshuff.cpp */,
@@ -1308,8 +1310,6 @@
                                A71CB15E130B04A2001E7287 /* anosimcommand.cpp */,
                                A7E9B66112D37EC300DA6239 /* binsequencecommand.h */,
                                A7E9B66012D37EC300DA6239 /* binsequencecommand.cpp */,
-                               A7E9B66B12D37EC400DA6239 /* bootstrapsharedcommand.h */,
-                               A7E9B66A12D37EC400DA6239 /* bootstrapsharedcommand.cpp */,
                                A7E9B67312D37EC400DA6239 /* catchallcommand.h */,
                                A7E9B67212D37EC400DA6239 /* catchallcommand.cpp */,
                                A7E9B67B12D37EC400DA6239 /* chimerabellerophoncommand.h */,
@@ -1350,8 +1350,6 @@
                                A7E9B6A812D37EC400DA6239 /* collectcommand.cpp */,
                                A7E9B6AD12D37EC400DA6239 /* collectsharedcommand.h */,
                                A7E9B6AC12D37EC400DA6239 /* collectsharedcommand.cpp */,
-                               A7E9B6B612D37EC400DA6239 /* consensuscommand.h */,
-                               A7E9B6B512D37EC400DA6239 /* consensuscommand.cpp */,
                                A7E9B6B812D37EC400DA6239 /* consensusseqscommand.h */,
                                A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */,
                                A7C3DC0A14FE457500FE1924 /* cooccurrencecommand.h */,
@@ -1422,6 +1420,8 @@
                                A7E9B73D12D37EC400DA6239 /* listseqscommand.cpp */,
                                A7FA10001302E096003860FE /* mantelcommand.h */,
                                A7FA10011302E096003860FE /* mantelcommand.cpp */,
+                               A724D2B4153C8600000A826F /* makebiomcommand.h */,
+                               A724D2B6153C8628000A826F /* makebiomcommand.cpp */,
                                A799F5B71309A3E000AEEFA0 /* makefastqcommand.h */,
                                A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */,
                                A7E9B74412D37EC400DA6239 /* makegroupcommand.h */,
@@ -1831,8 +1831,6 @@
                                A7E9B68F12D37EC400DA6239 /* classify.h */,
                                A7E9B73812D37EC400DA6239 /* knn.h */,
                                A7E9B73712D37EC400DA6239 /* knn.cpp */,
-                               A7E9B78912D37EC400DA6239 /* phylodiversity.cpp */,
-                               A7E9B78A12D37EC400DA6239 /* phylodiversity.h */,
                                A7E9B78D12D37EC400DA6239 /* phylosummary.cpp */,
                                A7E9B78E12D37EC400DA6239 /* phylosummary.h */,
                                A7E9B78F12D37EC400DA6239 /* phylotree.cpp */,
@@ -1884,6 +1882,8 @@
                                A713EBAB12DC7613000092AC /* readphylipvector.cpp */,
                                A7E9B84312D37EC400DA6239 /* splitmatrix.cpp */,
                                A7E9B84412D37EC400DA6239 /* splitmatrix.h */,
+                               A7D755D71535F665009BF21A /* treereader.h */,
+                               A7D755D91535F679009BF21A /* treereader.cpp */,
                        );
                        name = read;
                        sourceTree = "<group>";
@@ -1938,10 +1938,11 @@
                08FB7793FE84155DC02AAC07 /* Project object */ = {
                        isa = PBXProject;
                        attributes = {
+                               LastUpgradeCheck = 0420;
                                ORGANIZATIONNAME = "Schloss Lab";
                        };
                        buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */;
-                       compatibilityVersion = "Xcode 3.1";
+                       compatibilityVersion = "Xcode 3.2";
                        developmentRegion = English;
                        hasScannedForEncodings = 1;
                        knownRegions = (
@@ -1978,7 +1979,6 @@
                                A7E9B88C12D37EC400DA6239 /* blastdb.cpp in Sources */,
                                A7E9B88D12D37EC400DA6239 /* boneh.cpp in Sources */,
                                A7E9B88E12D37EC400DA6239 /* bootstrap.cpp in Sources */,
-                               A7E9B88F12D37EC400DA6239 /* bootstrapsharedcommand.cpp in Sources */,
                                A7E9B89012D37EC400DA6239 /* bstick.cpp in Sources */,
                                A7E9B89112D37EC400DA6239 /* calculator.cpp in Sources */,
                                A7E9B89212D37EC400DA6239 /* canberra.cpp in Sources */,
@@ -2013,7 +2013,7 @@
                                A7E9B8B012D37EC400DA6239 /* commandfactory.cpp in Sources */,
                                A7E9B8B112D37EC400DA6239 /* commandoptionparser.cpp in Sources */,
                                A7E9B8B212D37EC400DA6239 /* completelinkage.cpp in Sources */,
-                               A7E9B8B312D37EC400DA6239 /* consensuscommand.cpp in Sources */,
+                               A7E9B8B312D37EC400DA6239 /* consensus.cpp in Sources */,
                                A7E9B8B412D37EC400DA6239 /* consensusseqscommand.cpp in Sources */,
                                A7E9B8B512D37EC400DA6239 /* corraxescommand.cpp in Sources */,
                                A7E9B8B612D37EC400DA6239 /* coverage.cpp in Sources */,
@@ -2109,7 +2109,6 @@
                                A7E9B91312D37EC400DA6239 /* parsimony.cpp in Sources */,
                                A7E9B91412D37EC400DA6239 /* parsimonycommand.cpp in Sources */,
                                A7E9B91512D37EC400DA6239 /* pcoacommand.cpp in Sources */,
-                               A7E9B91612D37EC400DA6239 /* phylodiversity.cpp in Sources */,
                                A7E9B91712D37EC400DA6239 /* phylodiversitycommand.cpp in Sources */,
                                A7E9B91812D37EC400DA6239 /* phylosummary.cpp in Sources */,
                                A7E9B91912D37EC400DA6239 /* phylotree.cpp in Sources */,
@@ -2307,6 +2306,8 @@
                                A76CDD821510F143004C8458 /* prcseqscommand.cpp in Sources */,
                                A77EBD2F1523709100ED407C /* createdatabasecommand.cpp in Sources */,
                                A7876A26152A017C00A0AE86 /* subsample.cpp in Sources */,
+                               A7D755DA1535F679009BF21A /* treereader.cpp in Sources */,
+                               A724D2B7153C8628000A826F /* makebiomcommand.cpp in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
@@ -2319,7 +2320,6 @@
                                ALWAYS_SEARCH_USER_PATHS = NO;
                                COPY_PHASE_STRIP = NO;
                                GCC_DYNAMIC_NO_PIC = NO;
-                               GCC_ENABLE_FIX_AND_CONTINUE = YES;
                                GCC_MODEL_TUNING = G5;
                                GCC_OPTIMIZATION_LEVEL = 0;
                                INSTALL_PATH = /usr/local/bin;
@@ -2373,7 +2373,6 @@
                                        "-lncurses",
                                        "-lreadline",
                                );
-                               PREBINDING = NO;
                                SDKROOT = macosx10.6;
                                USER_HEADER_SEARCH_PATHS = "";
                        };
@@ -2411,7 +2410,6 @@
                                        "-lncurses",
                                        "-lreadline",
                                );
-                               PREBINDING = NO;
                                SDKROOT = macosx10.6;
                        };
                        name = Release;