]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
added get.dists and remove.dists commands. fixed bug in trim.seqs windows paralelliza...
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index 064019cb0e6b56f19eb6a3d1f2280f8505c8c33b..15a5cff06d869482c252cdc50e82c5ec0a75abdf 100644 (file)
                219C1DE01552C4BD004209F9 /* newcommandtemplate.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 219C1DDF1552C4BD004209F9 /* newcommandtemplate.cpp */; };
                219C1DE41559BCCF004209F9 /* getcoremicrobiomecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 219C1DE31559BCCD004209F9 /* getcoremicrobiomecommand.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 */; };
                83F25B0C163B031200ABE73D /* forest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 83F25B0A163B031200ABE73D /* forest.cpp */; };
                8DD76FB00486AB0100D96B5E /* mothur.1 in CopyFiles */ = {isa = PBXBuildFile; fileRef = C6A0FF2C0290799A04C91782 /* mothur.1 */; };
                A70056E6156A93D000924A2D /* getotulabelscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70056E5156A93D000924A2D /* getotulabelscommand.cpp */; };
                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 */; };
                A713EBAC12DC7613000092AC /* readphylipvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A713EBAB12DC7613000092AC /* readphylipvector.cpp */; };
                A713EBED12DC7C5E000092AC /* nmdscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */; };
                A71CB160130B04A2001E7287 /* anosimcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A71CB15E130B04A2001E7287 /* anosimcommand.cpp */; };
@@ -35,7 +38,9 @@
                A73DDBBA13C4A0D1006AAE38 /* clearmemorycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A73DDBB913C4A0D1006AAE38 /* clearmemorycommand.cpp */; };
                A73DDC3813C4BF64006AAE38 /* mothurmetastats.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A73DDC3713C4BF64006AAE38 /* mothurmetastats.cpp */; };
                A741FAD215D1688E0067BCC5 /* sequencecountparser.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A741FAD115D1688E0067BCC5 /* sequencecountparser.cpp */; };
+               A7496D2E167B531B00CC7D7C /* kruskalwalliscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7496D2C167B531B00CC7D7C /* kruskalwalliscommand.cpp */; };
                A74A9A9F148E881E00AB5E3E /* spline.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74A9A9E148E881E00AB5E3E /* spline.cpp */; };
+               A74C06E916A9C0A9008390A3 /* primerdesigncommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74C06E816A9C0A8008390A3 /* primerdesigncommand.cpp */; };
                A74D36B8137DAFAA00332B0C /* chimerauchimecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D36B7137DAFAA00332B0C /* chimerauchimecommand.cpp */; };
                A74D59A4159A1E2000043046 /* counttable.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D59A3159A1E2000043046 /* counttable.cpp */; };
                A754149714840CF7005850D1 /* summaryqualcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A754149614840CF7005850D1 /* summaryqualcommand.cpp */; };
                A79234D713C74BF6002B08E2 /* mothurfisher.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A79234D613C74BF6002B08E2 /* mothurfisher.cpp */; };
                A795840D13F13CD900F201D5 /* countgroupscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A795840C13F13CD900F201D5 /* countgroupscommand.cpp */; };
                A799F5B91309A3E000AEEFA0 /* makefastqcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */; };
+               A79EEF8616971D4A0006DEC1 /* filtersharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A79EEF8516971D4A0006DEC1 /* filtersharedcommand.cpp */; };
                A7A0671A1562946F0095C8C5 /* listotulabelscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7A067191562946F0095C8C5 /* listotulabelscommand.cpp */; };
                A7A0671F1562AC3E0095C8C5 /* makecontigscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7A0671E1562AC3E0095C8C5 /* makecontigscommand.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 */; };
                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 */; };
                7E6BE10812F710D8007ADDBE /* refchimeratest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = refchimeratest.h; sourceTree = "<group>"; };
                7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = refchimeratest.cpp; sourceTree = "<group>"; };
                7E78911B135F3E8600E725D2 /* eachgapdistignorens.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = eachgapdistignorens.h; sourceTree = "<group>"; };
+               834D9D561656D7C400E7FAB9 /* regularizedrandomforest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = regularizedrandomforest.cpp; sourceTree = "<group>"; };
+               834D9D571656D7C400E7FAB9 /* regularizedrandomforest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = regularizedrandomforest.h; sourceTree = "<group>"; };
+               834D9D5A1656DEC700E7FAB9 /* regularizeddecisiontree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = regularizeddecisiontree.cpp; sourceTree = "<group>"; };
+               834D9D5B1656DEC700E7FAB9 /* regularizeddecisiontree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = regularizeddecisiontree.h; sourceTree = "<group>"; };
                83F25B0A163B031200ABE73D /* forest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = forest.cpp; sourceTree = "<group>"; };
                83F25B0B163B031200ABE73D /* forest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = forest.h; sourceTree = "<group>"; };
                8DD76FB20486AB0100D96B5E /* mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = mothur; sourceTree = BUILT_PRODUCTS_DIR; };
                A70056E9156AB6D400924A2D /* removeotulabelscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removeotulabelscommand.h; sourceTree = "<group>"; };
                A70056EA156AB6E500924A2D /* removeotulabelscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removeotulabelscommand.cpp; sourceTree = "<group>"; };
                A70332B512D3A13400761E33 /* makefile */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.make; path = makefile; sourceTree = "<group>"; };
+               A7128B1A16B7001200723BE4 /* getdistscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getdistscommand.h; sourceTree = "<group>"; };
+               A7128B1C16B7002600723BE4 /* getdistscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getdistscommand.cpp; sourceTree = "<group>"; };
                A713EBAA12DC7613000092AC /* readphylipvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylipvector.h; sourceTree = "<group>"; };
                A713EBAB12DC7613000092AC /* readphylipvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylipvector.cpp; sourceTree = "<group>"; };
                A713EBEB12DC7C5E000092AC /* nmdscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nmdscommand.h; sourceTree = "<group>"; };
                A73DDC3713C4BF64006AAE38 /* mothurmetastats.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mothurmetastats.cpp; 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>"; };
+               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>"; };
                A74A9A9E148E881E00AB5E3E /* spline.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = spline.cpp; sourceTree = "<group>"; };
+               A74C06E616A9C097008390A3 /* primerdesigncommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = primerdesigncommand.h; sourceTree = "<group>"; };
+               A74C06E816A9C0A8008390A3 /* primerdesigncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = primerdesigncommand.cpp; sourceTree = "<group>"; };
                A74D36B6137DAFAA00332B0C /* chimerauchimecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerauchimecommand.h; sourceTree = "<group>"; };
                A74D36B7137DAFAA00332B0C /* chimerauchimecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerauchimecommand.cpp; sourceTree = "<group>"; };
                A74D59A3159A1E2000043046 /* counttable.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = counttable.cpp; sourceTree = "<group>"; };
                A795840C13F13CD900F201D5 /* countgroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = countgroupscommand.cpp; sourceTree = "<group>"; };
                A799F5B71309A3E000AEEFA0 /* makefastqcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = makefastqcommand.h; sourceTree = "<group>"; };
                A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = makefastqcommand.cpp; sourceTree = "<group>"; };
+               A79EEF8516971D4A0006DEC1 /* filtersharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = filtersharedcommand.cpp; sourceTree = "<group>"; };
+               A79EEF8816971D640006DEC1 /* filtersharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = filtersharedcommand.h; sourceTree = "<group>"; };
                A7A067191562946F0095C8C5 /* listotulabelscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listotulabelscommand.cpp; 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>"; };
                A7A61F2B130062E000E05B6B /* amovacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = amovacommand.h; sourceTree = "<group>"; };
                A7A61F2C130062E000E05B6B /* amovacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = amovacommand.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>"; };
                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>"; };
                                A77E193A161B289600DB1A2A /* rftreenode.cpp */,
                                83F25B0A163B031200ABE73D /* forest.cpp */,
                                83F25B0B163B031200ABE73D /* forest.h */,
+                               834D9D561656D7C400E7FAB9 /* regularizedrandomforest.cpp */,
+                               834D9D571656D7C400E7FAB9 /* regularizedrandomforest.h */,
+                               834D9D5A1656DEC700E7FAB9 /* regularizeddecisiontree.cpp */,
+                               834D9D5B1656DEC700E7FAB9 /* regularizeddecisiontree.h */,
                        );
                        name = randomforest;
                        sourceTree = "<group>";
                                A7E9B6CB12D37EC400DA6239 /* distancecommand.cpp */,
                                A7E9B6E412D37EC400DA6239 /* filterseqscommand.h */,
                                A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */,
+                               A79EEF8816971D640006DEC1 /* filtersharedcommand.h */,
+                               A79EEF8516971D4A0006DEC1 /* filtersharedcommand.cpp */,
                                A778FE69134CA6CA00C0BA33 /* getcommandinfocommand.h */,
                                A778FE6A134CA6CA00C0BA33 /* getcommandinfocommand.cpp */,
                                219C1DE51559BCF2004209F9 /* getcoremicrobiomecommand.h */,
                                219C1DE31559BCCD004209F9 /* getcoremicrobiomecommand.cpp */,
                                A7FE7C3E1330EA1000F7B327 /* getcurrentcommand.h */,
                                A7FE7C3F1330EA1000F7B327 /* getcurrentcommand.cpp */,
+                               A7128B1A16B7001200723BE4 /* getdistscommand.h */,
+                               A7128B1C16B7002600723BE4 /* getdistscommand.cpp */,
                                A7E9B6F312D37EC400DA6239 /* getgroupcommand.h */,
                                A7E9B6F212D37EC400DA6239 /* getgroupcommand.cpp */,
                                A7E9B6F512D37EC400DA6239 /* getgroupscommand.h */,
                                A75790581301749D00A30DAB /* homovacommand.cpp */,
                                A7E9B72C12D37EC400DA6239 /* indicatorcommand.h */,
                                A7E9B72B12D37EC400DA6239 /* indicatorcommand.cpp */,
+                               A7496D2D167B531B00CC7D7C /* kruskalwalliscommand.h */,
+                               A7496D2C167B531B00CC7D7C /* kruskalwalliscommand.cpp */,
                                A7E9B73C12D37EC400DA6239 /* libshuffcommand.h */,
                                A7E9B73B12D37EC400DA6239 /* libshuffcommand.cpp */,
                                A7A0671C156294810095C8C5 /* listotulabelscommand.h */,
                                A7E9B79512D37EC400DA6239 /* pipelinepdscommand.cpp */,
                                A7E9B79812D37EC400DA6239 /* preclustercommand.h */,
                                A7E9B79712D37EC400DA6239 /* preclustercommand.cpp */,
+                               A74C06E616A9C097008390A3 /* primerdesigncommand.h */,
+                               A74C06E816A9C0A8008390A3 /* primerdesigncommand.cpp */,
                                A7E9B7A212D37EC400DA6239 /* quitcommand.h */,
                                A7E9B7A112D37EC400DA6239 /* quitcommand.cpp */,
                                A7E9B7AC12D37EC400DA6239 /* rarefactcommand.h */,
                                A7E9B7AB12D37EC400DA6239 /* rarefactcommand.cpp */,
                                A7E9B7AF12D37EC400DA6239 /* rarefactsharedcommand.h */,
                                A7E9B7AE12D37EC400DA6239 /* rarefactsharedcommand.cpp */,
+                               A7B0231716B8245D006BA09E /* removedistscommand.h */,
+                               A7B0231416B8244B006BA09E /* removedistscommand.cpp */,
                                A7E9B7C412D37EC400DA6239 /* removegroupscommand.h */,
                                A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */,
                                A7E9B7C612D37EC400DA6239 /* removelineagecommand.h */,
                                A721AB72161C572A009860A1 /* kmertree.cpp in Sources */,
                                A721AB77161C573B009860A1 /* taxonomynode.cpp in Sources */,
                                83F25B0C163B031200ABE73D /* forest.cpp in Sources */,
+                               834D9D581656D7C400E7FAB9 /* regularizedrandomforest.cpp in Sources */,
+                               834D9D5C1656DEC800E7FAB9 /* regularizeddecisiontree.cpp in Sources */,
+                               A7496D2E167B531B00CC7D7C /* kruskalwalliscommand.cpp in Sources */,
+                               A79EEF8616971D4A0006DEC1 /* filtersharedcommand.cpp in Sources */,
+                               A74C06E916A9C0A9008390A3 /* primerdesigncommand.cpp in Sources */,
+                               A7128B1D16B7002A00723BE4 /* getdistscommand.cpp in Sources */,
+                               A7B0231516B8244C006BA09E /* removedistscommand.cpp in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };