modified trim.seqs to account for primers of different lengths

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

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 3ee1d81bc1944bdb301d2930b82b03cb51e2be63..eb9edec42e9c830b0e25c4da9464d7e0831623d1 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -7,6 +7,12 @@
        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>"; };
                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>"; };
@@ -552,6 +558,8 @@
                                A7DA20B0113FECD400BF472F /* nseqs.h */,
                                A7DA20B2113FECD400BF472F /* onegapdist.h */,
                                A7DA20B3113FECD400BF472F /* onegapignore.h */,
+                               A72B3A7B118B4D1B004B9F8D /* phylodiversity.h */,
+                               A72B3A7C118B4D1B004B9F8D /* phylodiversity.cpp */,
                                A7DA20BE113FECD400BF472F /* parsimony.cpp */,
                                A7DA20BF113FECD400BF472F /* parsimony.h */,
                                A7DA20CE113FECD400BF472F /* qstat.cpp */,
@@ -688,8 +696,10 @@
                                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 */,
@@ -706,56 +716,58 @@
                                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 */,
-                               A7DA20F4113FECD400BF472F /* reversecommand.cpp */,
+                               A7DA20F2113FECD400BF472F /* removeseqscommand.cpp */,
                                A7DA20F5113FECD400BF472F /* reversecommand.h */,
-                               A7DA20F8113FECD400BF472F /* screenseqscommand.cpp */,
+                               A7DA20F4113FECD400BF472F /* reversecommand.cpp */,
                                A7DA20F9113FECD400BF472F /* screenseqscommand.h */,
-                               A7DA20FA113FECD400BF472F /* secondarystructurecommand.cpp */,
+                               A7DA20F8113FECD400BF472F /* screenseqscommand.cpp */,
                                A7DA20FB113FECD400BF472F /* secondarystructurecommand.h */,
-                               A7DA20FC113FECD400BF472F /* seqsummarycommand.cpp */,
+                               A7DA20FA113FECD400BF472F /* secondarystructurecommand.cpp */,
                                A7DA20FD113FECD400BF472F /* seqsummarycommand.h */,
-                               A7DA2102113FECD400BF472F /* setdircommand.cpp */,
+                               A7DA20FC113FECD400BF472F /* seqsummarycommand.cpp */,
                                A7DA2103113FECD400BF472F /* setdircommand.h */,
+                               A7DA2102113FECD400BF472F /* setdircommand.cpp */,
                                A76C4A1011876BAF0009460B /* setlogfilecommand.h */,
                                A76C4A1111876BAF0009460B /* setlogfilecommand.cpp */,
-                               A7DA210F113FECD400BF472F /* sharedcommand.cpp */,
                                A7DA2110113FECD400BF472F /* sharedcommand.h */,
-                               A7DA2154113FECD400BF472F /* summarycommand.cpp */,
+                               A7DA210F113FECD400BF472F /* sharedcommand.cpp */,
                                A7DA2155113FECD400BF472F /* summarycommand.h */,
-                               A7DA2158113FECD400BF472F /* summarysharedcommand.cpp */,
+                               A7DA2154113FECD400BF472F /* summarycommand.cpp */,
                                A7DA2159113FECD400BF472F /* summarysharedcommand.h */,
-                               A7DA215A113FECD400BF472F /* systemcommand.cpp */,
+                               A7DA2158113FECD400BF472F /* summarysharedcommand.cpp */,
                                A7DA215B113FECD400BF472F /* systemcommand.h */,
-                               A7DA2161113FECD400BF472F /* treegroupscommand.cpp */,
+                               A7DA215A113FECD400BF472F /* systemcommand.cpp */,
                                A7DA2162113FECD400BF472F /* treegroupscommand.h */,
-                               A7DA2167113FECD400BF472F /* trimseqscommand.cpp */,
+                               A7DA2161113FECD400BF472F /* treegroupscommand.cpp */,
                                A7DA2168113FECD400BF472F /* trimseqscommand.h */,
-                               A7DA2169113FECD400BF472F /* unifracunweightedcommand.cpp */,
+                               A7DA2167113FECD400BF472F /* trimseqscommand.cpp */,
                                A7DA216A113FECD400BF472F /* unifracunweightedcommand.h */,
-                               A7DA216B113FECD400BF472F /* unifracweightedcommand.cpp */,
+                               A7DA2169113FECD400BF472F /* unifracunweightedcommand.cpp */,
                                A7DA216C113FECD400BF472F /* unifracweightedcommand.h */,
-                               A7DA2177113FECD400BF472F /* venncommand.cpp */,
+                               A7DA216B113FECD400BF472F /* unifracweightedcommand.cpp */,
                                A7DA2178113FECD400BF472F /* venncommand.h */,
+                               A7DA2177113FECD400BF472F /* venncommand.cpp */,
                        );
                        name = commands;
                        sourceTree = "<group>";