Merge remote-tracking branch 'origin/master'

diff --combined Mothur.xcodeproj/project.pbxproj
index df58a36026bed6961481c3e31efeccf6a8086810,79f445785da964b5ef5b8581b2d57e252ea9c7b3..1b298dfea5f58b9bd1f4ca1b09194967515a4de8
--- 1/Mothur.xcodeproj/project.pbxproj
--- 2/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@@ -10,6 -10,7 +10,7 @@@
                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 */; };
+               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 */; };
@@@ -367,8 -368,8 +368,8 @@@
                8DD76FAF0486AB0100D96B5E /* CopyFiles */ = {
                        isa = PBXCopyFilesBuildPhase;
                        buildActionMask = 8;
 -                      dstPath = /usr/share/man/man1/;
 -                      dstSubfolderSpec = 0;
 +                      dstPath = Users/SarahsWork/desktop/debug;
 +                      dstSubfolderSpec = 16;
                        files = (
                                8DD76FB00486AB0100D96B5E /* mothur.1 in CopyFiles */,
                        );
@@@ -384,6 -385,8 +385,8 @@@
                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>"; };
+               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; };
                A70056E5156A93D000924A2D /* getotulabelscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getotulabelscommand.cpp; sourceTree = "<group>"; };
                A70056E8156A93E300924A2D /* getotulabelscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getotulabelscommand.h; sourceTree = "<group>"; };
@@@ -1222,6 -1225,8 +1225,8 @@@
                                A77E1937161B201E00DB1A2A /* randomforest.cpp */,
                                A7386C201619CACB00651424 /* rftreenode.hpp */,
                                A77E193A161B289600DB1A2A /* rftreenode.cpp */,
+                               83F25B0A163B031200ABE73D /* forest.cpp */,
+                               83F25B0B163B031200ABE73D /* forest.h */,
                        );
                        name = randomforest;
                        sourceTree = "<group>";
@@@ -1530,6 -1535,8 +1535,6 @@@
                                A7E9B67112D37EC400DA6239 /* canberra.h */,
                                A7E9B67612D37EC400DA6239 /* chao1.cpp */,
                                A7E9B67712D37EC400DA6239 /* chao1.h */,
 -                              A7E9B6A412D37EC400DA6239 /* cmdargs.cpp */,
 -                              A7E9B6A512D37EC400DA6239 /* cmdargs.h */,
                                A7E9B6BB12D37EC400DA6239 /* coverage.cpp */,
                                A7E9B6BC12D37EC400DA6239 /* coverage.h */,
                                A7E9B6CA12D37EC400DA6239 /* dist.h */,
@@@ -1819,8 -1826,6 +1824,8 @@@
                        children = (
                                A7E9B69412D37EC400DA6239 /* clearcut.cpp */,
                                A7E9B69512D37EC400DA6239 /* clearcut.h */,
 +                              A7E9B6A412D37EC400DA6239 /* cmdargs.cpp */,
 +                              A7E9B6A512D37EC400DA6239 /* cmdargs.h */,
                                A7E9B6B312D37EC400DA6239 /* common.h */,
                                A7E9B6CF12D37EC400DA6239 /* distclearcut.cpp */,
                                A7E9B6D012D37EC400DA6239 /* distclearcut.h */,
@@@ -2280,6 -2285,7 +2285,7 @@@
                                A721AB71161C572A009860A1 /* kmernode.cpp in Sources */,
                                A721AB72161C572A009860A1 /* kmertree.cpp in Sources */,
                                A721AB77161C573B009860A1 /* taxonomynode.cpp in Sources */,
+                               83F25B0C163B031200ABE73D /* forest.cpp in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
@@@ -2292,12 -2298,9 +2298,12 @@@
                                ALWAYS_SEARCH_USER_PATHS = NO;
                                COPY_PHASE_STRIP = NO;
                                DEPLOYMENT_LOCATION = YES;
 +                              DSTROOT = TARGET_BUILD_DIR;
 +                              "DSTROOT[sdk=*]" = TARGET_BUILD_DIR;
                                GCC_DYNAMIC_NO_PIC = NO;
                                GCC_MODEL_TUNING = G5;
                                GCC_OPTIMIZATION_LEVEL = 3;
 +                              "INSTALL_PATH[sdk=*]" = TARGET_BUILD_DIR;
                                PRODUCT_NAME = mothur;
                                SDKROOT = macosx10.6;
                                SKIP_INSTALL = NO;
@@@ -2310,7 -2313,6 +2316,7 @@@
                                ALWAYS_SEARCH_USER_PATHS = NO;
                                DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";
                                DEPLOYMENT_LOCATION = YES;
 +                              DSTROOT = TARGET_BUILD_DIR;
                                GCC_MODEL_TUNING = G5;
                                GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_WARN_UNUSED_VALUE = YES;
@@@ -2404,7 -2406,7 +2410,7 @@@
                                1DEB928708733DD80010E9CD /* Release */,
                        );
                        defaultConfigurationIsVisible = 0;
 -                      defaultConfigurationName = Release;
 +                      defaultConfigurationName = Debug;
                };
                1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
                        isa = XCConfigurationList;
@@@ -2413,7 -2415,7 +2419,7 @@@
                                1DEB928B08733DD80010E9CD /* Release */,
                        );
                        defaultConfigurationIsVisible = 0;
 -                      defaultConfigurationName = Release;
 +                      defaultConfigurationName = Debug;
                };
  /* End XCConfigurationList section */
        };