Mothur.xcodeproj/project.pbxproj

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 234                 37D927D10F21331F001D4494 /* commandoptionparser.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandoptionparser.hpp; sourceTree = "<group>"; };
 235                 37D927D20F21331F001D4494 /* completelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = completelinkage.cpp; sourceTree = "<group>"; };
 236                 37D927D30F21331F001D4494 /* database.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = database.cpp; sourceTree = "<group>"; };
 237                 37D927D40F21331F001D4494 /* database.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = database.hpp; sourceTree = "<group>"; };
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 241                 37D927D80F21331F001D4494 /* engine.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = engine.hpp; sourceTree = "<group>"; };
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 243                 37D927DA0F21331F001D4494 /* errorchecking.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = errorchecking.h; sourceTree = "<group>"; };
 244                 37D927DB0F21331F001D4494 /* fastamap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fastamap.cpp; sourceTree = "<group>"; };
 245                 37D927DC0F21331F001D4494 /* fastamap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fastamap.h; sourceTree = "<group>"; };
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 247                 37D927DE0F21331F001D4494 /* fileoutput.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fileoutput.h; sourceTree = "<group>"; };
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 422                                 37D927D80F21331F001D4494 /* engine.hpp */,
 423                                 37D927D70F21331F001D4494 /* engine.cpp */,
 424                                 37D928B10F213472001D4494 /* errorcheckor */,
 425                                 37D927DE0F21331F001D4494 /* fileoutput.h */,
 426                                 37D927DD0F21331F001D4494 /* fileoutput.cpp */,
 427                                 37D927E00F21331F001D4494 /* globaldata.hpp */,
 428                                 37D927DF0F21331F001D4494 /* globaldata.cpp */,
 429                                 375873ED0F7D646F0040F377 /* heatmap.h */,
 430                                 375873EE0F7D646F0040F377 /* heatmap.cpp */,
 431                                 37D927E60F21331F001D4494 /* inputdata.h */,
 432                                 37D927E50F21331F001D4494 /* inputdata.cpp */,
 433                                 37D927EA0F21331F001D4494 /* kmer.hpp */,
 434                                 37D927E90F21331F001D4494 /* kmer.cpp */,
 435                                 37D927EC0F21331F001D4494 /* kmerdb.hpp */,
 436                                 37D927EB0F21331F001D4494 /* kmerdb.cpp */,
 437                                 37E3ED800F4D9D0D00B5DF02 /* mothur.h */,
 438                                 37D927EF0F21331F001D4494 /* mothur.cpp */,
 439                                 37D927F10F21331F001D4494 /* nameassignment.hpp */,
 440                                 37D927F00F21331F001D4494 /* nameassignment.cpp */,
 441                                 37D927F60F21331F001D4494 /* observable.h */,
 442                                 37D927FC0F21331F001D4494 /* progress.hpp */,
 443                                 37D927FB0F21331F001D4494 /* progress.cpp */,
 444                                 37D928040F21331F001D4494 /* raredisplay.h */,
 445                                 37D928030F21331F001D4494 /* raredisplay.cpp */,
 446                                 37D928060F21331F001D4494 /* rarefact.h */,
 447                                 37D928050F21331F001D4494 /* rarefact.cpp */,
 448                                 37D928090F21331F001D4494 /* rarefactioncurvedata.h */,
 449                                 37D928130F21331F001D4494 /* readmatrix.hpp */,
 450                                 37D928120F21331F001D4494 /* readmatrix.cpp */,
 451                                 37AD4DC80F28F3DD00AA2D49 /* readtree.h */,
 452                                 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */,
 453                                 37D9281D0F21331F001D4494 /* sequence.hpp */,
 454                                 37D9281C0F21331F001D4494 /* sequence.cpp */,
 455                                 37D928210F21331F001D4494 /* shared.h */,
 456                                 37D928200F21331F001D4494 /* shared.cpp */,
 457                                 37C7F3A70F8E90AD00E91C2B /* sharedutilities.h */,
 458                                 37C7F3A80F8E90AD00E91C2B /* sharedutilities.cpp */,
 459                                 37D928420F21331F001D4494 /* singlelinkage.cpp */,
 460                                 37D928480F21331F001D4494 /* summarydata.h */,
 461                                 37D928490F21331F001D4494 /* summarydisplay.h */,
 462                                 37519AB30F810FAE00FED5E8 /* venn.h */,
 463                                 37519AB40F810FAE00FED5E8 /* venn.cpp */,
 464                         );
 465                         name = Source;
 466                         sourceTree = "<group>";
 467                 };
 468                 1AB674ADFE9D54B511CA2CBB /* Products */ = {
 469                         isa = PBXGroup;
 470                         children = (
 471                                 8DD76F6C0486A84900D96B5E /* mothur */,
 472                         );
 473                         name = Products;
 474                         sourceTree = "<group>";
 475                 };
 476                 37D928A60F2133C0001D4494 /* calculators */ = {
 477                         isa = PBXGroup;
 478                         children = (
 479                                 37D927BE0F21331F001D4494 /* calculator.h */,
 480                                 3792948D0F2E271100B9034A /* treecalculator.h */,
 481                                 37D927BD0F21331F001D4494 /* calculator.cpp */,
 482                                 37D927B90F21331F001D4494 /* ace.h */,
 483                                 37D927B80F21331F001D4494 /* ace.cpp */,
 484                                 EB1216860F619B83004A865F /* bergerparker.h */,
 485                                 EB1216870F619B83004A865F /* bergerparker.cpp */,
 486                                 37D927BC0F21331F001D4494 /* bootstrap.h */,
 487                                 37D927BB0F21331F001D4494 /* bootstrap.cpp */,
 488                                 EB1216E30F61ACFB004A865F /* bstick.h */,
 489                                 EB1216E40F61ACFB004A865F /* bstick.cpp */,
 490                                 37D927C00F21331F001D4494 /* chao1.h */,
 491                                 37D927BF0F21331F001D4494 /* chao1.cpp */,
 492                                 375873E60F7D63E90040F377 /* coverage.h */,
 493                                 375873E50F7D63E90040F377 /* coverage.cpp */,
 494                                 EB9303F70F53517300E8EF26 /* geom.h */,
 495                                 EB9303F80F53517300E8EF26 /* geom.cpp */,
 496                                 EB9303E90F534D9400E8EF26 /* logsd.h */,
 497                                 EB9303EA0F534D9400E8EF26 /* logsd.cpp */,
 498                                 EB6E68170F5F1C780044E17B /* qstat.h */,
 499                                 EB6E68180F5F1C780044E17B /* qstat.cpp */,
 500                                 37D927E80F21331F001D4494 /* jackknife.h */,
 501                                 37D927E70F21331F001D4494 /* jackknife.cpp */,
 502                                 375873F90F7D64AB0040F377 /* nseqs.h */,
 503                                 37D927F50F21331F001D4494 /* npshannon.h */,
 504                                 37D927F40F21331F001D4494 /* npshannon.cpp */,
 505                                 379294880F2E258500B9034A /* parsimony.h */,
 506                                 379294890F2E258500B9034A /* parsimony.cpp */,
 507                                 37D928020F21331F001D4494 /* rarecalc.h */,
 508                                 37D928010F21331F001D4494 /* rarecalc.cpp */,
 509                                 37D9281F0F21331F001D4494 /* shannon.h */,
 510                                 37D9281E0F21331F001D4494 /* shannon.cpp */,
 511                                 37D928230F21331F001D4494 /* sharedace.h */,
 512                                 37D928220F21331F001D4494 /* sharedace.cpp */,
 513                                 37519A690F80E6EB00FED5E8 /* sharedanderbergs.h */,
 514                                 37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */,
 515                                 375873FB0F7D64DA0040F377 /* sharedbraycurtis.h */,
 516                                 375873FC0F7D64DA0040F377 /* sharedbraycurtis.cpp */,
 517                                 EB6F01590F6AC1670048081A /* sharedbdiversity.h */,
 518                                 EB6F015A0F6AC1670048081A /* sharedbdiversity.cpp */,
 519                                 37D928250F21331F001D4494 /* sharedchao1.h */,
 520                                 37D928240F21331F001D4494 /* sharedchao1.cpp */,
 521                                 37D928290F21331F001D4494 /* sharedjabund.h */,
 522                                 37D928280F21331F001D4494 /* sharedjabund.cpp */,
 523                                 37D9282B0F21331F001D4494 /* sharedjclass.h */,
 524                                 37D9282A0F21331F001D4494 /* sharedjclass.cpp */,
 525                                 37D9282D0F21331F001D4494 /* sharedjest.h */,
 526                                 37D9282C0F21331F001D4494 /* sharedjest.cpp */,
 527                                 EB1217210F61C9AC004A865F /* sharedkstest.h */,
 528                                 EB1217220F61C9AC004A865F /* sharedkstest.cpp */,
 529                                 375874000F7D64EF0040F377 /* sharedkulczynski.h */,
 530                                 375873FE0F7D64EF0040F377 /* sharedkulczynski.cpp */,
 531                                 375874030F7D64EF0040F377 /* sharedkulczynskicody.h */,
 532                                 375874020F7D64EF0040F377 /* sharedkulczynskicody.cpp */,
 533                                 375874010F7D64EF0040F377 /* sharedlennon.h */,
 534                                 375873FF0F7D64EF0040F377 /* sharedlennon.cpp */,
 535                                 375874070F7D64FC0040F377 /* sharedmorisitahorn.h */,
 536                                 375874080F7D64FC0040F377 /* sharedmorisitahorn.cpp */,
 537                                 375874090F7D64FC0040F377 /* sharedochiai.h */,
 538                                 3758740B0F7D64FC0040F377 /* sharedochiai.cpp */,
 539                                 3758740A0F7D64FC0040F377 /* sharednseqs.h */,
 540                                 37D928350F21331F001D4494 /* sharedsobs.h */,
 541                                 37D928340F21331F001D4494 /* sharedsobs.cpp */,
 542                                 37AFC71D0F445386005F492D /* sharedsobscollectsummary.h */,
 543                                 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */,
 544                                 37D928370F21331F001D4494 /* sharedsorabund.h */,
 545                                 37D928360F21331F001D4494 /* sharedsorabund.cpp */,
 546                                 37D928390F21331F001D4494 /* sharedsorclass.h */,
 547                                 37D928380F21331F001D4494 /* sharedsorclass.cpp */,
 548                                 37D9283B0F21331F001D4494 /* sharedsorest.h */,
 549                                 37D9283A0F21331F001D4494 /* sharedsorest.cpp */,
 550                                 37D9283D0F21331F001D4494 /* sharedthetan.h */,
 551                                 37D9283C0F21331F001D4494 /* sharedthetan.cpp */,
 552                                 37D9283F0F21331F001D4494 /* sharedthetayc.h */,
 553                                 37D9283E0F21331F001D4494 /* sharedthetayc.cpp */,
 554                                 37D928410F21331F001D4494 /* simpson.h */,
 555                                 37D928400F21331F001D4494 /* simpson.cpp */,
 556                                 37D928430F21331F001D4494 /* sobs.h */,
 557                                 374610810F40652400460C57 /* unweighted.h */,
 558                                 374610820F40652400460C57 /* unweighted.cpp */,
 559                                 37D9284E0F21331F001D4494 /* uvest.h */,
 560                                 37D9284D0F21331F001D4494 /* uvest.cpp */,
 561                                 3746107C0F4064D100460C57 /* weighted.h */,
 562                                 3746107D0F4064D100460C57 /* weighted.cpp */,
 563                         );
 564                         name = calculators;
 565                         sourceTree = "<group>";
 566                 };
 567                 37D928A90F2133E5001D4494 /* commands */ = {
 568                         isa = PBXGroup;
 569                         children = (
 570                                 37D927CD0F21331F001D4494 /* command.hpp */,
 571                                 37C1D9710F86506E0059E3F0 /* binsequencecommand.h */,
 572                                 37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */,
 573                                 37D927C40F21331F001D4494 /* clustercommand.h */,
 574                                 37D927C30F21331F001D4494 /* clustercommand.cpp */,
 575                                 37D927C80F21331F001D4494 /* collectcommand.h */,
 576                                 37D927C70F21331F001D4494 /* collectcommand.cpp */,
 577                                 37D927CC0F21331F001D4494 /* collectsharedcommand.h */,
 578                                 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */,
 579                                 37B28F660F27590100808A62 /* deconvolutecommand.h */,
 580                                 37B28F670F27590100808A62 /* deconvolutecommand.cpp */,
 581                                 A70B53A50F4CD7AD0064797E /* getgroupcommand.h */,
 582                                 A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */,
 583                                 A70B53A70F4CD7AD0064797E /* getlabelcommand.h */,
 584                                 A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */,
 585                                 A70B53A90F4CD7AD0064797E /* getlinecommand.h */,
 586                                 A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */,
 587                                 370B88050F8A4EE4005AB382 /* getoturepcommand.h */,
 588                                 370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */,
 589                                 375873F10F7D64800040F377 /* heatmapcommand.h */,
 590                                 375873F00F7D64800040F377 /* heatmapcommand.cpp */,
 591                                 37D927E40F21331F001D4494 /* helpcommand.h */,
 592                                 37D927E30F21331F001D4494 /* helpcommand.cpp */,
 593                                 375873F40F7D648F0040F377 /* libshuffcommand.h */,
 594                                 375873F30F7D648F0040F377 /* libshuffcommand.cpp */,
 595                                 375873F60F7D649C0040F377 /* nocommands.cpp */,
 596                                 375873F70F7D649C0040F377 /* nocommands.h */,
 597                                 37D927FA0F21331F001D4494 /* parselistcommand.h */,
 598                                 37D927F90F21331F001D4494 /* parselistcommand.cpp */,
 599                                 3792946E0F2E191800B9034A /* parsimonycommand.h */,
 600                                 3792946F0F2E191800B9034A /* parsimonycommand.cpp */,
 601                                 37D927FE0F21331F001D4494 /* quitcommand.h */,
 602                                 37D927FD0F21331F001D4494 /* quitcommand.cpp */,
 603                                 37D928080F21331F001D4494 /* rarefactcommand.h */,
 604                                 37D928070F21331F001D4494 /* rarefactcommand.cpp */,
 605                                 37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */,
 606                                 37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */,
 607                                 372E12940F263D5A0095CF7E /* readdistcommand.h */,
 608                                 372E12950F263D5A0095CF7E /* readdistcommand.cpp */,
 609                                 372E126E0F26365B0095CF7E /* readotucommand.h */,
 610                                 372E126F0F26365B0095CF7E /* readotucommand.cpp */,
 611                                 37E5F4900F2A3DA800F8D827 /* readtreecommand.h */,
 612                                 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */,
 613                                 37D928270F21331F001D4494 /* sharedcommand.h */,
 614                                 37D928260F21331F001D4494 /* sharedcommand.cpp */,
 615                                 37D928470F21331F001D4494 /* summarycommand.h */,
 616                                 37D928460F21331F001D4494 /* summarycommand.cpp */,
 617                                 37D9284B0F21331F001D4494 /* summarysharedcommand.h */,
 618                                 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */,
 619                                 3731C1F10F8CFC0A0065A2AD /* treegroupscommand.h */,
 620                                 3731C1F20F8CFC0A0065A2AD /* treegroupscommand.cpp */,
 621                                 3746109B0F40657600460C57 /* unifracunweightedcommand.h */,
 622                                 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */,
 623                                 374610760F40645300460C57 /* unifracweightedcommand.h */,
 624                                 374610770F40645300460C57 /* unifracweightedcommand.cpp */,
 625                                 37519A9F0F810D0200FED5E8 /* venncommand.h */,
 626                                 37519AA00F810D0200FED5E8 /* venncommand.cpp */,
 627                         );
 628                         name = commands;
 629                         sourceTree = "<group>";
 630                 };
 631                 37D928AC0F213420001D4494 /* containers */ = {
 632                         isa = PBXGroup;
 633                         children = (
 634                                 37D927D50F21331F001D4494 /* datavector.hpp */,
 635                                 37D927DC0F21331F001D4494 /* fastamap.h */,
 636                                 37D927DB0F21331F001D4494 /* fastamap.cpp */,
 637                                 375873EA0F7D64520040F377 /* fullmatrix.h */,
 638                                 375873EB0F7D64520040F377 /* fullmatrix.cpp */,
 639                                 37D927E20F21331F001D4494 /* groupmap.h */,
 640                                 37D927E10F21331F001D4494 /* groupmap.cpp */,
 641                                 37D927EE0F21331F001D4494 /* listvector.hpp */,
 642                                 37D927ED0F21331F001D4494 /* listvector.cpp */,
 643                                 37D927F80F21331F001D4494 /* ordervector.hpp */,
 644                                 37D927F70F21331F001D4494 /* ordervector.cpp */,
 645                                 37D928000F21331F001D4494 /* rabundvector.hpp */,
 646                                 37D927FF0F21331F001D4494 /* rabundvector.cpp */,
 647                                 37D9281B0F21331F001D4494 /* sabundvector.hpp */,
 648                                 37D9281A0F21331F001D4494 /* sabundvector.cpp */,
 649                                 37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */,
 650                                 37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */,
 651                                 37D9282F0F21331F001D4494 /* sharedordervector.h */,
 652                                 37D9282E0F21331F001D4494 /* sharedordervector.cpp */,
 653                                 37D928310F21331F001D4494 /* sharedrabundvector.h */,
 654                                 37D928300F21331F001D4494 /* sharedrabundvector.cpp */,
 655                                 37D928330F21331F001D4494 /* sharedsabundvector.h */,
 656                                 37D928320F21331F001D4494 /* sharedsabundvector.cpp */,
 657                                 37D928450F21331F001D4494 /* sparsematrix.hpp */,
 658                                 37D928440F21331F001D4494 /* sparsematrix.cpp */,
 659                                 37AD4DB90F28E2FE00AA2D49 /* tree.h */,
 660                                 37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */,
 661                                 379293C10F2DE73400B9034A /* treemap.h */,
 662                                 379293C20F2DE73400B9034A /* treemap.cpp */,
 663                                 37E5F3E10F29FD4200F8D827 /* treenode.h */,
 664                                 37E5F3E20F29FD4200F8D827 /* treenode.cpp */,
 665                         );
 666                         name = containers;
 667                         sourceTree = "<group>";
 668                 };
 669                 37D928B10F213472001D4494 /* errorcheckor */ = {
 670                         isa = PBXGroup;
 671                         children = (
 672                                 37D927DA0F21331F001D4494 /* errorchecking.h */,
 673                                 37D927D90F21331F001D4494 /* errorchecking.cpp */,
 674                                 37D928500F21331F001D4494 /* validcalculator.h */,
 675                                 37D9284F0F21331F001D4494 /* validcalculator.cpp */,
 676                                 37D928520F21331F001D4494 /* validcommands.h */,
 677                                 37D928510F21331F001D4494 /* validcommands.cpp */,
 678                                 37D928540F21331F001D4494 /* validparameter.h */,
 679                                 37D928530F21331F001D4494 /* validparameter.cpp */,
 680                         );
 681                         name = errorcheckor;
 682                         sourceTree = "<group>";
 683                 };
 684                 C6859E8C029090F304C91782 /* Documentation */ = {
 685                         isa = PBXGroup;
 686                         children = (
 687                                 C6859E8B029090EE04C91782 /* Mothur.1 */,
 688                         );
 689                         name = Documentation;
 690                         sourceTree = "<group>";
 691                 };
 692 /* End PBXGroup section */
 693
 694 /* Begin PBXNativeTarget section */
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 696                         isa = PBXNativeTarget;
 697                         buildConfigurationList = 1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "mothur" */;
 698                         buildPhases = (
 699                                 8DD76F640486A84900D96B5E /* Sources */,
 700                                 8DD76F660486A84900D96B5E /* Frameworks */,
 701                                 8DD76F690486A84900D96B5E /* CopyFiles */,
 702                         );
 703                         buildRules = (
 704                         );
 705                         dependencies = (
 706                         );
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 708                         productInstallPath = "$(HOME)/bin";
 709                         productName = Mothur;
 710                         productReference = 8DD76F6C0486A84900D96B5E /* mothur */;
 711                         productType = "com.apple.product-type.tool";
 712                 };
 713 /* End PBXNativeTarget section */
 714
 715 /* Begin PBXProject section */
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 717                         isa = PBXProject;
 718                         buildConfigurationList = 1DEB923508733DC60010E9CD /* Build configuration list for PBXProject "Mothur" */;
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 720                         hasScannedForEncodings = 1;
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 722                         projectDirPath = "";
 723                         projectRoot = "";
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 727                 };
 728 /* End PBXProject section */
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 880                         name = Release;
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 885                                 GCC_OPTIMIZATION_LEVEL = 3;
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