From 58cf1d08fee8c64334979075fa57bcafb035a2ed Mon Sep 17 00:00:00 2001 From: pschloss Date: Fri, 30 Jan 2009 12:49:01 +0000 Subject: [PATCH] When Pat tried to compile mothur in Ubuntu linux, there were a number of minor problems that needed to be fixed in the code --- Mothur.xcodeproj/project.pbxproj | 4 ++++ ace.h | 1 - bootstrap.h | 3 +-- chao1.h | 3 +-- clustercommand.h | 3 +-- collect.cpp | 5 ++++- collectcommand.h | 3 +-- collectdisplay.h | 2 +- collectorscurvedata.h | 2 +- collectsharedcommand.h | 3 +-- commandfactory.cpp | 1 - deconvolutecommand.h | 2 +- display.h | 2 +- engine.cpp | 7 +++---- errorchecking.h | 3 +-- fastamap.h | 2 +- fileoutput.cpp | 2 +- fileoutput.h | 1 - groupmap.h | 3 +-- helpcommand.h | 3 +-- inputdata.h | 2 +- jackknife.h | 3 +-- listvector.hpp | 1 - nocommand.h | 3 +-- npshannon.h | 3 +-- parselistcommand.h | 3 +-- quitcommand.h | 4 ++-- rarecalc.h | 2 -- rarefactcommand.h | 3 +-- rarefactsharedcommand.h | 3 +-- readdistcommand.cpp | 2 +- readdistcommand.h | 3 +-- readotucommand.cpp | 2 +- readotucommand.h | 3 +-- readtree.cpp | 2 +- readtree.h | 2 +- readtreecommand.cpp | 3 ++- readtreecommand.h | 9 +-------- shannon.h | 1 - shared.h | 3 +-- sharedace.h | 4 +--- sharedchao1.cpp | 3 ++- sharedchao1.h | 4 ++-- sharedcommand.h | 3 +-- sharedjabund.cpp | 1 + sharedjabund.h | 3 +-- sharedjclass.cpp | 1 + sharedjclass.h | 4 +--- sharedjest.cpp | 3 +-- sharedjest.h | 3 --- sharedlistvector.h | 2 -- sharedordervector.h | 1 - sharedrabundvector.h | 1 - sharedsabundvector.h | 2 -- sharedsobs.h | 1 - sharedsorabund.h | 1 - sharedsorclass.h | 3 +-- sharedsorest.h | 1 - sharedthetan.cpp | 1 + sharedthetan.h | 3 +-- sharedthetayc.h | 4 ++-- simpson.h | 3 +-- sobs.h | 4 ++-- summarycommand.h | 3 +-- summarydisplay.h | 2 +- summarysharedcommand.h | 3 +-- tree.h | 5 +---- treemap.cpp | 2 +- treemap.h | 3 +-- treenode.cpp | 2 +- treenode.h | 2 +- uvest.h | 5 +++-- validcalculator.h | 8 +++++--- validcommands.cpp | 2 +- validcommands.h | 8 ++++++-- validparameter.cpp | 2 +- validparameter.h | 8 ++++++-- 77 files changed, 93 insertions(+), 130 deletions(-) diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index 0a3c22c..e773981 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -85,6 +85,7 @@ 37D9289F0F21331F001D4494 /* validparameter.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928530F21331F001D4494 /* validparameter.cpp */; }; 37E5F3E30F29FD4200F8D827 /* treenode.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37E5F3E20F29FD4200F8D827 /* treenode.cpp */; }; 37E5F4920F2A3DA800F8D827 /* readtreecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */; }; + 7E44EBD10F3235D900B0D45D /* makefile in Sources */ = {isa = PBXBuildFile; fileRef = 7E44EBD00F32358B00B0D45D /* makefile */; }; 8DD76F6A0486A84900D96B5E /* Mothur.1 in CopyFiles */ = {isa = PBXBuildFile; fileRef = C6859E8B029090EE04C91782 /* Mothur.1 */; }; /* End PBXBuildFile section */ @@ -265,6 +266,7 @@ 37E5F3E20F29FD4200F8D827 /* treenode.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treenode.cpp; sourceTree = SOURCE_ROOT; }; 37E5F4900F2A3DA800F8D827 /* readtreecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtreecommand.h; sourceTree = SOURCE_ROOT; }; 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtreecommand.cpp; sourceTree = SOURCE_ROOT; }; + 7E44EBD00F32358B00B0D45D /* makefile */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.make; path = makefile; sourceTree = ""; }; 8DD76F6C0486A84900D96B5E /* mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = mothur; sourceTree = BUILT_PRODUCTS_DIR; }; C6859E8B029090EE04C91782 /* Mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = Mothur.1; sourceTree = ""; }; /* End PBXFileReference section */ @@ -313,6 +315,7 @@ 37D927D60F21331F001D4494 /* display.h */, 37D927D80F21331F001D4494 /* engine.hpp */, 37D927D70F21331F001D4494 /* engine.cpp */, + 7E44EBD00F32358B00B0D45D /* makefile */, 37D928B10F213472001D4494 /* errorcheckor */, 37D927DE0F21331F001D4494 /* fileoutput.h */, 37D927DD0F21331F001D4494 /* fileoutput.cpp */, @@ -629,6 +632,7 @@ 37E5F3E30F29FD4200F8D827 /* treenode.cpp in Sources */, 37E5F4920F2A3DA800F8D827 /* readtreecommand.cpp in Sources */, 379293C30F2DE73400B9034A /* treemap.cpp in Sources */, + 7E44EBD10F3235D900B0D45D /* makefile in Sources */, ); runOnlyForDeploymentPostprocessing = 0; }; diff --git a/ace.h b/ace.h index 19188fa..4c4a69d 100644 --- a/ace.h +++ b/ace.h @@ -13,7 +13,6 @@ /* This class implements the Ace estimator on a single group. It is a child of the calculator class. */ -#include #include "calculator.h" /***********************************************************************/ diff --git a/bootstrap.h b/bootstrap.h index 71d2c26..7c72ca2 100644 --- a/bootstrap.h +++ b/bootstrap.h @@ -12,7 +12,6 @@ /* This class implements the Bootstrap estimator on single group. It is a child of the calculator class. */ -#include #include "calculator.h" /***********************************************************************/ @@ -29,4 +28,4 @@ public: /***********************************************************************/ -#endif \ No newline at end of file +#endif diff --git a/chao1.h b/chao1.h index 3a7cfc7..548e1a7 100644 --- a/chao1.h +++ b/chao1.h @@ -9,7 +9,6 @@ * */ -#include #include "calculator.h" /* This class implements the Ace estimator on single group. @@ -28,4 +27,4 @@ public: /***********************************************************************/ -#endif \ No newline at end of file +#endif diff --git a/clustercommand.h b/clustercommand.h index 1487b3e..5dbeb73 100644 --- a/clustercommand.h +++ b/clustercommand.h @@ -9,7 +9,6 @@ * */ -#include #include #include #include "globaldata.hpp" @@ -55,4 +54,4 @@ private: void printData(string label); }; -#endif \ No newline at end of file +#endif diff --git a/collect.cpp b/collect.cpp index 7f589ce..0a92218 100644 --- a/collect.cpp +++ b/collect.cpp @@ -148,6 +148,7 @@ try { } /**************************************************************************************/ + void Collect::getGroupComb() { string group; @@ -163,4 +164,6 @@ void Collect::getGroupComb() { n++; } -} \ No newline at end of file +} + +/**************************************************************************************/ diff --git a/collectcommand.h b/collectcommand.h index 633f345..b92b350 100644 --- a/collectcommand.h +++ b/collectcommand.h @@ -9,7 +9,6 @@ * */ -#include #include #include #include @@ -55,4 +54,4 @@ private: }; -#endif \ No newline at end of file +#endif diff --git a/collectdisplay.h b/collectdisplay.h index 7127573..367a188 100644 --- a/collectdisplay.h +++ b/collectdisplay.h @@ -51,4 +51,4 @@ private: /***********************************************************************/ -#endif \ No newline at end of file +#endif diff --git a/collectorscurvedata.h b/collectorscurvedata.h index e6f6278..403c23c 100644 --- a/collectorscurvedata.h +++ b/collectorscurvedata.h @@ -3,7 +3,7 @@ #include #include "sabundvector.hpp" -#include "sharedRAbundvector.h" +#include "sharedrabundvector.h" #include "display.h" #include "observable.h" diff --git a/collectsharedcommand.h b/collectsharedcommand.h index 3737c11..6a8f96f 100644 --- a/collectsharedcommand.h +++ b/collectsharedcommand.h @@ -9,7 +9,6 @@ * */ -#include #include #include #include @@ -57,4 +56,4 @@ private: }; -#endif \ No newline at end of file +#endif diff --git a/commandfactory.cpp b/commandfactory.cpp index ed6aebe..0a065cd 100644 --- a/commandfactory.cpp +++ b/commandfactory.cpp @@ -78,4 +78,3 @@ Command* CommandFactory::getCommand(string commandName){ } /***********************************************************/ -/***********************************************************/ \ No newline at end of file diff --git a/deconvolutecommand.h b/deconvolutecommand.h index 6b05704..b9b2084 100644 --- a/deconvolutecommand.h +++ b/deconvolutecommand.h @@ -37,4 +37,4 @@ private: }; -#endif \ No newline at end of file +#endif diff --git a/display.h b/display.h index e526e56..f8daae2 100644 --- a/display.h +++ b/display.h @@ -26,4 +26,4 @@ private: /***********************************************************************/ -#endif \ No newline at end of file +#endif diff --git a/engine.cpp b/engine.cpp index e1bc23d..1ca98b0 100644 --- a/engine.cpp +++ b/engine.cpp @@ -59,15 +59,14 @@ bool InteractEngine::getInput(){ bool errorFree; ErrorCheck* errorCheckor = new ErrorCheck(); - cout << "MOTHUR v2.0 (Martha)" << endl; - cout << "Last updated: 1/07/2009" << endl << endl; - cout << "(Distance-based OTU and Richness)" << endl << endl; + cout << "mothur v1.0" << endl; + cout << "Last updated: 1/29/2009" << endl << endl; cout << "by" << endl; cout << "Patrick D. Schloss" << endl << endl; cout << "Department of Microbiology" << endl; cout << "The University of Massachusetts" << endl; cout << "pschloss@micro.umass.edu" << endl; - cout << "http://schloss.micro.umass.edu" << endl << endl << endl; + cout << "http://schloss.micro.umass.edu/mothur" << endl << endl << endl; cout << "Distributed under the GNU General Public License" << endl << endl; cout << "Type 'help()' for information on the commands that are available" << endl << endl; cout << "Type 'quit()' to exit program" << endl; diff --git a/errorchecking.h b/errorchecking.h index 756f676..d1e2f82 100644 --- a/errorchecking.h +++ b/errorchecking.h @@ -9,7 +9,6 @@ * */ -#include #include #include #include "globaldata.hpp" @@ -44,4 +43,4 @@ class ErrorCheck { vector singleEsimators, sharedEstimators, rareEstimators, summaryEstimators, sharedRareEstimators; }; -#endif \ No newline at end of file +#endif diff --git a/fastamap.h b/fastamap.h index 9eab853..864a2d0 100644 --- a/fastamap.h +++ b/fastamap.h @@ -51,4 +51,4 @@ private: map::iterator it; }; -#endif \ No newline at end of file +#endif diff --git a/fileoutput.cpp b/fileoutput.cpp index c8df770..2f7639f 100644 --- a/fileoutput.cpp +++ b/fileoutput.cpp @@ -283,7 +283,7 @@ void OneColumnFile::resetFile(){ /***********************************************************************/ /***********************************************************************/ -SharedOneColumnFile::~OneColumnFile(){ +SharedOneColumnFile::~SharedOneColumnFile(){ inFile.close(); outFile.close(); diff --git a/fileoutput.h b/fileoutput.h index b7837d2..3f90cd5 100644 --- a/fileoutput.h +++ b/fileoutput.h @@ -107,4 +107,3 @@ private: #endif - diff --git a/groupmap.h b/groupmap.h index 263fc84..a3b923c 100644 --- a/groupmap.h +++ b/groupmap.h @@ -9,7 +9,6 @@ * */ -#include #include #include #include @@ -37,4 +36,4 @@ private: map groupmap; //sequence name and groupname }; -#endif \ No newline at end of file +#endif diff --git a/helpcommand.h b/helpcommand.h index 4ea4628..6d95d86 100644 --- a/helpcommand.h +++ b/helpcommand.h @@ -11,7 +11,6 @@ /* This class is designed to aid the user in running mothur. */ -#include #include "command.hpp" #include "globaldata.hpp" @@ -29,4 +28,4 @@ private: }; -#endif \ No newline at end of file +#endif diff --git a/inputdata.h b/inputdata.h index 6d814c5..abb343e 100644 --- a/inputdata.h +++ b/inputdata.h @@ -35,4 +35,4 @@ private: }; -#endif \ No newline at end of file +#endif diff --git a/jackknife.h b/jackknife.h index 45f9287..ec920e0 100644 --- a/jackknife.h +++ b/jackknife.h @@ -10,7 +10,6 @@ * */ -#include #include "calculator.h" /* This class implements the JackKnife estimator on single group. @@ -35,4 +34,4 @@ private: /***********************************************************************/ -#endif \ No newline at end of file +#endif diff --git a/listvector.hpp b/listvector.hpp index e195f4e..f4eaca0 100644 --- a/listvector.hpp +++ b/listvector.hpp @@ -1,7 +1,6 @@ #ifndef LIST_H #define LIST_H -#include #include "datavector.hpp" #include #include diff --git a/nocommand.h b/nocommand.h index ce202e4..b529392 100644 --- a/nocommand.h +++ b/nocommand.h @@ -11,7 +11,6 @@ /* This command is run if the user enters an invalid command. */ -#include #include "command.hpp" class NoCommand : public Command { @@ -25,4 +24,4 @@ private: }; -#endif \ No newline at end of file +#endif diff --git a/npshannon.h b/npshannon.h index 4a633b3..9272409 100644 --- a/npshannon.h +++ b/npshannon.h @@ -13,7 +13,6 @@ /* This class implements the NPShannon estimator on single group. It is a child of the calculator class. */ -#include #include "calculator.h" /***********************************************************************/ @@ -30,4 +29,4 @@ private: /***********************************************************************/ -#endif \ No newline at end of file +#endif diff --git a/parselistcommand.h b/parselistcommand.h index 73c1070..4358762 100644 --- a/parselistcommand.h +++ b/parselistcommand.h @@ -9,7 +9,6 @@ * */ -#include #include #include #include @@ -53,4 +52,4 @@ private: string fileroot; }; -#endif \ No newline at end of file +#endif diff --git a/quitcommand.h b/quitcommand.h index c54e7f2..7f7b7e2 100644 --- a/quitcommand.h +++ b/quitcommand.h @@ -9,7 +9,6 @@ * */ -#include #include "command.hpp" /* The quit() command: @@ -27,4 +26,5 @@ public: private: }; -#endif \ No newline at end of file + +#endif diff --git a/rarecalc.h b/rarecalc.h index 1079b96..99964ec 100644 --- a/rarecalc.h +++ b/rarecalc.h @@ -11,8 +11,6 @@ /* This class is not currently used by Mothur */ - -#include #include "calculator.h" /***********************************************************************/ diff --git a/rarefactcommand.h b/rarefactcommand.h index b1b706c..0da5f0c 100644 --- a/rarefactcommand.h +++ b/rarefactcommand.h @@ -9,7 +9,6 @@ * */ -#include #include #include #include @@ -54,4 +53,4 @@ private: int freq, nIters; }; -#endif \ No newline at end of file +#endif diff --git a/rarefactsharedcommand.h b/rarefactsharedcommand.h index 1d87710..ab87024 100644 --- a/rarefactsharedcommand.h +++ b/rarefactsharedcommand.h @@ -9,7 +9,6 @@ * */ -#include #include #include #include @@ -54,4 +53,4 @@ private: }; -#endif \ No newline at end of file +#endif diff --git a/readdistcommand.cpp b/readdistcommand.cpp index 4feddfd..4cf5c4e 100644 --- a/readdistcommand.cpp +++ b/readdistcommand.cpp @@ -70,4 +70,4 @@ int ReadDistCommand::execute(){ cout << "An unknown error has occurred in the ReadDistCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; exit(1); } -} \ No newline at end of file +} diff --git a/readdistcommand.h b/readdistcommand.h index 3dfda1b..4f38d03 100644 --- a/readdistcommand.h +++ b/readdistcommand.h @@ -9,7 +9,6 @@ * */ -#include #include #include #include "command.hpp" @@ -40,4 +39,4 @@ private: NameAssignment* nameMap; }; -#endif \ No newline at end of file +#endif diff --git a/readotucommand.cpp b/readotucommand.cpp index c7e83e4..eeb8cd6 100644 --- a/readotucommand.cpp +++ b/readotucommand.cpp @@ -61,4 +61,4 @@ int ReadOtuCommand::execute(){ exit(1); } } -//********************************************************************************************************************** \ No newline at end of file +//********************************************************************************************************************** diff --git a/readotucommand.h b/readotucommand.h index 6974158..f00369b 100644 --- a/readotucommand.h +++ b/readotucommand.h @@ -9,7 +9,6 @@ * */ -#include #include #include #include "command.hpp" @@ -50,4 +49,4 @@ private: string filename; }; -#endif \ No newline at end of file +#endif diff --git a/readtree.cpp b/readtree.cpp index 9b96861..47da6d6 100644 --- a/readtree.cpp +++ b/readtree.cpp @@ -255,4 +255,4 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) { } /**************************************************************************************************/ /**************************************************************************************************/ - \ No newline at end of file + diff --git a/readtree.h b/readtree.h index d363cd6..1abef8a 100644 --- a/readtree.h +++ b/readtree.h @@ -60,4 +60,4 @@ private: /****************************************************************************/ -#endif \ No newline at end of file +#endif diff --git a/readtreecommand.cpp b/readtreecommand.cpp index 452c0ec..7cca943 100644 --- a/readtreecommand.cpp +++ b/readtreecommand.cpp @@ -60,4 +60,5 @@ int ReadTreeCommand::execute(){ exit(1); } } -//********************************************************************************************************************** \ No newline at end of file + +//********************************************************************************************************************** diff --git a/readtreecommand.h b/readtreecommand.h index 0810ab0..e9424b2 100644 --- a/readtreecommand.h +++ b/readtreecommand.h @@ -10,7 +10,6 @@ * */ -#include #include #include #include "command.hpp" @@ -33,10 +32,4 @@ private: }; - - - - - - -#endif \ No newline at end of file +#endif diff --git a/shannon.h b/shannon.h index 223bc90..e594c09 100644 --- a/shannon.h +++ b/shannon.h @@ -13,7 +13,6 @@ It is a child of the calculator class. */ -#include #include "calculator.h" /***********************************************************************/ diff --git a/shared.h b/shared.h index 0607c13..8625d8b 100644 --- a/shared.h +++ b/shared.h @@ -12,7 +12,6 @@ using namespace std; -#include #include #include #include @@ -37,4 +36,4 @@ class Shared { vector< map > sharedRAbund; //contains all the info needed to create the .shared file not sure if we will need }; -#endif \ No newline at end of file +#endif diff --git a/sharedace.h b/sharedace.h index fead251..c73f153 100644 --- a/sharedace.h +++ b/sharedace.h @@ -12,8 +12,6 @@ /* This class implements the SharedAce estimator on two groups. It is a child of the calculator class. */ - -#include #include "calculator.h" /***********************************************************************/ @@ -29,5 +27,5 @@ private: }; /***********************************************************************/ -#endif +#endif diff --git a/sharedchao1.cpp b/sharedchao1.cpp index 0536528..824115f 100644 --- a/sharedchao1.cpp +++ b/sharedchao1.cpp @@ -68,4 +68,5 @@ EstOutput SharedChao1::getValues(SharedRAbundVector* sharedA, SharedRAbundVector } } -/***********************************************************************/ \ No newline at end of file + +/***********************************************************************/ diff --git a/sharedchao1.h b/sharedchao1.h index 86f718f..bba4342 100644 --- a/sharedchao1.h +++ b/sharedchao1.h @@ -13,7 +13,6 @@ It is a child of the calculator class. */ -#include #include "calculator.h" /***********************************************************************/ @@ -27,4 +26,5 @@ public: }; /***********************************************************************/ -#endif \ No newline at end of file + +#endif diff --git a/sharedcommand.h b/sharedcommand.h index 318fe98..b3b3e6f 100644 --- a/sharedcommand.h +++ b/sharedcommand.h @@ -9,7 +9,6 @@ * */ -#include #include #include #include @@ -48,4 +47,4 @@ private: }; -#endif \ No newline at end of file +#endif diff --git a/sharedjabund.cpp b/sharedjabund.cpp index 9cd938e..1c0b6ed 100644 --- a/sharedjabund.cpp +++ b/sharedjabund.cpp @@ -35,4 +35,5 @@ EstOutput SharedJAbund::getValues(SharedRAbundVector* shared1, SharedRAbundVecto exit(1); } } + /***********************************************************************/ diff --git a/sharedjabund.h b/sharedjabund.h index cba2d98..426f204 100644 --- a/sharedjabund.h +++ b/sharedjabund.h @@ -13,7 +13,6 @@ It is a child of the calculator class. */ -#include #include "calculator.h" /***********************************************************************/ @@ -31,4 +30,4 @@ private: /***********************************************************************/ -#endif \ No newline at end of file +#endif diff --git a/sharedjclass.cpp b/sharedjclass.cpp index 52591f5..6557a0f 100644 --- a/sharedjclass.cpp +++ b/sharedjclass.cpp @@ -48,4 +48,5 @@ EstOutput SharedJclass::getValues(SharedRAbundVector* shared1, SharedRAbundVecto exit(1); } } + /***********************************************************************/ diff --git a/sharedjclass.h b/sharedjclass.h index c35abff..301518b 100644 --- a/sharedjclass.h +++ b/sharedjclass.h @@ -12,8 +12,6 @@ /* This class implements the SharedJclass estimator on two groups. It is a child of the calculator class. */ - -#include #include "calculator.h" /***********************************************************************/ @@ -30,4 +28,4 @@ private: /***********************************************************************/ -#endif \ No newline at end of file +#endif diff --git a/sharedjest.cpp b/sharedjest.cpp index ba62e33..5a3b6b8 100644 --- a/sharedjest.cpp +++ b/sharedjest.cpp @@ -54,6 +54,5 @@ EstOutput SharedJest::getValues(SharedRAbundVector* shared1, SharedRAbundVector* exit(1); } } -/***********************************************************************/ - +/***********************************************************************/ diff --git a/sharedjest.h b/sharedjest.h index 19f36f9..405e68c 100644 --- a/sharedjest.h +++ b/sharedjest.h @@ -13,11 +13,8 @@ It is a child of the calculator class. */ -#include #include "calculator.h" - - /***********************************************************************/ class SharedJest : public Calculator { diff --git a/sharedlistvector.h b/sharedlistvector.h index 492997e..f62248d 100644 --- a/sharedlistvector.h +++ b/sharedlistvector.h @@ -10,7 +10,6 @@ * */ -#include #include "datavector.hpp" #include "groupmap.h" #include "globaldata.hpp" @@ -69,4 +68,3 @@ private: }; #endif - diff --git a/sharedordervector.h b/sharedordervector.h index f925964..b1b4a65 100644 --- a/sharedordervector.h +++ b/sharedordervector.h @@ -25,7 +25,6 @@ struct individual { int abundance; }; -#include #include "sabundvector.hpp" #include "rabundvector.hpp" #include "sharedrabundvector.h" diff --git a/sharedrabundvector.h b/sharedrabundvector.h index b69bc30..5547f89 100644 --- a/sharedrabundvector.h +++ b/sharedrabundvector.h @@ -10,7 +10,6 @@ * */ -#include #include "datavector.hpp" #include "sharedordervector.h" #include "sharedsabundvector.h" diff --git a/sharedsabundvector.h b/sharedsabundvector.h index 60b9364..64b8983 100644 --- a/sharedsabundvector.h +++ b/sharedsabundvector.h @@ -11,8 +11,6 @@ * */ - -#include #include "datavector.hpp" #include "rabundvector.hpp" #include "ordervector.hpp" diff --git a/sharedsobs.h b/sharedsobs.h index 3a7037e..a4c5b9b 100644 --- a/sharedsobs.h +++ b/sharedsobs.h @@ -13,7 +13,6 @@ It is a child of the calculator class. */ -#include #include "calculator.h" /***********************************************************************/ diff --git a/sharedsorabund.h b/sharedsorabund.h index 7fd6434..e1ca45a 100644 --- a/sharedsorabund.h +++ b/sharedsorabund.h @@ -13,7 +13,6 @@ It is a child of the calculator class. */ -#include #include "calculator.h" /***********************************************************************/ diff --git a/sharedsorclass.h b/sharedsorclass.h index d8702ff..7a5e282 100644 --- a/sharedsorclass.h +++ b/sharedsorclass.h @@ -13,7 +13,6 @@ It is a child of the calculator class. */ -#include #include "calculator.h" /***********************************************************************/ @@ -29,4 +28,4 @@ private: }; /***********************************************************************/ -#endif \ No newline at end of file +#endif diff --git a/sharedsorest.h b/sharedsorest.h index 1795f66..1589ccc 100644 --- a/sharedsorest.h +++ b/sharedsorest.h @@ -13,7 +13,6 @@ It is a child of the calculator class. */ -#include #include "calculator.h" /***********************************************************************/ diff --git a/sharedthetan.cpp b/sharedthetan.cpp index 3293689..3c97d89 100644 --- a/sharedthetan.cpp +++ b/sharedthetan.cpp @@ -59,4 +59,5 @@ EstOutput SharedThetaN::getValues(SharedRAbundVector* shared1, SharedRAbundVecto exit(1); } } + /***********************************************************************/ diff --git a/sharedthetan.h b/sharedthetan.h index b6f2c87..02b9f87 100644 --- a/sharedthetan.h +++ b/sharedthetan.h @@ -13,7 +13,6 @@ It is a child of the calculator class. */ -#include #include "calculator.h" /***********************************************************************/ @@ -30,4 +29,4 @@ private: /***********************************************************************/ -#endif \ No newline at end of file +#endif diff --git a/sharedthetayc.h b/sharedthetayc.h index 9c69fb1..c3c0000 100644 --- a/sharedthetayc.h +++ b/sharedthetayc.h @@ -13,7 +13,6 @@ It is a child of the calculator class. */ -#include #include "calculator.h" /***********************************************************************/ @@ -29,5 +28,6 @@ private: }; /***********************************************************************/ - #endif + +#endif diff --git a/simpson.h b/simpson.h index 968d5a1..66f4c13 100644 --- a/simpson.h +++ b/simpson.h @@ -13,7 +13,6 @@ It is a child of the calculator class. */ -#include #include "calculator.h" /***********************************************************************/ @@ -28,4 +27,4 @@ public: /***********************************************************************/ -#endif \ No newline at end of file +#endif diff --git a/sobs.h b/sobs.h index 3162f70..c2136b5 100644 --- a/sobs.h +++ b/sobs.h @@ -1,5 +1,6 @@ #ifndef SOBS_H #define SOBS_H + /* * sobs.h * Dotur @@ -13,7 +14,6 @@ It is a child of the calculator class. */ -#include #include "calculator.h" /***********************************************************************/ @@ -32,4 +32,4 @@ public: /***********************************************************************/ -#endif \ No newline at end of file +#endif diff --git a/summarycommand.h b/summarycommand.h index 1f24cd4..c03a6c6 100644 --- a/summarycommand.h +++ b/summarycommand.h @@ -9,7 +9,6 @@ * */ -#include #include #include #include @@ -49,4 +48,4 @@ private: string outputFileName; ofstream outputFileHandle; }; -#endif \ No newline at end of file +#endif diff --git a/summarydisplay.h b/summarydisplay.h index 42e6e19..89e610b 100644 --- a/summarydisplay.h +++ b/summarydisplay.h @@ -32,4 +32,4 @@ private: /***********************************************************************/ -#endif \ No newline at end of file +#endif diff --git a/summarysharedcommand.h b/summarysharedcommand.h index 24ce04b..9ce3b69 100644 --- a/summarysharedcommand.h +++ b/summarysharedcommand.h @@ -9,7 +9,6 @@ * */ -#include #include #include #include @@ -62,4 +61,4 @@ private: }; -#endif \ No newline at end of file +#endif diff --git a/tree.h b/tree.h index 63c7d5f..872283d 100644 --- a/tree.h +++ b/tree.h @@ -44,7 +44,4 @@ class Tree { string filename; }; - - - -#endif \ No newline at end of file +#endif diff --git a/treemap.cpp b/treemap.cpp index 58379da..6fb8536 100644 --- a/treemap.cpp +++ b/treemap.cpp @@ -113,4 +113,4 @@ void TreeMap::print(ostream& output){ } } -/************************************************************/ \ No newline at end of file +/************************************************************/ diff --git a/treemap.h b/treemap.h index 20bbcfe..d9617f5 100644 --- a/treemap.h +++ b/treemap.h @@ -9,7 +9,6 @@ * */ -#include #include #include #include @@ -48,4 +47,4 @@ private: map treemap; //sequence name and groupname }; -#endif \ No newline at end of file +#endif diff --git a/treenode.cpp b/treenode.cpp index 6cd99f9..b31fefd 100644 --- a/treenode.cpp +++ b/treenode.cpp @@ -68,4 +68,4 @@ void Node::printNode(ostream& out) { exit(1); } } -/****************************************************************/ \ No newline at end of file +/****************************************************************/ diff --git a/treenode.h b/treenode.h index d17e7b3..8bd0559 100644 --- a/treenode.h +++ b/treenode.h @@ -53,4 +53,4 @@ class Node { int vectorIndex; }; -#endif \ No newline at end of file +#endif diff --git a/uvest.h b/uvest.h index 7c7ac6f..8906976 100644 --- a/uvest.h +++ b/uvest.h @@ -15,10 +15,11 @@ It is used by sharedJAbund and SharedSorensonAbund. */ using namespace std; -#include #include #include #include +#include + #include "sharedrabundvector.h" typedef vector EstOutput; @@ -30,4 +31,4 @@ class UVEst { }; /***********************************************************************/ -#endif \ No newline at end of file +#endif diff --git a/validcalculator.h b/validcalculator.h index 36a1174..b23c24f 100644 --- a/validcalculator.h +++ b/validcalculator.h @@ -1,3 +1,6 @@ +#ifndef VALIDCALCULATOR_H +#define VALIDCALCULATOR_H + /* * validcalculator.h * Dotur @@ -8,7 +11,6 @@ */ using namespace std; -#include #include #include #include @@ -37,6 +39,6 @@ class ValidCalculators { void initialSharedRarefact(); void initialSummary(); void initialSharedSummary(); - - }; + +#endif diff --git a/validcommands.cpp b/validcommands.cpp index 3a72a2b..734e0ce 100644 --- a/validcommands.cpp +++ b/validcommands.cpp @@ -66,4 +66,4 @@ bool ValidCommands::isValidCommand(string command) { } } -/***********************************************************************/ \ No newline at end of file +/***********************************************************************/ diff --git a/validcommands.h b/validcommands.h index 658d5e4..1955497 100644 --- a/validcommands.h +++ b/validcommands.h @@ -1,3 +1,6 @@ +#ifndef VALIDCOMMANDS_H +#define VALIDCOMMANDS_H + /* * validcommands.h * Dotur @@ -8,7 +11,6 @@ */ using namespace std; -#include #include #include #include @@ -26,4 +28,6 @@ class ValidCommands { private: map commands; -}; \ No newline at end of file +}; + +#endif diff --git a/validparameter.cpp b/validparameter.cpp index 70287c9..1f6e1ef 100644 --- a/validparameter.cpp +++ b/validparameter.cpp @@ -79,4 +79,4 @@ bool ValidParameters::isValidParameter(string parameter) { } } -/***********************************************************************/ \ No newline at end of file +/***********************************************************************/ diff --git a/validparameter.h b/validparameter.h index d3fb2b7..e0477aa 100644 --- a/validparameter.h +++ b/validparameter.h @@ -1,3 +1,6 @@ +#ifndef VALIDPARAMETERS_H +#define VALIDPARAMETERS_H + /* * validparameter.h * Dotur @@ -8,7 +11,6 @@ */ using namespace std; -#include #include #include #include @@ -27,4 +29,6 @@ class ValidParameters { private: map parameters; -}; \ No newline at end of file +}; + +#endif -- 2.39.2