Mothur.xcodeproj/project.pbxproj

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 121                 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtree.cpp; sourceTree = SOURCE_ROOT; };
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 123                 37B28F670F27590100808A62 /* deconvolutecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deconvolutecommand.cpp; sourceTree = SOURCE_ROOT; };
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 125                 37D927B90F21331F001D4494 /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = SOURCE_ROOT; };
 126                 37D927BA0F21331F001D4494 /* averagelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = averagelinkage.cpp; sourceTree = SOURCE_ROOT; };
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 128                 37D927BC0F21331F001D4494 /* bootstrap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bootstrap.h; sourceTree = SOURCE_ROOT; };
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 130                 37D927BE0F21331F001D4494 /* calculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = calculator.h; sourceTree = SOURCE_ROOT; };
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 132                 37D927C00F21331F001D4494 /* chao1.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chao1.h; sourceTree = SOURCE_ROOT; };
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 134                 37D927C20F21331F001D4494 /* cluster.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = cluster.hpp; sourceTree = SOURCE_ROOT; };
 135                 37D927C30F21331F001D4494 /* clustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clustercommand.cpp; sourceTree = SOURCE_ROOT; };
 136                 37D927C40F21331F001D4494 /* clustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clustercommand.h; sourceTree = SOURCE_ROOT; };
 137                 37D927C50F21331F001D4494 /* collect.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collect.cpp; sourceTree = SOURCE_ROOT; };
 138                 37D927C60F21331F001D4494 /* collect.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collect.h; sourceTree = SOURCE_ROOT; };
 139                 37D927C70F21331F001D4494 /* collectcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collectcommand.cpp; sourceTree = SOURCE_ROOT; };
 140                 37D927C80F21331F001D4494 /* collectcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectcommand.h; sourceTree = SOURCE_ROOT; };
 141                 37D927C90F21331F001D4494 /* collectdisplay.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectdisplay.h; sourceTree = SOURCE_ROOT; };
 142                 37D927CA0F21331F001D4494 /* collectorscurvedata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectorscurvedata.h; sourceTree = SOURCE_ROOT; };
 143                 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collectsharedcommand.cpp; sourceTree = SOURCE_ROOT; };
 144                 37D927CC0F21331F001D4494 /* collectsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectsharedcommand.h; sourceTree = SOURCE_ROOT; };
 145                 37D927CD0F21331F001D4494 /* command.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = command.hpp; sourceTree = SOURCE_ROOT; };
 146                 37D927CF0F21331F001D4494 /* commandfactory.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandfactory.hpp; sourceTree = SOURCE_ROOT; };
 147                 37D927D00F21331F001D4494 /* commandoptionparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = commandoptionparser.cpp; sourceTree = SOURCE_ROOT; };
 148                 37D927D10F21331F001D4494 /* commandoptionparser.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandoptionparser.hpp; sourceTree = SOURCE_ROOT; };
 149                 37D927D20F21331F001D4494 /* completelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = completelinkage.cpp; sourceTree = SOURCE_ROOT; };
 150                 37D927D30F21331F001D4494 /* database.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = database.cpp; sourceTree = SOURCE_ROOT; };
 151                 37D927D40F21331F001D4494 /* database.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = database.hpp; sourceTree = SOURCE_ROOT; };
 152                 37D927D50F21331F001D4494 /* datavector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = datavector.hpp; sourceTree = SOURCE_ROOT; };
 153                 37D927D60F21331F001D4494 /* display.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = display.h; sourceTree = SOURCE_ROOT; };
 154                 37D927D70F21331F001D4494 /* engine.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = engine.cpp; sourceTree = SOURCE_ROOT; };
 155                 37D927D80F21331F001D4494 /* engine.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = engine.hpp; sourceTree = SOURCE_ROOT; };
 156                 37D927D90F21331F001D4494 /* errorchecking.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = errorchecking.cpp; sourceTree = SOURCE_ROOT; };
 157                 37D927DA0F21331F001D4494 /* errorchecking.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = errorchecking.h; sourceTree = SOURCE_ROOT; };
 158                 37D927DB0F21331F001D4494 /* fastamap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fastamap.cpp; sourceTree = SOURCE_ROOT; };
 159                 37D927DC0F21331F001D4494 /* fastamap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fastamap.h; sourceTree = SOURCE_ROOT; };
 160                 37D927DD0F21331F001D4494 /* fileoutput.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fileoutput.cpp; sourceTree = SOURCE_ROOT; };
 161                 37D927DE0F21331F001D4494 /* fileoutput.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fileoutput.h; sourceTree = SOURCE_ROOT; };
 162                 37D927DF0F21331F001D4494 /* globaldata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = globaldata.cpp; sourceTree = SOURCE_ROOT; };
 163                 37D927E00F21331F001D4494 /* globaldata.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = globaldata.hpp; sourceTree = SOURCE_ROOT; };
 164                 37D927E10F21331F001D4494 /* groupmap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = groupmap.cpp; sourceTree = SOURCE_ROOT; };
 165                 37D927E20F21331F001D4494 /* groupmap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = groupmap.h; sourceTree = SOURCE_ROOT; };
 166                 37D927E30F21331F001D4494 /* helpcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = helpcommand.cpp; sourceTree = SOURCE_ROOT; };
 167                 37D927E40F21331F001D4494 /* helpcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = helpcommand.h; sourceTree = SOURCE_ROOT; };
 168                 37D927E50F21331F001D4494 /* inputdata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = inputdata.cpp; sourceTree = SOURCE_ROOT; };
 169                 37D927E60F21331F001D4494 /* inputdata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = inputdata.h; sourceTree = SOURCE_ROOT; };
 170                 37D927E70F21331F001D4494 /* jackknife.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = jackknife.cpp; sourceTree = SOURCE_ROOT; };
 171                 37D927E80F21331F001D4494 /* jackknife.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = jackknife.h; sourceTree = SOURCE_ROOT; };
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 173                 37D927EA0F21331F001D4494 /* kmer.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = kmer.hpp; sourceTree = SOURCE_ROOT; };
 174                 37D927EB0F21331F001D4494 /* kmerdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = kmerdb.cpp; sourceTree = SOURCE_ROOT; };
 175                 37D927EC0F21331F001D4494 /* kmerdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = kmerdb.hpp; sourceTree = SOURCE_ROOT; };
 176                 37D927ED0F21331F001D4494 /* listvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listvector.cpp; sourceTree = SOURCE_ROOT; };
 177                 37D927EE0F21331F001D4494 /* listvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = listvector.hpp; sourceTree = SOURCE_ROOT; };
 178                 37D927EF0F21331F001D4494 /* mothur.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mothur.cpp; sourceTree = SOURCE_ROOT; };
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 180                 37D927F10F21331F001D4494 /* nameassignment.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nameassignment.hpp; sourceTree = SOURCE_ROOT; };
 181                 37D927F20F21331F001D4494 /* nocommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nocommand.cpp; sourceTree = SOURCE_ROOT; };
 182                 37D927F30F21331F001D4494 /* nocommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nocommand.h; sourceTree = SOURCE_ROOT; };
 183                 37D927F40F21331F001D4494 /* npshannon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = npshannon.cpp; sourceTree = SOURCE_ROOT; };
 184                 37D927F50F21331F001D4494 /* npshannon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = npshannon.h; sourceTree = SOURCE_ROOT; };
 185                 37D927F60F21331F001D4494 /* observable.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = observable.h; sourceTree = SOURCE_ROOT; };
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 189                 37D927FA0F21331F001D4494 /* parselistcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parselistcommand.h; sourceTree = SOURCE_ROOT; };
 190                 37D927FB0F21331F001D4494 /* progress.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = progress.cpp; sourceTree = SOURCE_ROOT; };
 191                 37D927FC0F21331F001D4494 /* progress.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = progress.hpp; sourceTree = SOURCE_ROOT; };
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 281 /* End PBXFileReference section */
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 292
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 295                         isa = PBXGroup;
 296                         children = (
 297                                 08FB7795FE84155DC02AAC07 /* Source */,
 298                                 C6859E8C029090F304C91782 /* Documentation */,
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 306                         children = (
 307                                 37D927BA0F21331F001D4494 /* averagelinkage.cpp */,
 308                                 37D928A60F2133C0001D4494 /* calculators */,
 309                                 37D927C20F21331F001D4494 /* cluster.hpp */,
 310                                 37D927C10F21331F001D4494 /* cluster.cpp */,
 311                                 37D928A90F2133E5001D4494 /* commands */,
 312                                 37D927C60F21331F001D4494 /* collect.h */,
 313                                 37D927C50F21331F001D4494 /* collect.cpp */,
 314                                 37D927C90F21331F001D4494 /* collectdisplay.h */,
 315                                 37D928AC0F213420001D4494 /* containers */,
 316                                 37D927CA0F21331F001D4494 /* collectorscurvedata.h */,
 317                                 37D927CF0F21331F001D4494 /* commandfactory.hpp */,
 318                                 372E12EC0F264D320095CF7E /* commandfactory.cpp */,
 319                                 37D927D10F21331F001D4494 /* commandoptionparser.hpp */,
 320                                 37D927D00F21331F001D4494 /* commandoptionparser.cpp */,
 321                                 37D927D20F21331F001D4494 /* completelinkage.cpp */,
 322                                 37D927D40F21331F001D4494 /* database.hpp */,
 323                                 37D927D30F21331F001D4494 /* database.cpp */,
 324                                 37D927D60F21331F001D4494 /* display.h */,
 325                                 37D927D80F21331F001D4494 /* engine.hpp */,
 326                                 37D927D70F21331F001D4494 /* engine.cpp */,
 327                                 7E44EBD00F32358B00B0D45D /* makefile */,
 328                                 37D928B10F213472001D4494 /* errorcheckor */,
 329                                 37D927DE0F21331F001D4494 /* fileoutput.h */,
 330                                 37D927DD0F21331F001D4494 /* fileoutput.cpp */,
 331                                 37D927E00F21331F001D4494 /* globaldata.hpp */,
 332                                 37D927DF0F21331F001D4494 /* globaldata.cpp */,
 333                                 37D927E60F21331F001D4494 /* inputdata.h */,
 334                                 37D927E50F21331F001D4494 /* inputdata.cpp */,
 335                                 37D927EA0F21331F001D4494 /* kmer.hpp */,
 336                                 37D927E90F21331F001D4494 /* kmer.cpp */,
 337                                 37D927EC0F21331F001D4494 /* kmerdb.hpp */,
 338                                 37D927EB0F21331F001D4494 /* kmerdb.cpp */,
 339                                 37D927EF0F21331F001D4494 /* mothur.cpp */,
 340                                 37D927F10F21331F001D4494 /* nameassignment.hpp */,
 341                                 37D927F00F21331F001D4494 /* nameassignment.cpp */,
 342                                 37D927F60F21331F001D4494 /* observable.h */,
 343                                 37D927FC0F21331F001D4494 /* progress.hpp */,
 344                                 37D927FB0F21331F001D4494 /* progress.cpp */,
 345                                 37D928040F21331F001D4494 /* raredisplay.h */,
 346                                 37D928030F21331F001D4494 /* raredisplay.cpp */,
 347                                 37D928060F21331F001D4494 /* rarefact.h */,
 348                                 37D928050F21331F001D4494 /* rarefact.cpp */,
 349                                 37D928090F21331F001D4494 /* rarefactioncurvedata.h */,
 350                                 37D928130F21331F001D4494 /* readmatrix.hpp */,
 351                                 37D928120F21331F001D4494 /* readmatrix.cpp */,
 352                                 37AD4DC80F28F3DD00AA2D49 /* readtree.h */,
 353                                 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */,
 354                                 37D9281D0F21331F001D4494 /* sequence.hpp */,
 355                                 37D9281C0F21331F001D4494 /* sequence.cpp */,
 356                                 37D928210F21331F001D4494 /* shared.h */,
 357                                 37D928200F21331F001D4494 /* shared.cpp */,
 358                                 37D928420F21331F001D4494 /* singlelinkage.cpp */,
 359                                 37D928450F21331F001D4494 /* sparsematrix.hpp */,
 360                                 37D928440F21331F001D4494 /* sparsematrix.cpp */,
 361                                 37D928480F21331F001D4494 /* summarydata.h */,
 362                                 37D928490F21331F001D4494 /* summarydisplay.h */,
 363                                 37D9284C0F21331F001D4494 /* utilities.hpp */,
 364                         );
 365                         name = Source;
 366                         sourceTree = SOURCE_ROOT;
 367                 };
 368                 1AB674ADFE9D54B511CA2CBB /* Products */ = {
 369                         isa = PBXGroup;
 370                         children = (
 371                                 8DD76F6C0486A84900D96B5E /* mothur */,
 372                         );
 373                         name = Products;
 374                         sourceTree = "<group>";
 375                 };
 376                 37D928A60F2133C0001D4494 /* calculators */ = {
 377                         isa = PBXGroup;
 378                         children = (
 379                                 37D927BE0F21331F001D4494 /* calculator.h */,
 380                                 37D927BD0F21331F001D4494 /* calculator.cpp */,
 381                                 37D927B90F21331F001D4494 /* ace.h */,
 382                                 37D927B80F21331F001D4494 /* ace.cpp */,
 383                                 37D927BC0F21331F001D4494 /* bootstrap.h */,
 384                                 37D927BB0F21331F001D4494 /* bootstrap.cpp */,
 385                                 37D927C00F21331F001D4494 /* chao1.h */,
 386                                 37D927BF0F21331F001D4494 /* chao1.cpp */,
 387                                 37D927E80F21331F001D4494 /* jackknife.h */,
 388                                 37D927E70F21331F001D4494 /* jackknife.cpp */,
 389                                 37D927F50F21331F001D4494 /* npshannon.h */,
 390                                 37D927F40F21331F001D4494 /* npshannon.cpp */,
 391                                 37D928020F21331F001D4494 /* rarecalc.h */,
 392                                 37D928010F21331F001D4494 /* rarecalc.cpp */,
 393                                 37D9281F0F21331F001D4494 /* shannon.h */,
 394                                 37D9281E0F21331F001D4494 /* shannon.cpp */,
 395                                 37D928230F21331F001D4494 /* sharedace.h */,
 396                                 37D928220F21331F001D4494 /* sharedace.cpp */,
 397                                 37D928250F21331F001D4494 /* sharedchao1.h */,
 398                                 37D928240F21331F001D4494 /* sharedchao1.cpp */,
 399                                 37D928290F21331F001D4494 /* sharedjabund.h */,
 400                                 37D928280F21331F001D4494 /* sharedjabund.cpp */,
 401                                 37D9282B0F21331F001D4494 /* sharedjclass.h */,
 402                                 37D9282A0F21331F001D4494 /* sharedjclass.cpp */,
 403                                 37D9282D0F21331F001D4494 /* sharedjest.h */,
 404                                 37D9282C0F21331F001D4494 /* sharedjest.cpp */,
 405                                 37D928350F21331F001D4494 /* sharedsobs.h */,
 406                                 37D928340F21331F001D4494 /* sharedsobs.cpp */,
 407                                 37D928370F21331F001D4494 /* sharedsorabund.h */,
 408                                 37D928360F21331F001D4494 /* sharedsorabund.cpp */,
 409                                 37D928390F21331F001D4494 /* sharedsorclass.h */,
 410                                 37D928380F21331F001D4494 /* sharedsorclass.cpp */,
 411                                 37D9283B0F21331F001D4494 /* sharedsorest.h */,
 412                                 37D9283A0F21331F001D4494 /* sharedsorest.cpp */,
 413                                 37D9283C0F21331F001D4494 /* sharedthetan.cpp */,
 414                                 37D9283D0F21331F001D4494 /* sharedthetan.h */,
 415                                 37D9283F0F21331F001D4494 /* sharedthetayc.h */,
 416                                 37D9283E0F21331F001D4494 /* sharedthetayc.cpp */,
 417                                 37D928410F21331F001D4494 /* simpson.h */,
 418                                 37D928400F21331F001D4494 /* simpson.cpp */,
 419                                 37D928430F21331F001D4494 /* sobs.h */,
 420                                 37D9284E0F21331F001D4494 /* uvest.h */,
 421                                 37D9284D0F21331F001D4494 /* uvest.cpp */,
 422                         );
 423                         name = calculators;
 424                         sourceTree = SOURCE_ROOT;
 425                 };
 426                 37D928A90F2133E5001D4494 /* commands */ = {
 427                         isa = PBXGroup;
 428                         children = (
 429                                 37D927CD0F21331F001D4494 /* command.hpp */,
 430                                 37D927C40F21331F001D4494 /* clustercommand.h */,
 431                                 37D927C30F21331F001D4494 /* clustercommand.cpp */,
 432                                 37D927C80F21331F001D4494 /* collectcommand.h */,
 433                                 37D927C70F21331F001D4494 /* collectcommand.cpp */,
 434                                 37D927CC0F21331F001D4494 /* collectsharedcommand.h */,
 435                                 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */,
 436                                 37B28F660F27590100808A62 /* deconvolutecommand.h */,
 437                                 37B28F670F27590100808A62 /* deconvolutecommand.cpp */,
 438                                 EBA52D2A0F378B0F00122C15 /* getgroupcommand.h */,
 439                                 EBA52D2B0F378B0F00122C15 /* getgroupcommand.cpp */,
 440                                 EBFD67820F33876C00883537 /* getlabelcommand.h */,
 441                                 EBFD67830F33876C00883537 /* getlabelcommand.cpp */,
 442                                 EBFD67E60F339AAA00883537 /* getlinecommand.h */,
 443                                 EBFD67E70F339AAA00883537 /* getlinecommand.cpp */,
 444                                 37D927E40F21331F001D4494 /* helpcommand.h */,
 445                                 37D927E30F21331F001D4494 /* helpcommand.cpp */,
 446                                 37D927F20F21331F001D4494 /* nocommand.cpp */,
 447                                 37D927F30F21331F001D4494 /* nocommand.h */,
 448                                 37D927FA0F21331F001D4494 /* parselistcommand.h */,
 449                                 37D927F90F21331F001D4494 /* parselistcommand.cpp */,
 450                                 37D928080F21331F001D4494 /* rarefactcommand.h */,
 451                                 37D928070F21331F001D4494 /* rarefactcommand.cpp */,
 452                                 37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */,
 453                                 37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */,
 454                                 372E12940F263D5A0095CF7E /* readdistcommand.h */,
 455                                 372E12950F263D5A0095CF7E /* readdistcommand.cpp */,
 456                                 372E126E0F26365B0095CF7E /* readotucommand.h */,
 457                                 372E126F0F26365B0095CF7E /* readotucommand.cpp */,
 458                                 37E5F4900F2A3DA800F8D827 /* readtreecommand.h */,
 459                                 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */,
 460                                 37D928270F21331F001D4494 /* sharedcommand.h */,
 461                                 37D928260F21331F001D4494 /* sharedcommand.cpp */,
 462                                 37D928470F21331F001D4494 /* summarycommand.h */,
 463                                 37D928460F21331F001D4494 /* summarycommand.cpp */,
 464                                 37D9284B0F21331F001D4494 /* summarysharedcommand.h */,
 465                                 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */,
 466                                 37D927FE0F21331F001D4494 /* quitcommand.h */,
 467                                 37D927FD0F21331F001D4494 /* quitcommand.cpp */,
 468                         );
 469                         name = commands;
 470                         sourceTree = SOURCE_ROOT;
 471                 };
 472                 37D928AC0F213420001D4494 /* containers */ = {
 473                         isa = PBXGroup;
 474                         children = (
 475                                 37D927D50F21331F001D4494 /* datavector.hpp */,
 476                                 37D927DC0F21331F001D4494 /* fastamap.h */,
 477                                 37D927DB0F21331F001D4494 /* fastamap.cpp */,
 478                                 37D927E20F21331F001D4494 /* groupmap.h */,
 479                                 37D927E10F21331F001D4494 /* groupmap.cpp */,
 480                                 37D927EE0F21331F001D4494 /* listvector.hpp */,
 481                                 37D927ED0F21331F001D4494 /* listvector.cpp */,
 482                                 37D927F80F21331F001D4494 /* ordervector.hpp */,
 483                                 37D927F70F21331F001D4494 /* ordervector.cpp */,
 484                                 37D928000F21331F001D4494 /* rabundvector.hpp */,
 485                                 37D927FF0F21331F001D4494 /* rabundvector.cpp */,
 486                                 37D9281B0F21331F001D4494 /* sabundvector.hpp */,
 487                                 37D9281A0F21331F001D4494 /* sabundvector.cpp */,
 488                                 37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */,
 489                                 37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */,
 490                                 37D9282F0F21331F001D4494 /* sharedordervector.h */,
 491                                 37D9282E0F21331F001D4494 /* sharedordervector.cpp */,
 492                                 37D928310F21331F001D4494 /* sharedrabundvector.h */,
 493                                 37D928300F21331F001D4494 /* sharedrabundvector.cpp */,
 494                                 37D928330F21331F001D4494 /* sharedsabundvector.h */,
 495                                 37D928320F21331F001D4494 /* sharedsabundvector.cpp */,
 496                                 37AD4DB90F28E2FE00AA2D49 /* tree.h */,
 497                                 37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */,
 498                                 379293C10F2DE73400B9034A /* treemap.h */,
 499                                 379293C20F2DE73400B9034A /* treemap.cpp */,
 500                                 37E5F3E10F29FD4200F8D827 /* treenode.h */,
 501                                 37E5F3E20F29FD4200F8D827 /* treenode.cpp */,
 502                         );
 503                         name = containers;
 504                         sourceTree = SOURCE_ROOT;
 505                 };
 506                 37D928B10F213472001D4494 /* errorcheckor */ = {
 507                         isa = PBXGroup;
 508                         children = (
 509                                 37D927DA0F21331F001D4494 /* errorchecking.h */,
 510                                 37D927D90F21331F001D4494 /* errorchecking.cpp */,
 511                                 37D928500F21331F001D4494 /* validcalculator.h */,
 512                                 37D9284F0F21331F001D4494 /* validcalculator.cpp */,
 513                                 37D928520F21331F001D4494 /* validcommands.h */,
 514                                 37D928510F21331F001D4494 /* validcommands.cpp */,
 515                                 37D928540F21331F001D4494 /* validparameter.h */,
 516                                 37D928530F21331F001D4494 /* validparameter.cpp */,
 517                         );
 518                         name = errorcheckor;
 519                         sourceTree = SOURCE_ROOT;
 520                 };
 521                 C6859E8C029090F304C91782 /* Documentation */ = {
 522                         isa = PBXGroup;
 523                         children = (
 524                                 C6859E8B029090EE04C91782 /* Mothur.1 */,
 525                         );
 526                         name = Documentation;
 527                         sourceTree = "<group>";
 528                 };
 529 /* End PBXGroup section */
 530
 531 /* Begin PBXNativeTarget section */
 532                 8DD76F620486A84900D96B5E /* mothur */ = {
 533                         isa = PBXNativeTarget;
 534                         buildConfigurationList = 1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "mothur" */;
 535                         buildPhases = (
 536                                 8DD76F640486A84900D96B5E /* Sources */,
 537                                 8DD76F660486A84900D96B5E /* Frameworks */,
 538                                 8DD76F690486A84900D96B5E /* CopyFiles */,
 539                         );
 540                         buildRules = (
 541                         );
 542                         dependencies = (
 543                         );
 544                         name = mothur;
 545                         productInstallPath = "$(HOME)/bin";
 546                         productName = Mothur;
 547                         productReference = 8DD76F6C0486A84900D96B5E /* mothur */;
 548                         productType = "com.apple.product-type.tool";
 549                 };
 550 /* End PBXNativeTarget section */
 551
 552 /* Begin PBXProject section */
 553                 08FB7793FE84155DC02AAC07 /* Project object */ = {
 554                         isa = PBXProject;
 555                         buildConfigurationList = 1DEB923508733DC60010E9CD /* Build configuration list for PBXProject "Mothur" */;
 556                         compatibilityVersion = "Xcode 3.0";
 557                         hasScannedForEncodings = 1;
 558                         mainGroup = 08FB7794FE84155DC02AAC07 /* Mothur */;
 559                         projectDirPath = "";
 560                         projectRoot = "";
 561                         targets = (
 562                                 8DD76F620486A84900D96B5E /* mothur */,
 563                         );
 564                 };
 565 /* End PBXProject section */
 566
 567 /* Begin PBXSourcesBuildPhase section */
 568                 8DD76F640486A84900D96B5E /* Sources */ = {
 569                         isa = PBXSourcesBuildPhase;
 570                         buildActionMask = 2147483647;
 571                         files = (
 572                                 37D928550F21331F001D4494 /* ace.cpp in Sources */,
 573                                 37D928560F21331F001D4494 /* averagelinkage.cpp in Sources */,
 574                                 37D928570F21331F001D4494 /* bootstrap.cpp in Sources */,
 575                                 37D928580F21331F001D4494 /* calculator.cpp in Sources */,
 576                                 37D928590F21331F001D4494 /* chao1.cpp in Sources */,
 577                                 37D9285A0F21331F001D4494 /* cluster.cpp in Sources */,
 578                                 37D9285B0F21331F001D4494 /* clustercommand.cpp in Sources */,
 579                                 37D9285C0F21331F001D4494 /* collect.cpp in Sources */,
 580                                 37D9285D0F21331F001D4494 /* collectcommand.cpp in Sources */,
 581                                 37D9285E0F21331F001D4494 /* collectsharedcommand.cpp in Sources */,
 582                                 37D928600F21331F001D4494 /* commandoptionparser.cpp in Sources */,
 583                                 37D928610F21331F001D4494 /* completelinkage.cpp in Sources */,
 584                                 37D928620F21331F001D4494 /* database.cpp in Sources */,
 585                                 37D928630F21331F001D4494 /* engine.cpp in Sources */,
 586                                 37D928640F21331F001D4494 /* errorchecking.cpp in Sources */,
 587                                 37D928650F21331F001D4494 /* fastamap.cpp in Sources */,
 588                                 37D928660F21331F001D4494 /* fileoutput.cpp in Sources */,
 589                                 37D928670F21331F001D4494 /* globaldata.cpp in Sources */,
 590                                 37D928680F21331F001D4494 /* groupmap.cpp in Sources */,
 591                                 37D928690F21331F001D4494 /* helpcommand.cpp in Sources */,
 592                                 37D9286A0F21331F001D4494 /* inputdata.cpp in Sources */,
 593                                 37D9286B0F21331F001D4494 /* jackknife.cpp in Sources */,
 594                                 37D9286C0F21331F001D4494 /* kmer.cpp in Sources */,
 595                                 37D9286D0F21331F001D4494 /* kmerdb.cpp in Sources */,
 596                                 37D9286E0F21331F001D4494 /* listvector.cpp in Sources */,
 597                                 37D9286F0F21331F001D4494 /* mothur.cpp in Sources */,
 598                                 37D928700F21331F001D4494 /* nameassignment.cpp in Sources */,
 599                                 37D928710F21331F001D4494 /* nocommand.cpp in Sources */,
 600                                 37D928720F21331F001D4494 /* npshannon.cpp in Sources */,
 601                                 37D928730F21331F001D4494 /* ordervector.cpp in Sources */,
 602                                 37D928740F21331F001D4494 /* parselistcommand.cpp in Sources */,
 603                                 37D928750F21331F001D4494 /* progress.cpp in Sources */,
 604                                 37D928760F21331F001D4494 /* quitcommand.cpp in Sources */,
 605                                 37D928770F21331F001D4494 /* rabundvector.cpp in Sources */,
 606                                 37D928780F21331F001D4494 /* rarecalc.cpp in Sources */,
 607                                 37D928790F21331F001D4494 /* raredisplay.cpp in Sources */,
 608                                 37D9287A0F21331F001D4494 /* rarefact.cpp in Sources */,
 609                                 37D9287B0F21331F001D4494 /* rarefactcommand.cpp in Sources */,
 610                                 37D9287C0F21331F001D4494 /* rarefactsharedcommand.cpp in Sources */,
 611                                 37D928800F21331F001D4494 /* readmatrix.cpp in Sources */,
 612                                 37D928840F21331F001D4494 /* sabundvector.cpp in Sources */,
 613                                 37D928850F21331F001D4494 /* sequence.cpp in Sources */,
 614                                 37D928860F21331F001D4494 /* shannon.cpp in Sources */,
 615                                 37D928870F21331F001D4494 /* shared.cpp in Sources */,
 616                                 37D928880F21331F001D4494 /* sharedace.cpp in Sources */,
 617                                 37D928890F21331F001D4494 /* sharedchao1.cpp in Sources */,
 618                                 37D9288A0F21331F001D4494 /* sharedcommand.cpp in Sources */,
 619                                 37D9288B0F21331F001D4494 /* sharedjabund.cpp in Sources */,
 620                                 37D9288C0F21331F001D4494 /* sharedjclass.cpp in Sources */,
 621                                 37D9288D0F21331F001D4494 /* sharedjest.cpp in Sources */,
 622                                 37D9288E0F21331F001D4494 /* sharedordervector.cpp in Sources */,
 623                                 37D9288F0F21331F001D4494 /* sharedrabundvector.cpp in Sources */,
 624                                 37D928900F21331F001D4494 /* sharedsabundvector.cpp in Sources */,
 625                                 37D928910F21331F001D4494 /* sharedsobs.cpp in Sources */,
 626                                 37D928920F21331F001D4494 /* sharedsorabund.cpp in Sources */,
 627                                 37D928930F21331F001D4494 /* sharedsorclass.cpp in Sources */,
 628                                 37D928940F21331F001D4494 /* sharedsorest.cpp in Sources */,
 629                                 37D928950F21331F001D4494 /* sharedthetan.cpp in Sources */,
 630                                 37D928960F21331F001D4494 /* sharedthetayc.cpp in Sources */,
 631                                 37D928970F21331F001D4494 /* simpson.cpp in Sources */,
 632                                 37D928980F21331F001D4494 /* singlelinkage.cpp in Sources */,
 633                                 37D928990F21331F001D4494 /* sparsematrix.cpp in Sources */,
 634                                 37D9289A0F21331F001D4494 /* summarycommand.cpp in Sources */,
 635                                 37D9289B0F21331F001D4494 /* summarysharedcommand.cpp in Sources */,
 636                                 37D9289C0F21331F001D4494 /* uvest.cpp in Sources */,
 637                                 37D9289D0F21331F001D4494 /* validcalculator.cpp in Sources */,
 638                                 37D9289E0F21331F001D4494 /* validcommands.cpp in Sources */,
 639                                 37D9289F0F21331F001D4494 /* validparameter.cpp in Sources */,
 640                                 372E12700F26365B0095CF7E /* readotucommand.cpp in Sources */,
 641                                 372E12960F263D5A0095CF7E /* readdistcommand.cpp in Sources */,
 642                                 372E12ED0F264D320095CF7E /* commandfactory.cpp in Sources */,
 643                                 37B28F680F27590100808A62 /* deconvolutecommand.cpp in Sources */,
 644                                 37AD4CE40F28AEA300AA2D49 /* sharedlistvector.cpp in Sources */,
 645                                 37AD4DBB0F28E2FE00AA2D49 /* tree.cpp in Sources */,
 646                                 37AD4DCA0F28F3DD00AA2D49 /* readtree.cpp in Sources */,
 647                                 37E5F3E30F29FD4200F8D827 /* treenode.cpp in Sources */,
 648                                 37E5F4920F2A3DA800F8D827 /* readtreecommand.cpp in Sources */,
 649                                 379293C30F2DE73400B9034A /* treemap.cpp in Sources */,
 650                                 7E44EBD10F3235D900B0D45D /* makefile in Sources */,
 651                                 EBFD67840F33876C00883537 /* getlabelcommand.cpp in Sources */,
 652                                 EBFD67E80F339AAA00883537 /* getlinecommand.cpp in Sources */,
 653                                 EBA52D2C0F378B0F00122C15 /* getgroupcommand.cpp in Sources */,
 654                         );
 655                         runOnlyForDeploymentPostprocessing = 0;
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 657 /* End PBXSourcesBuildPhase section */
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 662                         buildSettings = {
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 666                                 GCC_MODEL_TUNING = G5;
 667                                 GCC_OPTIMIZATION_LEVEL = 0;
 668                                 GCC_PREPROCESSOR_DEFINITIONS = (
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 670                                         "_GLIBCXX_DEBUG_PEDANTIC=1",
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 672                                 INSTALL_PATH = /usr/local/bin;
 673                                 PRODUCT_NAME = mothur;
 674                                 ZERO_LINK = YES;
 675                         };
 676                         name = Debug;
 677                 };
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 684                                 PRODUCT_NAME = mothur;
 685                         };
 686                         name = Release;
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 689                         isa = XCBuildConfiguration;
 690                         buildSettings = {
 691                                 GCC_OPTIMIZATION_LEVEL = 3;
 692                                 GCC_WARN_ABOUT_RETURN_TYPE = YES;
 693                                 GCC_WARN_UNUSED_VARIABLE = YES;
 694                                 PREBINDING = NO;
 695                                 SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
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 697                         name = Debug;
 698                 };
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 700                         isa = XCBuildConfiguration;
 701                         buildSettings = {
 702                                 ARCHS = (
 703                                         ppc,
 704                                         i386,
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 709                                 PREBINDING = NO;
 710                                 SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
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 714 /* End XCBuildConfiguration section */
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 716 /* Begin XCConfigurationList section */
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 718                         isa = XCConfigurationList;
 719                         buildConfigurations = (
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 726                 1DEB923508733DC60010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
 727                         isa = XCConfigurationList;
 728                         buildConfigurations = (
 729                                 1DEB923608733DC60010E9CD /* Debug */,
 730                                 1DEB923708733DC60010E9CD /* Release */,
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 738 }