added hcluster command and fixed some bugs, namely one with smart distancing.

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

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 59291a3d80849c433545b63e555c8f0af52084c9..252c02eef75714e8610af6e8a5a7403a0b07bdc4 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -164,8 +164,15 @@
                A70B53AC0F4CD7AD0064797E /* getlinecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */; };
                A70DECD91063D8B40057C03C /* secondarystructurecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70DECD81063D8B40057C03C /* secondarystructurecommand.cpp */; };
                A7283FF81056CAE100D0CC69 /* chimeracheckrdp.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7283FF71056CAE100D0CC69 /* chimeracheckrdp.cpp */; };
+               A729ACD010848E6100139801 /* hclustercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A729ACCF10848E6100139801 /* hclustercommand.cpp */; };
+               A729ACE410849BBE00139801 /* hcluster.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A729ACE310849BBE00139801 /* hcluster.cpp */; };
+               A73329CF1083B3B3003B10C5 /* getlistcountcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A73329CE1083B3B3003B10C5 /* getlistcountcommand.cpp */; };
+               A751ACEA1098B283003D0911 /* readcluster.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A751ACE91098B283003D0911 /* readcluster.cpp */; };
                A75B887E104C16860083C454 /* ccode.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A75B887B104C16860083C454 /* ccode.cpp */; };
+               A7B04493106CC3E60046FC83 /* chimeraslayer.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7B04492106CC3E60046FC83 /* chimeraslayer.cpp */; };
+               A7B0450E106CEEC90046FC83 /* slayer.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7B0450D106CEEC90046FC83 /* slayer.cpp */; };
                A7E4A783106913F900688F62 /* getsharedotucommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E4A782106913F900688F62 /* getsharedotucommand.cpp */; };
+               A7E4A824106A9AD700688F62 /* maligner.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E4A823106A9AD700688F62 /* maligner.cpp */; };
                EB1216880F619B83004A865F /* bergerparker.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB1216870F619B83004A865F /* bergerparker.cpp */; };
                EB1216E50F61ACFB004A865F /* bstick.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB1216E40F61ACFB004A865F /* bstick.cpp */; };
                EB1217230F61C9AC004A865F /* sharedkstest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB1217220F61C9AC004A865F /* sharedkstest.cpp */; };
@@ -517,14 +524,28 @@
                A70B53A70F4CD7AD0064797E /* getlabelcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlabelcommand.h; sourceTree = SOURCE_ROOT; };
                A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlinecommand.cpp; sourceTree = SOURCE_ROOT; };
                A70B53A90F4CD7AD0064797E /* getlinecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlinecommand.h; sourceTree = SOURCE_ROOT; };
-               A70DECD71063D8B40057C03C /* secondarystructurecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = secondarystructurecommand.h; sourceTree = "<group>"; };
-               A70DECD81063D8B40057C03C /* secondarystructurecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = secondarystructurecommand.cpp; sourceTree = "<group>"; };
+               A70DECD71063D8B40057C03C /* secondarystructurecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = secondarystructurecommand.h; sourceTree = SOURCE_ROOT; };
+               A70DECD81063D8B40057C03C /* secondarystructurecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = secondarystructurecommand.cpp; sourceTree = SOURCE_ROOT; };
                A7283FF61056CAE100D0CC69 /* chimeracheckrdp.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeracheckrdp.h; sourceTree = SOURCE_ROOT; };
                A7283FF71056CAE100D0CC69 /* chimeracheckrdp.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeracheckrdp.cpp; sourceTree = SOURCE_ROOT; };
+               A729ACCE10848E6100139801 /* hclustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = hclustercommand.h; sourceTree = SOURCE_ROOT; };
+               A729ACCF10848E6100139801 /* hclustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = hclustercommand.cpp; sourceTree = SOURCE_ROOT; };
+               A729ACE210849BBE00139801 /* hcluster.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = hcluster.h; sourceTree = SOURCE_ROOT; };
+               A729ACE310849BBE00139801 /* hcluster.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = hcluster.cpp; sourceTree = SOURCE_ROOT; };
+               A73329CD1083B3B3003B10C5 /* getlistcountcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlistcountcommand.h; sourceTree = SOURCE_ROOT; };
+               A73329CE1083B3B3003B10C5 /* getlistcountcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlistcountcommand.cpp; sourceTree = SOURCE_ROOT; };
+               A751ACE81098B283003D0911 /* readcluster.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readcluster.h; sourceTree = SOURCE_ROOT; };
+               A751ACE91098B283003D0911 /* readcluster.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readcluster.cpp; sourceTree = SOURCE_ROOT; };
                A75B887B104C16860083C454 /* ccode.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ccode.cpp; sourceTree = SOURCE_ROOT; };
                A75B887C104C16860083C454 /* ccode.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ccode.h; sourceTree = SOURCE_ROOT; };
-               A7E4A781106913F900688F62 /* getsharedotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getsharedotucommand.h; sourceTree = "<group>"; };
-               A7E4A782106913F900688F62 /* getsharedotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getsharedotucommand.cpp; sourceTree = "<group>"; };
+               A7B04491106CC3E60046FC83 /* chimeraslayer.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraslayer.h; sourceTree = SOURCE_ROOT; };
+               A7B04492106CC3E60046FC83 /* chimeraslayer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraslayer.cpp; sourceTree = SOURCE_ROOT; };
+               A7B0450C106CEEC90046FC83 /* slayer.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = slayer.h; sourceTree = SOURCE_ROOT; };
+               A7B0450D106CEEC90046FC83 /* slayer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = slayer.cpp; sourceTree = SOURCE_ROOT; };
+               A7E4A781106913F900688F62 /* getsharedotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getsharedotucommand.h; sourceTree = SOURCE_ROOT; };
+               A7E4A782106913F900688F62 /* getsharedotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getsharedotucommand.cpp; sourceTree = SOURCE_ROOT; };
+               A7E4A822106A9AD700688F62 /* maligner.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = maligner.h; sourceTree = SOURCE_ROOT; };
+               A7E4A823106A9AD700688F62 /* maligner.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = maligner.cpp; sourceTree = SOURCE_ROOT; };
                C6859E8B029090EE04C91782 /* Mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = Mothur.1; sourceTree = "<group>"; };
                EB1216860F619B83004A865F /* bergerparker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bergerparker.h; sourceTree = SOURCE_ROOT; };
                EB1216870F619B83004A865F /* bergerparker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bergerparker.cpp; sourceTree = SOURCE_ROOT; };
@@ -573,6 +594,8 @@
                                374F2FE81006346600E97C66 /* chimera */,
                                37D927C20F21331F001D4494 /* cluster.hpp */,
                                37D927C10F21331F001D4494 /* cluster.cpp */,
+                               A729ACE210849BBE00139801 /* hcluster.h */,
+                               A729ACE310849BBE00139801 /* hcluster.cpp */,
                                37D928A90F2133E5001D4494 /* commands */,
                                37D927C60F21331F001D4494 /* collect.h */,
                                37D927C50F21331F001D4494 /* collect.cpp */,
@@ -606,8 +629,6 @@
                                7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */,
                                37E3ED800F4D9D0D00B5DF02 /* mothur.h */,
                                37D927EF0F21331F001D4494 /* mothur.cpp */,
-                               37D927F10F21331F001D4494 /* nameassignment.hpp */,
-                               37D927F00F21331F001D4494 /* nameassignment.cpp */,
                                373C691E0FC1C98600137ACD /* nast.hpp */,
                                373C691D0FC1C98600137ACD /* nast.cpp */,
                                373C692A0FC1C9EB00137ACD /* nastreport.hpp */,
@@ -661,10 +682,16 @@
                                A75B887B104C16860083C454 /* ccode.cpp */,
                                A7283FF61056CAE100D0CC69 /* chimeracheckrdp.h */,
                                A7283FF71056CAE100D0CC69 /* chimeracheckrdp.cpp */,
+                               A7B04491106CC3E60046FC83 /* chimeraslayer.h */,
+                               A7B04492106CC3E60046FC83 /* chimeraslayer.cpp */,
                                372A55531017922B00C5194B /* decalc.h */,
                                372A55541017922B00C5194B /* decalc.cpp */,
+                               A7E4A822106A9AD700688F62 /* maligner.h */,
+                               A7E4A823106A9AD700688F62 /* maligner.cpp */,
                                374F301110063B6F00E97C66 /* pintail.h */,
                                374F301210063B6F00E97C66 /* pintail.cpp */,
+                               A7B0450C106CEEC90046FC83 /* slayer.h */,
+                               A7B0450D106CEEC90046FC83 /* slayer.cpp */,
                        );
                        name = chimera;
                        sourceTree = "<group>";
@@ -672,6 +699,8 @@
                3796441D0FB9B9650081FDB6 /* read */ = {
                        isa = PBXGroup;
                        children = (
+                               A751ACE81098B283003D0911 /* readcluster.h */,
+                               A751ACE91098B283003D0911 /* readcluster.cpp */,
                                375AA1340F9E433D008EF9B8 /* readcolumn.h */,
                                375AA1330F9E433D008EF9B8 /* readcolumn.cpp */,
                                37D928130F21331F001D4494 /* readmatrix.hpp */,
@@ -830,6 +859,8 @@
                                A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */,
                                A70B53A90F4CD7AD0064797E /* getlinecommand.h */,
                                A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */,
+                               A73329CD1083B3B3003B10C5 /* getlistcountcommand.h */,
+                               A73329CE1083B3B3003B10C5 /* getlistcountcommand.cpp */,
                                370B88050F8A4EE4005AB382 /* getoturepcommand.h */,
                                370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */,
                                3749273D0FD5956B0031C06B /* getrabundcommand.h */,
@@ -840,6 +871,8 @@
                                37B73CA51004D89A008C4B41 /* getseqscommand.cpp */,
                                A7E4A781106913F900688F62 /* getsharedotucommand.h */,
                                A7E4A782106913F900688F62 /* getsharedotucommand.cpp */,
+                               A729ACCE10848E6100139801 /* hclustercommand.h */,
+                               A729ACCF10848E6100139801 /* hclustercommand.cpp */,
                                375873F10F7D64800040F377 /* heatmapcommand.h */,
                                375873F00F7D64800040F377 /* heatmapcommand.cpp */,
                                378598640FDD497000EF9D03 /* heatmapsimcommand.h */,
@@ -928,6 +961,8 @@
                                37D927EB0F21331F001D4494 /* kmerdb.cpp */,
                                37D927EE0F21331F001D4494 /* listvector.hpp */,
                                37D927ED0F21331F001D4494 /* listvector.cpp */,
+                               37D927F10F21331F001D4494 /* nameassignment.hpp */,
+                               37D927F00F21331F001D4494 /* nameassignment.cpp */,
                                37D927F80F21331F001D4494 /* ordervector.hpp */,
                                37D927F70F21331F001D4494 /* ordervector.cpp */,
                                37D928000F21331F001D4494 /* rabundvector.hpp */,
@@ -1191,6 +1226,13 @@
                                A7283FF81056CAE100D0CC69 /* chimeracheckrdp.cpp in Sources */,
                                A70DECD91063D8B40057C03C /* secondarystructurecommand.cpp in Sources */,
                                A7E4A783106913F900688F62 /* getsharedotucommand.cpp in Sources */,
+                               A7E4A824106A9AD700688F62 /* maligner.cpp in Sources */,
+                               A7B04493106CC3E60046FC83 /* chimeraslayer.cpp in Sources */,
+                               A7B0450E106CEEC90046FC83 /* slayer.cpp in Sources */,
+                               A73329CF1083B3B3003B10C5 /* getlistcountcommand.cpp in Sources */,
+                               A729ACD010848E6100139801 /* hclustercommand.cpp in Sources */,
+                               A729ACE410849BBE00139801 /* hcluster.cpp in Sources */,
+                               A751ACEA1098B283003D0911 /* readcluster.cpp in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };