modified freq parameter be a percentage of numSeqs, added catchall command - not...

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

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index ce6918c8449ed7b857386c30c75a5537e74767cd..5b5981b1608c62ffbc486921d3c1f3e5cdc8dcb8 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -7,6 +7,14 @@
        objects = {
 
 /* Begin PBXFileReference section */
+               A703FE931194645F002C397E /* makegroupcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = makegroupcommand.h; sourceTree = SOURCE_ROOT; };
+               A703FE941194645F002C397E /* makegroupcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = makegroupcommand.cpp; sourceTree = SOURCE_ROOT; };
+               A72B3A62118B37FD004B9F8D /* phylodiversitycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylodiversitycommand.h; sourceTree = "<group>"; };
+               A72B3A63118B37FD004B9F8D /* phylodiversitycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversitycommand.cpp; sourceTree = "<group>"; };
+               A72B3A7B118B4D1B004B9F8D /* phylodiversity.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylodiversity.h; sourceTree = "<group>"; };
+               A72B3A7C118B4D1B004B9F8D /* phylodiversity.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversity.cpp; sourceTree = "<group>"; };
+               A73953DA11987ED100B0B160 /* chopseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chopseqscommand.h; sourceTree = "<group>"; };
+               A73953DB11987ED100B0B160 /* chopseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chopseqscommand.cpp; sourceTree = "<group>"; };
                A747E79B1163442A00FB9042 /* chimeracheckcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeracheckcommand.h; sourceTree = "<group>"; };
                A747E79C1163442A00FB9042 /* chimeracheckcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeracheckcommand.cpp; sourceTree = "<group>"; };
                A747E81C116365E000FB9042 /* chimeraslayercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraslayercommand.h; sourceTree = "<group>"; };
@@ -22,6 +30,10 @@
                A7825503116519F70002E2DD /* chimerabellerophoncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerabellerophoncommand.cpp; sourceTree = "<group>"; };
                A78434881162224F00100BE0 /* chimeraccodecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraccodecommand.h; sourceTree = "<group>"; };
                A78434891162224F00100BE0 /* chimeraccodecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraccodecommand.cpp; sourceTree = "<group>"; };
+               A7D215C811996C6E00F13F13 /* clearcutcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clearcutcommand.h; sourceTree = "<group>"; };
+               A7D215C911996C6E00F13F13 /* clearcutcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clearcutcommand.cpp; sourceTree = "<group>"; };
+               A7D216061199C47F00F13F13 /* catchallcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = catchallcommand.h; sourceTree = "<group>"; };
+               A7D216071199C47F00F13F13 /* catchallcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = catchallcommand.cpp; sourceTree = "<group>"; };
                A7DA1FEC113FECD400BF472F /* ace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ace.cpp; sourceTree = "<group>"; };
                A7DA1FED113FECD400BF472F /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = "<group>"; };
                A7DA1FEE113FECD400BF472F /* aligncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = aligncommand.cpp; sourceTree = "<group>"; };
@@ -552,6 +564,8 @@
                                A7DA20B0113FECD400BF472F /* nseqs.h */,
                                A7DA20B2113FECD400BF472F /* onegapdist.h */,
                                A7DA20B3113FECD400BF472F /* onegapignore.h */,
+                               A72B3A7B118B4D1B004B9F8D /* phylodiversity.h */,
+                               A72B3A7C118B4D1B004B9F8D /* phylodiversity.cpp */,
                                A7DA20BE113FECD400BF472F /* parsimony.cpp */,
                                A7DA20BF113FECD400BF472F /* parsimony.h */,
                                A7DA20CE113FECD400BF472F /* qstat.cpp */,
@@ -634,20 +648,26 @@
                                A7DA1FFE113FECD400BF472F /* binsequencecommand.h */,
                                A7DA2007113FECD400BF472F /* bootstrapsharedcommand.cpp */,
                                A7DA2008113FECD400BF472F /* bootstrapsharedcommand.h */,
+                               A7D216061199C47F00F13F13 /* catchallcommand.h */,
+                               A7D216071199C47F00F13F13 /* catchallcommand.cpp */,
                                A7DA2017113FECD400BF472F /* chimeraseqscommand.cpp */,
+                               A78434881162224F00100BE0 /* chimeraccodecommand.h */,
                                A7DA2018113FECD400BF472F /* chimeraseqscommand.h */,
                                A7825502116519F70002E2DD /* chimerabellerophoncommand.h */,
                                A7825503116519F70002E2DD /* chimerabellerophoncommand.cpp */,
                                A747E79B1163442A00FB9042 /* chimeracheckcommand.h */,
                                A747E79C1163442A00FB9042 /* chimeracheckcommand.cpp */,
-                               A78434881162224F00100BE0 /* chimeraccodecommand.h */,
                                A78434891162224F00100BE0 /* chimeraccodecommand.cpp */,
                                A78254461164D7790002E2DD /* chimerapintailcommand.h */,
                                A78254471164D7790002E2DD /* chimerapintailcommand.cpp */,
                                A747E81C116365E000FB9042 /* chimeraslayercommand.h */,
                                A747E81D116365E000FB9042 /* chimeraslayercommand.cpp */,
-                               A7DA201D113FECD400BF472F /* classifyseqscommand.cpp */,
+                               A73953DA11987ED100B0B160 /* chopseqscommand.h */,
+                               A73953DB11987ED100B0B160 /* chopseqscommand.cpp */,
                                A7DA201E113FECD400BF472F /* classifyseqscommand.h */,
+                               A7DA201D113FECD400BF472F /* classifyseqscommand.cpp */,
+                               A7D215C811996C6E00F13F13 /* clearcutcommand.h */,
+                               A7D215C911996C6E00F13F13 /* clearcutcommand.cpp */,
                                A7DA2021113FECD400BF472F /* clustercommand.cpp */,
                                A7DA2022113FECD400BF472F /* clustercommand.h */,
                                A7DA2025113FECD400BF472F /* collectcommand.cpp */,
@@ -674,8 +694,8 @@
                                A7DA2063113FECD400BF472F /* getrabundcommand.h */,
                                A7DA2064113FECD400BF472F /* getsabundcommand.cpp */,
                                A7DA2065113FECD400BF472F /* getsabundcommand.h */,
-                               A7DA2066113FECD400BF472F /* getseqscommand.cpp */,
                                A7DA2067113FECD400BF472F /* getseqscommand.h */,
+                               A7DA2066113FECD400BF472F /* getseqscommand.cpp */,
                                A7DA2068113FECD400BF472F /* getsharedotucommand.cpp */,
                                A7DA2069113FECD400BF472F /* getsharedotucommand.h */,
                                A7DA2074113FECD400BF472F /* hclustercommand.cpp */,
@@ -688,8 +708,10 @@
                                A7DA207F113FECD400BF472F /* helpcommand.h */,
                                A7DA208D113FECD400BF472F /* libshuffcommand.cpp */,
                                A7DA208E113FECD400BF472F /* libshuffcommand.h */,
-                               A7DA208F113FECD400BF472F /* listseqscommand.cpp */,
                                A7DA2090113FECD400BF472F /* listseqscommand.h */,
+                               A7DA208F113FECD400BF472F /* listseqscommand.cpp */,
+                               A703FE931194645F002C397E /* makegroupcommand.h */,
+                               A703FE941194645F002C397E /* makegroupcommand.cpp */,
                                A7DA2098113FECD400BF472F /* matrixoutputcommand.cpp */,
                                A7DA2099113FECD400BF472F /* matrixoutputcommand.h */,
                                A7DA209A113FECD400BF472F /* mergefilecommand.cpp */,
@@ -706,26 +728,28 @@
                                A7E8338C115BBDAA00739EC4 /* parsesffcommand.h */,
                                A7DA20C0113FECD400BF472F /* parsimonycommand.cpp */,
                                A7DA20C1113FECD400BF472F /* parsimonycommand.h */,
-                               A7DA20C2113FECD400BF472F /* pcacommand.cpp */,
                                A7DA20C3113FECD400BF472F /* pcacommand.h */,
-                               A7DA20C6113FECD400BF472F /* phylotypecommand.cpp */,
+                               A7DA20C2113FECD400BF472F /* pcacommand.cpp */,
+                               A72B3A62118B37FD004B9F8D /* phylodiversitycommand.h */,
+                               A72B3A63118B37FD004B9F8D /* phylodiversitycommand.cpp */,
                                A7DA20C7113FECD400BF472F /* phylotypecommand.h */,
-                               A7DA20CA113FECD400BF472F /* preclustercommand.cpp */,
+                               A7DA20C6113FECD400BF472F /* phylotypecommand.cpp */,
                                A7DA20CB113FECD400BF472F /* preclustercommand.h */,
-                               A7DA20D0113FECD400BF472F /* quitcommand.cpp */,
+                               A7DA20CA113FECD400BF472F /* preclustercommand.cpp */,
                                A7DA20D1113FECD400BF472F /* quitcommand.h */,
-                               A7DA20DA113FECD400BF472F /* rarefactcommand.cpp */,
+                               A7DA20D0113FECD400BF472F /* quitcommand.cpp */,
                                A7DA20DB113FECD400BF472F /* rarefactcommand.h */,
-                               A7DA20DD113FECD400BF472F /* rarefactsharedcommand.cpp */,
+                               A7DA20DA113FECD400BF472F /* rarefactcommand.cpp */,
                                A7DA20DE113FECD400BF472F /* rarefactsharedcommand.h */,
-                               A7DA20E5113FECD400BF472F /* readdistcommand.cpp */,
+                               A7DA20DD113FECD400BF472F /* rarefactsharedcommand.cpp */,
                                A7DA20E6113FECD400BF472F /* readdistcommand.h */,
-                               A7DA20EA113FECD400BF472F /* readotucommand.cpp */,
+                               A7DA20E5113FECD400BF472F /* readdistcommand.cpp */,
                                A7DA20EB113FECD400BF472F /* readotucommand.h */,
-                               A7DA20F0113FECD400BF472F /* readtreecommand.cpp */,
+                               A7DA20EA113FECD400BF472F /* readotucommand.cpp */,
                                A7DA20F1113FECD400BF472F /* readtreecommand.h */,
-                               A7DA20F2113FECD400BF472F /* removeseqscommand.cpp */,
+                               A7DA20F0113FECD400BF472F /* readtreecommand.cpp */,
                                A7DA20F3113FECD400BF472F /* removeseqscommand.h */,
+                               A7DA20F2113FECD400BF472F /* removeseqscommand.cpp */,
                                A7DA20F5113FECD400BF472F /* reversecommand.h */,
                                A7DA20F4113FECD400BF472F /* reversecommand.cpp */,
                                A7DA20F9113FECD400BF472F /* screenseqscommand.h */,