fixed trim.seqs bug with qtrim parameter and added num=1 special case to database...

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

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 7a32b803547870fb6ad5c2f96f8a7835504fd1b7..1b87a4f360376eb978f94c7a1e846ec2a18ffb7c 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -9,6 +9,8 @@
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                A70332B712D3A13400761E33 /* makefile in Sources */ = {isa = PBXBuildFile; fileRef = A70332B512D3A13400761E33 /* makefile */; };
+               A713EBAC12DC7613000092AC /* readphylipvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A713EBAB12DC7613000092AC /* readphylipvector.cpp */; };
+               A713EBED12DC7C5E000092AC /* nmdscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */; };
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@@ -157,7 +159,7 @@
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                A7E9B91412D37EC400DA6239 /* parsimonycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */; };
-               A7E9B91512D37EC400DA6239 /* pcacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78712D37EC400DA6239 /* pcacommand.cpp */; };
+               A7E9B91512D37EC400DA6239 /* pcoacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */; };
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@@ -280,6 +282,8 @@
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                A7E9B98F12D37EC400DA6239 /* whittaker.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87F12D37EC400DA6239 /* whittaker.cpp */; };
+               A7FC480E12D788F20055BC5C /* linearalgebra.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FC480D12D788F20055BC5C /* linearalgebra.cpp */; };
+               A7FC486712D795D60055BC5C /* pcacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FC486612D795D60055BC5C /* pcacommand.cpp */; };
 /* End PBXBuildFile section */
 
 /* Begin PBXCopyFilesBuildPhase section */
@@ -298,6 +302,10 @@
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                A70332B512D3A13400761E33 /* makefile */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.make; path = makefile; sourceTree = "<group>"; };
+               A713EBAA12DC7613000092AC /* readphylipvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylipvector.h; sourceTree = "<group>"; };
+               A713EBAB12DC7613000092AC /* readphylipvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylipvector.cpp; sourceTree = "<group>"; };
+               A713EBEB12DC7C5E000092AC /* nmdscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nmdscommand.h; sourceTree = "<group>"; };
+               A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nmdscommand.cpp; sourceTree = "<group>"; };
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@@ -610,8 +618,8 @@
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+               A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcoacommand.cpp; sourceTree = "<group>"; };
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@@ -860,6 +868,10 @@
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+               A7FC480D12D788F20055BC5C /* linearalgebra.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = linearalgebra.cpp; sourceTree = "<group>"; };
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@@ -930,6 +942,8 @@
                                A7E9B72D12D37EC400DA6239 /* inputdata.cpp */,
                                A7E9B73912D37EC400DA6239 /* libshuff.cpp */,
                                A7E9B73A12D37EC400DA6239 /* libshuff.h */,
+                               A7FC480C12D788F20055BC5C /* linearalgebra.h */,
+                               A7FC480D12D788F20055BC5C /* linearalgebra.cpp */,
                                A7E9BA5612D39BD800DA6239 /* metastats */,
                                A7E9B75B12D37EC400DA6239 /* mothur.cpp */,
                                A7E9B75C12D37EC400DA6239 /* mothur.h */,
@@ -1100,6 +1114,8 @@
                                A7E9B76912D37EC400DA6239 /* nocommands.cpp */,
                                A7E9B76B12D37EC400DA6239 /* normalizesharedcommand.cpp */,
                                A7E9B76C12D37EC400DA6239 /* normalizesharedcommand.h */,
+                               A713EBEB12DC7C5E000092AC /* nmdscommand.h */,
+                               A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */,
                                A7E9B77912D37EC400DA6239 /* otuhierarchycommand.cpp */,
                                A7E9B77A12D37EC400DA6239 /* otuhierarchycommand.h */,
                                A7E9B77D12D37EC400DA6239 /* pairwiseseqscommand.cpp */,
@@ -1110,8 +1126,10 @@
                                A7E9B78212D37EC400DA6239 /* parselistscommand.h */,
                                A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */,
                                A7E9B78612D37EC400DA6239 /* parsimonycommand.h */,
-                               A7E9B78712D37EC400DA6239 /* pcacommand.cpp */,
-                               A7E9B78812D37EC400DA6239 /* pcacommand.h */,
+                               A7FC486512D795D60055BC5C /* pcacommand.h */,
+                               A7FC486612D795D60055BC5C /* pcacommand.cpp */,
+                               A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */,
+                               A7E9B78812D37EC400DA6239 /* pcoacommand.h */,
                                A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */,
                                A7E9B78C12D37EC400DA6239 /* phylodiversitycommand.h */,
                                A7E9B79112D37EC400DA6239 /* phylotypecommand.cpp */,
@@ -1511,6 +1529,8 @@
                                A7E9B7BE12D37EC400DA6239 /* readphylip.h */,
                                A7E9B7BF12D37EC400DA6239 /* readtree.cpp */,
                                A7E9B7C012D37EC400DA6239 /* readtree.h */,
+                               A713EBAA12DC7613000092AC /* readphylipvector.h */,
+                               A713EBAB12DC7613000092AC /* readphylipvector.cpp */,
                                A7E9B84312D37EC400DA6239 /* splitmatrix.cpp */,
                                A7E9B84412D37EC400DA6239 /* splitmatrix.h */,
                        );
@@ -1732,7 +1752,7 @@
                                A7E9B91212D37EC400DA6239 /* parselistscommand.cpp in Sources */,
                                A7E9B91312D37EC400DA6239 /* parsimony.cpp in Sources */,
                                A7E9B91412D37EC400DA6239 /* parsimonycommand.cpp in Sources */,
-                               A7E9B91512D37EC400DA6239 /* pcacommand.cpp in Sources */,
+                               A7E9B91512D37EC400DA6239 /* pcoacommand.cpp in Sources */,
                                A7E9B91612D37EC400DA6239 /* phylodiversity.cpp in Sources */,
                                A7E9B91712D37EC400DA6239 /* phylodiversitycommand.cpp in Sources */,
                                A7E9B91812D37EC400DA6239 /* phylosummary.cpp in Sources */,
@@ -1856,6 +1876,10 @@
                                A7E9B98E12D37EC400DA6239 /* weightedlinkage.cpp in Sources */,
                                A7E9B98F12D37EC400DA6239 /* whittaker.cpp in Sources */,
                                A70332B712D3A13400761E33 /* makefile in Sources */,
+                               A7FC480E12D788F20055BC5C /* linearalgebra.cpp in Sources */,
+                               A7FC486712D795D60055BC5C /* pcacommand.cpp in Sources */,
+                               A713EBAC12DC7613000092AC /* readphylipvector.cpp in Sources */,
+                               A713EBED12DC7C5E000092AC /* nmdscommand.cpp in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };