From bfbc55964f1977da72c2cea984288a427d370a59 Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Thu, 19 Feb 2009 14:45:41 +0000
Subject: [PATCH] added mothur.h and fixed includes in many files

---
 Mothur.xcodeproj/project.pbxproj | 12 +++++----
 averagelinkage.cpp               |  2 +-
 calculator.h                     |  9 +------
 cluster.cpp                      |  1 -
 cluster.hpp                      |  4 +--
 clustercommand.h                 |  4 +--
 collectcommand.h                 |  3 ---
 collectorscurvedata.h            |  2 +-
 collectsharedcommand.h           |  4 +--
 command.hpp                      |  4 +--
 commandfactory.cpp               |  2 +-
 commandoptionparser.cpp          |  4 +--
 completelinkage.cpp              |  2 +-
 database.cpp                     |  6 +----
 datavector.hpp                   |  5 +---
 deconvolutecommand.h             |  2 --
 display.h                        |  2 +-
 engine.cpp                       |  7 -----
 engine.hpp                       |  4 +--
 errorchecking.cpp                |  3 +--
 errorchecking.h                  |  3 +--
 fastamap.h                       |  5 +---
 fileoutput.h                     |  5 +---
 getgroupcommand.cpp              |  3 ---
 getgroupcommand.h                |  2 --
 getlabelcommand.cpp              |  3 ---
 getlabelcommand.h                |  2 --
 getlinecommand.cpp               |  4 ---
 getlinecommand.h                 |  2 --
 globaldata.hpp                   | 11 +-------
 groupmap.h                       |  5 +---
 inputdata.h                      |  5 +---
 kmer.cpp                         |  4 +--
 kmerdb.cpp                       |  6 +----
 listvector.cpp                   |  4 +--
 listvector.hpp                   |  2 --
 mothur.cpp                       |  9 ++-----
 mothur.h                         | 44 ++++++++++++++++++++++++++++++++
 nameassignment.cpp               |  4 ---
 nameassignment.hpp               |  3 +--
 nocommand.cpp                    |  2 +-
 ordervector.cpp                  |  3 +--
 parselistcommand.h               |  3 ---
 parsimonycommand.h               |  5 ----
 progress.cpp                     |  4 +--
 progress.hpp                     |  3 ++-
 rabundvector.cpp                 |  3 +--
 raredisplay.h                    |  2 +-
 rarefactcommand.h                |  3 ---
 rarefactioncurvedata.h           |  2 +-
 rarefactsharedcommand.h          |  3 ---
 readdistcommand.h                |  2 --
 readmatrix.cpp                   |  4 ---
 readotucommand.h                 |  2 --
 readsharedcommand.h              |  3 +--
 readtree.h                       |  2 --
 readtreecommand.h                |  2 --
 sabundvector.cpp                 |  2 --
 sequence.cpp                     |  3 ---
 sequence.hpp                     |  2 +-
 shared.h                         |  7 -----
 sharedcommand.h                  |  3 ---
 sharedlistvector.cpp             |  4 +--
 sharedlistvector.h               |  2 --
 sharedordervector.cpp            |  2 +-
 sharedrabundvector.cpp           |  3 ---
 sharedsabundvector.cpp           |  2 --
 singlelinkage.cpp                |  2 +-
 sparsematrix.cpp                 |  4 ---
 sparsematrix.hpp                 |  2 +-
 summarycommand.h                 |  3 ---
 summarydata.h                    |  2 +-
 summarydisplay.h                 |  5 +---
 summarysharedcommand.h           |  4 +--
 treecalculator.h                 |  7 +----
 treemap.h                        |  5 +---
 treenode.h                       |  7 +----
 unifracunweightedcommand.h       |  5 ----
 unifracweightedcommand.h         |  5 ----
 utilities.hpp                    |  9 +------
 uvest.h                          |  6 +----
 validcalculator.h                |  4 +--
 validcommands.h                  |  4 +--
 validparameter.h                 |  4 +--
 84 files changed, 103 insertions(+), 261 deletions(-)
 create mode 100644 mothur.h

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 1047135..ac5bd2d 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -289,6 +289,7 @@
 		37D928520F21331F001D4494 /* validcommands.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validcommands.h; sourceTree = "<group>"; };
 		37D928530F21331F001D4494 /* validparameter.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validparameter.cpp; sourceTree = "<group>"; };
 		37D928540F21331F001D4494 /* validparameter.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validparameter.h; sourceTree = "<group>"; };
+		37E3ED800F4D9D0D00B5DF02 /* mothur.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mothur.h; sourceTree = "<group>"; };
 		37E5F3E10F29FD4200F8D827 /* treenode.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treenode.h; sourceTree = "<group>"; };
 		37E5F3E20F29FD4200F8D827 /* treenode.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treenode.cpp; sourceTree = "<group>"; };
 		37E5F4900F2A3DA800F8D827 /* readtreecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtreecommand.h; sourceTree = "<group>"; };
@@ -358,6 +359,7 @@
 				37D927E90F21331F001D4494 /* kmer.cpp */,
 				37D927EC0F21331F001D4494 /* kmerdb.hpp */,
 				37D927EB0F21331F001D4494 /* kmerdb.cpp */,
+				37E3ED800F4D9D0D00B5DF02 /* mothur.h */,
 				37D927EF0F21331F001D4494 /* mothur.cpp */,
 				37D927F10F21331F001D4494 /* nameassignment.hpp */,
 				37D927F00F21331F001D4494 /* nameassignment.cpp */,
@@ -437,8 +439,8 @@
 				37D928380F21331F001D4494 /* sharedsorclass.cpp */,
 				37D9283B0F21331F001D4494 /* sharedsorest.h */,
 				37D9283A0F21331F001D4494 /* sharedsorest.cpp */,
-				37D9283C0F21331F001D4494 /* sharedthetan.cpp */,
 				37D9283D0F21331F001D4494 /* sharedthetan.h */,
+				37D9283C0F21331F001D4494 /* sharedthetan.cpp */,
 				37D9283F0F21331F001D4494 /* sharedthetayc.h */,
 				37D9283E0F21331F001D4494 /* sharedthetayc.cpp */,
 				37D928410F21331F001D4494 /* simpson.h */,
@@ -466,16 +468,16 @@
 				37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */,
 				37B28F660F27590100808A62 /* deconvolutecommand.h */,
 				37B28F670F27590100808A62 /* deconvolutecommand.cpp */,
-				A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */,
 				A70B53A50F4CD7AD0064797E /* getgroupcommand.h */,
-				A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */,
+				A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */,
 				A70B53A70F4CD7AD0064797E /* getlabelcommand.h */,
-				A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */,
+				A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */,
 				A70B53A90F4CD7AD0064797E /* getlinecommand.h */,
+				A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */,
 				37D927E40F21331F001D4494 /* helpcommand.h */,
 				37D927E30F21331F001D4494 /* helpcommand.cpp */,
-				37D927F20F21331F001D4494 /* nocommand.cpp */,
 				37D927F30F21331F001D4494 /* nocommand.h */,
+				37D927F20F21331F001D4494 /* nocommand.cpp */,
 				37D927FA0F21331F001D4494 /* parselistcommand.h */,
 				37D927F90F21331F001D4494 /* parselistcommand.cpp */,
 				3792946E0F2E191800B9034A /* parsimonycommand.h */,
diff --git a/averagelinkage.cpp b/averagelinkage.cpp
index 43b3e5b..ec619ca 100644
--- a/averagelinkage.cpp
+++ b/averagelinkage.cpp
@@ -4,7 +4,7 @@
 #include "cluster.hpp"
 #include "rabundvector.hpp"
 #include "sparsematrix.hpp"
-#include <exception>
+#include "mothur.h"
 
 /* This class implements the average UPGMA, average neighbor clustering algorithm */
 
diff --git a/calculator.h b/calculator.h
index c119892..8c935af 100644
--- a/calculator.h
+++ b/calculator.h
@@ -3,14 +3,7 @@
 
 using namespace std;
 
-#include <vector>
-#include <cmath>
-#include <iostream>
-#include <fstream>
-#include <math.h>
-#include <string>
-#include <map>
-#include <algorithm>
+#include "mothur.h"
 #include "utilities.hpp"
 #include "sabundvector.hpp"
 #include "sharedsabundvector.h"
diff --git a/cluster.cpp b/cluster.cpp
index 5bd0099..81360b4 100644
--- a/cluster.cpp
+++ b/cluster.cpp
@@ -10,7 +10,6 @@
 #include "cluster.hpp"
 #include "rabundvector.hpp"
 #include "listvector.hpp"
-#include <exception>
 
 /***********************************************************************/
 
diff --git a/cluster.hpp b/cluster.hpp
index a673027..208ccbf 100644
--- a/cluster.hpp
+++ b/cluster.hpp
@@ -3,9 +3,7 @@
 
 using namespace std;
 
-#include <iostream>
-#include <list>
-
+#include "mothur.h"
 #include "utilities.hpp"
 #include "sparsematrix.hpp"
 #include "rabundvector.hpp"
diff --git a/clustercommand.h b/clustercommand.h
index 5dbeb73..ad41a45 100644
--- a/clustercommand.h
+++ b/clustercommand.h
@@ -9,10 +9,8 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include "globaldata.hpp"
 #include "command.hpp"
+#include "globaldata.hpp"
 #include "rabundvector.hpp"
 #include "sabundvector.hpp"
 #include "listvector.hpp"
diff --git a/collectcommand.h b/collectcommand.h
index 64362ef..93b5607 100644
--- a/collectcommand.h
+++ b/collectcommand.h
@@ -9,9 +9,6 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
 #include "command.hpp"
 #include "ordervector.hpp"
 #include "inputdata.h"
diff --git a/collectorscurvedata.h b/collectorscurvedata.h
index 403c23c..af81c39 100644
--- a/collectorscurvedata.h
+++ b/collectorscurvedata.h
@@ -1,7 +1,7 @@
 #ifndef COLLECTORSCURVEDATA_H
 #define COLLECTORSCURVEDATA_H
 
-#include <set>
+#include "mothur.h"
 #include "sabundvector.hpp"
 #include "sharedrabundvector.h"
 #include "display.h"
diff --git a/collectsharedcommand.h b/collectsharedcommand.h
index ffc4278..6e9d5cc 100644
--- a/collectsharedcommand.h
+++ b/collectsharedcommand.h
@@ -9,9 +9,7 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
+
 #include "command.hpp"
 #include "sharedordervector.h"
 #include "sharedlistvector.h"
diff --git a/command.hpp b/command.hpp
index 6d734e0..e418de8 100644
--- a/command.hpp
+++ b/command.hpp
@@ -14,9 +14,7 @@
 
 using namespace std;
 
-#include <iostream>
-#include <fstream>
-
+#include "mothur.h"
 
 class Command {
 	public:
diff --git a/commandfactory.cpp b/commandfactory.cpp
index 840eaac..e05f8df 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -31,7 +31,7 @@
 #include "parsimonycommand.h"
 #include "unifracunweightedcommand.h"
 #include "unifracweightedcommand.h"
-#include <exception>
+#include "mothur.h"
 
 
 /***********************************************************/
diff --git a/commandoptionparser.cpp b/commandoptionparser.cpp
index 893d0d9..dcfcf43 100644
--- a/commandoptionparser.cpp
+++ b/commandoptionparser.cpp
@@ -7,14 +7,12 @@
  *
  */
 
-#include <string>
 
 using namespace std;
 
 #include "globaldata.hpp"
 #include "commandoptionparser.hpp"
-#include <exception>
-#include <iostream>
+#include "mothur.h"
 
 //**********************************************************************************************************************
 //This Function parses through the command line and pulls out the command then sends the options to  the parseGlobalData
diff --git a/completelinkage.cpp b/completelinkage.cpp
index 69b68a0..3c779b9 100644
--- a/completelinkage.cpp
+++ b/completelinkage.cpp
@@ -1,6 +1,6 @@
 
 #include "cluster.hpp"
-#include <exception>
+#include "mothur.h"
 
 /***********************************************************************/
 
diff --git a/database.cpp b/database.cpp
index 153876f..b661d41 100644
--- a/database.cpp
+++ b/database.cpp
@@ -9,11 +9,7 @@
 
 using namespace std;
 
-#include <string>
-#include <vector>
-#include <fstream>
-#include <iostream>
-
+#include "mothur.h"
 #include "sequence.hpp"
 #include "database.hpp"
 
diff --git a/datavector.hpp b/datavector.hpp
index 426a757..73058a9 100644
--- a/datavector.hpp
+++ b/datavector.hpp
@@ -3,10 +3,7 @@
 
 using namespace std;
 
-#include <iostream>
-#include <string>
-#include <vector>
-#include <map>
+#include "mothur.h"
 
 /* This class is parent to listvector, ordervector, rabundvector, sabundvector, sharedordervector, sharedrabundvector, sharedsabundvector. 
 	The child classes all contain OTU information in different forms. */
diff --git a/deconvolutecommand.h b/deconvolutecommand.h
index 2ccc20a..c80bb36 100644
--- a/deconvolutecommand.h
+++ b/deconvolutecommand.h
@@ -9,8 +9,6 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
 #include "command.hpp"
 #include "utilities.hpp"
 #include "fastamap.h"
diff --git a/display.h b/display.h
index f8daae2..17867c8 100644
--- a/display.h
+++ b/display.h
@@ -5,7 +5,7 @@
 #include "sharedsabundvector.h"
 #include "calculator.h"
 #include "fileoutput.h"
-#include <vector>
+
 
 using namespace std;
 
diff --git a/engine.cpp b/engine.cpp
index e251f00..5e56479 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -12,13 +12,6 @@
  */
 using namespace std;
 
-#include <string>
-#include <iostream>
-#include <iomanip>
-#include <fstream>
-#include <vector>
-#include <set>
-#include <exception>
 
 #include "utilities.hpp"
 #include "globaldata.hpp"
diff --git a/engine.hpp b/engine.hpp
index 7990d17..c04cd4e 100644
--- a/engine.hpp
+++ b/engine.hpp
@@ -12,9 +12,7 @@
  
 
 
-#include <vector>
-#include <set>
-#include <string>
+#include "mothur.h"
 
 using namespace std;
 
diff --git a/errorchecking.cpp b/errorchecking.cpp
index 5446572..dccb679 100644
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -8,7 +8,6 @@
  */
 
 #include "errorchecking.h"
-#include <math.h>
 
 /*******************************************************/
 
@@ -65,7 +64,7 @@ void ErrorCheck::refresh() {
 		"summary",            //22
 		"sharedrarefaction",  //23
 		"sharedsummary",      //24
-		"comparegroups",      //25
+		"groups",			  //25
 		"abund",              //26
 		};
 	
diff --git a/errorchecking.h b/errorchecking.h
index 8b3c0ca..8bf6857 100644
--- a/errorchecking.h
+++ b/errorchecking.h
@@ -9,8 +9,7 @@
  *
  */
 
-#include <iostream>
-#include <map>
+#include "mothur.h"
 #include "globaldata.hpp"
 #include "validcommands.h"
 #include "validparameter.h"
diff --git a/fastamap.h b/fastamap.h
index 8ba2fc6..169974b 100644
--- a/fastamap.h
+++ b/fastamap.h
@@ -12,10 +12,7 @@
  
 using namespace std;
  
-#include <iostream>
-#include <fstream>
-#include <string>
-#include <map>
+#include "mothur.h"
 #include "utilities.hpp"
 
 
diff --git a/fileoutput.h b/fileoutput.h
index 3f90cd5..b578421 100644
--- a/fileoutput.h
+++ b/fileoutput.h
@@ -1,10 +1,7 @@
 #ifndef FILEOUTPUT_H
 #define FILEOUTPUT_H
 
-#include <iostream>
-#include <fstream>
-#include <iomanip>
-#include <vector>
+#include "mothur.h"
 #include "utilities.hpp"
 #include "globaldata.hpp"
 
diff --git a/getgroupcommand.cpp b/getgroupcommand.cpp
index 393be4e..59987a3 100644
--- a/getgroupcommand.cpp
+++ b/getgroupcommand.cpp
@@ -10,9 +10,6 @@
 #include "getgroupcommand.h"
 
 
-
-
-
 GetgroupCommand::GetgroupCommand(){
 	try {
 		globaldata = GlobalData::getInstance();
diff --git a/getgroupcommand.h b/getgroupcommand.h
index 00c1b51..b296735 100644
--- a/getgroupcommand.h
+++ b/getgroupcommand.h
@@ -10,8 +10,6 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
 #include "command.hpp"
 #include "readmatrix.hpp"
 
diff --git a/getlabelcommand.cpp b/getlabelcommand.cpp
index baabc21..c5a59ac 100644
--- a/getlabelcommand.cpp
+++ b/getlabelcommand.cpp
@@ -11,9 +11,6 @@
 
 
 
-
-
-
 GetlabelCommand::GetlabelCommand(){
 	try {
 		globaldata = GlobalData::getInstance();
diff --git a/getlabelcommand.h b/getlabelcommand.h
index ae4c4db..d3797ac 100644
--- a/getlabelcommand.h
+++ b/getlabelcommand.h
@@ -10,8 +10,6 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
 #include "command.hpp"
 #include "readmatrix.hpp"
 
diff --git a/getlinecommand.cpp b/getlinecommand.cpp
index 63dde60..a7ca17f 100644
--- a/getlinecommand.cpp
+++ b/getlinecommand.cpp
@@ -10,10 +10,6 @@
 #include "getlinecommand.h"
 
 
-
-
-
-
 GetlineCommand::GetlineCommand(){
 	try {
 		globaldata = GlobalData::getInstance();
diff --git a/getlinecommand.h b/getlinecommand.h
index 295fe99..7953f9f 100644
--- a/getlinecommand.h
+++ b/getlinecommand.h
@@ -10,8 +10,6 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
 #include "command.hpp"
 #include "readmatrix.hpp"
 
diff --git a/globaldata.hpp b/globaldata.hpp
index 31a63b6..1bccc34 100644
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -1,16 +1,7 @@
 #ifndef GLOBALDATA_HPP
 #define GLOBALDATA_HPP
 
-#include <string>
-#include <vector>
-#include <set>
-#include <iostream>
-#include <iomanip>
-#include <map>
-#include <sstream>
-#include <stdexcept>
-#include <exception>
-
+#include "mothur.h"
 #include "groupmap.h"
 #include "treemap.h"
 
diff --git a/groupmap.h b/groupmap.h
index de69ca4..d03880d 100644
--- a/groupmap.h
+++ b/groupmap.h
@@ -9,10 +9,7 @@
  *
  */
 
-#include <map>
-#include <string>
-#include <iostream>
-#include <fstream>
+#include "mothur.h"
 #include "utilities.hpp"
 
 /* This class is a representation of the groupfile.  It is used by all the shared commands to determine what group a 
diff --git a/inputdata.h b/inputdata.h
index b6912b3..1352e94 100644
--- a/inputdata.h
+++ b/inputdata.h
@@ -1,10 +1,7 @@
 #ifndef INPUTDATA_H
 #define INPUTDATA_H
 
-#include <iostream>
-#include <iomanip>
-#include <string>
-#include <fstream>
+#include "mothur.h"
 #include "ordervector.hpp"
 #include "sharedlistvector.h"
 #include "sharedordervector.h"
diff --git a/kmer.cpp b/kmer.cpp
index 2c27833..5f962a6 100644
--- a/kmer.cpp
+++ b/kmer.cpp
@@ -9,9 +9,7 @@
 
 using namespace std;
 
-#include <string>
-#include <vector>
-
+#include "mothur.h"
 #include "kmer.hpp"
 
 /**************************************************************************************************/
diff --git a/kmerdb.cpp b/kmerdb.cpp
index e15bb91..a5094f0 100644
--- a/kmerdb.cpp
+++ b/kmerdb.cpp
@@ -9,11 +9,7 @@
 
 using namespace std;
 
-#include <vector>
-#include <string>
-#include <fstream>
-#include <iostream>
-
+#include "mothur.h"
 #include "sequence.hpp"
 #include "kmer.hpp"
 #include "database.hpp"
diff --git a/listvector.cpp b/listvector.cpp
index 3018efe..9005dc0 100644
--- a/listvector.cpp
+++ b/listvector.cpp
@@ -9,12 +9,10 @@
 
 using namespace std;
 
-#include <map>
-#include <exception>
+
 #include "sabundvector.hpp"
 #include "rabundvector.hpp"
 #include "ordervector.hpp"
-#include "datavector.hpp"
 #include "utilities.hpp"
 #include "listvector.hpp"
 
diff --git a/listvector.hpp b/listvector.hpp
index f4eaca0..801537d 100644
--- a/listvector.hpp
+++ b/listvector.hpp
@@ -2,8 +2,6 @@
 #define LIST_H
 
 #include "datavector.hpp"
-#include <iostream>
-#include <map>
 
 /* This class is a child to datavector.  It represents OTU information at a certain distance. 
 	A list vector can be converted into and ordervector, rabundvector or sabundvector.
diff --git a/mothur.cpp b/mothur.cpp
index 2b3f8f5..3a91aa6 100644
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -6,13 +6,8 @@
  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
  *
  */
-#include <string>
-#include <iostream>
-#include <iomanip>
-#include <fstream>
-#include <sstream>
-#include <exception>
-
+ 
+#include "mothur.h"
 #include "engine.hpp"
 #include "globaldata.hpp"
 
diff --git a/mothur.h b/mothur.h
new file mode 100644
index 0000000..e5c3890
--- /dev/null
+++ b/mothur.h
@@ -0,0 +1,44 @@
+#ifndef MOTHUR_H
+#define MOTHUR_H
+
+using namespace std;
+
+
+/*
+ *  mothur.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 2/19/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+/* This file contains all the standard incudes we use in the project. */
+
+
+//io libraries
+#include <iostream>
+#include <iomanip>
+#include <fstream>
+#include <sstream>
+
+//exception
+#include <stdexcept>
+#include <exception>
+#include <cstdlib> 
+
+
+//containers
+#include <vector>
+#include <set>
+#include <map>
+#include <string>
+#include <list>
+
+//math
+#include <cmath>
+#include <math.h>
+#include <algorithm>
+
+#endif
+
diff --git a/nameassignment.cpp b/nameassignment.cpp
index 1f2feac..cd9ef4e 100644
--- a/nameassignment.cpp
+++ b/nameassignment.cpp
@@ -1,9 +1,5 @@
 using namespace std;
 
-#include <string>
-#include <map>
-#include <exception>
-
 #include "nameassignment.hpp"
 
 //**********************************************************************************************************************
diff --git a/nameassignment.hpp b/nameassignment.hpp
index f3a99fb..3d21e32 100644
--- a/nameassignment.hpp
+++ b/nameassignment.hpp
@@ -3,8 +3,7 @@
 
 using namespace std;
 
-#include <string>
-#include <map>
+#include "mothur.h"
 #include "utilities.hpp"
 #include "listvector.hpp"
 
diff --git a/nocommand.cpp b/nocommand.cpp
index b9cb61a..9cbf3d3 100644
--- a/nocommand.cpp
+++ b/nocommand.cpp
@@ -21,7 +21,7 @@ NoCommand::~NoCommand(){}
 
 int NoCommand::execute(){
 	//Could choose to give more help here?fdsah
-	cout << "Invalid command - choices are read.dist(), read.otu(), read.tree(), cluster(), deconvolute(), collect.single(), collect.shared(), rarefaction.single(), summary.single(), summary.shared(), quit(), help()." << "\n";
+	cout << "Invalid command." << "\n";
 	cout << "For more information on command parameters use the help() command." << "\n";
 	return 0;
 }
diff --git a/ordervector.cpp b/ordervector.cpp
index 8732c8a..333c280 100644
--- a/ordervector.cpp
+++ b/ordervector.cpp
@@ -10,9 +10,8 @@
 using namespace std;
 
 #include "ordervector.hpp"
-#include "datavector.hpp"
 #include "utilities.hpp"
-#include <exception>
+
 
 /***********************************************************************/
 
diff --git a/parselistcommand.h b/parselistcommand.h
index 4358762..bf8ee5d 100644
--- a/parselistcommand.h
+++ b/parselistcommand.h
@@ -9,9 +9,6 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <map>
 #include "command.hpp"
 #include "rabundvector.hpp"
 #include "sharedlistvector.h"
diff --git a/parsimonycommand.h b/parsimonycommand.h
index e854294..bd52fa6 100644
--- a/parsimonycommand.h
+++ b/parsimonycommand.h
@@ -9,11 +9,6 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
-#include <map>
-#include <cmath>
 #include "command.hpp"
 #include "parsimony.h"
 #include "treemap.h"
diff --git a/progress.cpp b/progress.cpp
index 94ad416..eec8f09 100644
--- a/progress.cpp
+++ b/progress.cpp
@@ -7,10 +7,8 @@
  *
  */
 
-#include <iostream>
-#include <string>
+
 #include "progress.hpp"
-#include <exception>
 
 using namespace std;
 
diff --git a/progress.hpp b/progress.hpp
index 82eed70..ae0303c 100644
--- a/progress.hpp
+++ b/progress.hpp
@@ -1,7 +1,8 @@
 #ifndef PROGRESS_H
 #define PROGRESS_H
 
-#include <string>
+#include "mothur.h"
+
 using namespace std;
 
 class Progress {
diff --git a/rabundvector.cpp b/rabundvector.cpp
index fd7f3ac..d6b7d12 100644
--- a/rabundvector.cpp
+++ b/rabundvector.cpp
@@ -8,9 +8,8 @@
  */
 using namespace std;
  
-#include "datavector.hpp"
+
 #include "utilities.hpp"
-#include <exception>
 #include "rabundvector.hpp"
 #include "sabundvector.hpp"
 #include "ordervector.hpp"
diff --git a/raredisplay.h b/raredisplay.h
index ad6a389..50e2121 100644
--- a/raredisplay.h
+++ b/raredisplay.h
@@ -5,7 +5,7 @@
 #include "calculator.h"
 #include "fileoutput.h"
 #include "display.h"
-#include <vector>
+
 
 using namespace std;
 
diff --git a/rarefactcommand.h b/rarefactcommand.h
index 058d7dd..28be17c 100644
--- a/rarefactcommand.h
+++ b/rarefactcommand.h
@@ -9,9 +9,6 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
 #include "command.hpp"
 #include "ordervector.hpp"
 #include "inputdata.h"
diff --git a/rarefactioncurvedata.h b/rarefactioncurvedata.h
index e08f9d7..9d97b80 100644
--- a/rarefactioncurvedata.h
+++ b/rarefactioncurvedata.h
@@ -1,7 +1,7 @@
 #ifndef RAREFACTIONCURVEDATA_H
 #define RAREFACTIONCURVEDATA_H
 
-#include <set>
+#include "mothur.h"
 #include "sabundvector.hpp"
 #include "display.h"
 #include "observable.h"
diff --git a/rarefactsharedcommand.h b/rarefactsharedcommand.h
index a0afb96..54a6a95 100644
--- a/rarefactsharedcommand.h
+++ b/rarefactsharedcommand.h
@@ -9,9 +9,6 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
 #include "command.hpp"
 #include "sharedordervector.h"
 #include "sharedlistvector.h"
diff --git a/readdistcommand.h b/readdistcommand.h
index 4f38d03..bd4a913 100644
--- a/readdistcommand.h
+++ b/readdistcommand.h
@@ -9,8 +9,6 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
 #include "command.hpp"
 #include "readmatrix.hpp"
 
diff --git a/readmatrix.cpp b/readmatrix.cpp
index 72dd799..2d98124 100644
--- a/readmatrix.cpp
+++ b/readmatrix.cpp
@@ -9,15 +9,11 @@
 
 using namespace std;
 
-#include <string>
-#include <map>
 #include "utilities.hpp"
 #include "sparsematrix.hpp"
 #include "progress.hpp"
 #include "listvector.hpp"
 #include "rabundvector.hpp"
-#include <exception>
-
 #include "readmatrix.hpp"
 
 
diff --git a/readotucommand.h b/readotucommand.h
index f00369b..7bd1ead 100644
--- a/readotucommand.h
+++ b/readotucommand.h
@@ -9,8 +9,6 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
 #include "command.hpp"
 #include "readmatrix.hpp"
 #include "inputdata.h"
diff --git a/readsharedcommand.h b/readsharedcommand.h
index 8e7f290..6cb16b3 100644
--- a/readsharedcommand.h
+++ b/readsharedcommand.h
@@ -8,8 +8,7 @@
  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
-#include <iostream>
-#include <fstream>
+
 #include "command.hpp"
 #include "readmatrix.hpp"
 #include "inputdata.h"
diff --git a/readtree.h b/readtree.h
index 653a853..bee4d94 100644
--- a/readtree.h
+++ b/readtree.h
@@ -11,8 +11,6 @@
 
 using namespace std;
 
-#include <string>
-#include <iostream>
 #include "globaldata.hpp"
 #include "utilities.hpp"
 #include "tree.h"
diff --git a/readtreecommand.h b/readtreecommand.h
index e9424b2..2ee72a1 100644
--- a/readtreecommand.h
+++ b/readtreecommand.h
@@ -10,8 +10,6 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
 #include "command.hpp"
 #include "readtree.h"
 #include "treemap.h"
diff --git a/sabundvector.cpp b/sabundvector.cpp
index 4a926b2..a785619 100644
--- a/sabundvector.cpp
+++ b/sabundvector.cpp
@@ -9,9 +9,7 @@
 using namespace std;
 
 #include "sabundvector.hpp"
-#include "datavector.hpp"
 #include "utilities.hpp"
-#include <exception>
 
 /***********************************************************************/
 
diff --git a/sequence.cpp b/sequence.cpp
index 3f64db5..7bc8b05 100644
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -9,9 +9,6 @@
 
 using namespace std;
 
-#include <string>
-#include <fstream>
-
 #include "sequence.hpp"
 
 //********************************************************************************************************************
diff --git a/sequence.hpp b/sequence.hpp
index 32063ef..e094fb5 100644
--- a/sequence.hpp
+++ b/sequence.hpp
@@ -11,7 +11,7 @@
  */
 using namespace std;
 
-#include <string>
+#include "mothur.h"
 
 
 /**************************************************************************************************/
diff --git a/shared.h b/shared.h
index 8625d8b..fd9179e 100644
--- a/shared.h
+++ b/shared.h
@@ -12,13 +12,6 @@
  
 using namespace std;
 
-#include <iostream>
-#include <fstream>
-#include <iomanip>
-#include <vector>
-#include <string>
-#include <sstream>
-#include <map>
 #include "sharedrabundvector.h"
 #include "sharedlistvector.h"
 #include "globaldata.hpp"
diff --git a/sharedcommand.h b/sharedcommand.h
index b3b3e6f..20e2ddb 100644
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -9,9 +9,6 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <map>
 #include "command.hpp"
 #include "sharedlistvector.h"
 #include "inputdata.h"
diff --git a/sharedlistvector.cpp b/sharedlistvector.cpp
index 81dd728..00aef79 100644
--- a/sharedlistvector.cpp
+++ b/sharedlistvector.cpp
@@ -10,12 +10,10 @@
 
 using namespace std;
 
-#include <map>
-#include <exception>
+
 #include "sabundvector.hpp"
 #include "rabundvector.hpp"
 #include "ordervector.hpp"
-#include "datavector.hpp"
 #include "utilities.hpp"
 #include "sharedlistvector.h"
 #include "sharedordervector.h"
diff --git a/sharedlistvector.h b/sharedlistvector.h
index f62248d..53fe1b1 100644
--- a/sharedlistvector.h
+++ b/sharedlistvector.h
@@ -15,8 +15,6 @@
 #include "globaldata.hpp"
 #include "sharedrabundvector.h"
 #include "sharedsabundvector.h"
-#include <iostream>
-#include <map>
 
 /* This class is a child to datavector.  It represents OTU information at a certain distance. 
 	A sharedlistvector can be converted into a sharedordervector, sharedrabundvector or sharedsabundvectorand 
diff --git a/sharedordervector.cpp b/sharedordervector.cpp
index 6aeb4ce..a1eff83 100644
--- a/sharedordervector.cpp
+++ b/sharedordervector.cpp
@@ -12,7 +12,7 @@ using namespace std;
 
 #include "sharedordervector.h"
 #include "utilities.hpp"
-#include <exception>
+
 
 /***********************************************************************/
 
diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp
index a2b7936..b35b06d 100644
--- a/sharedrabundvector.cpp
+++ b/sharedrabundvector.cpp
@@ -11,10 +11,7 @@
 using namespace std;
 
 #include "sharedrabundvector.h" 
-#include "datavector.hpp"
 #include "utilities.hpp"
-#include <exception>
-#include "sharedrabundvector.h"
 #include "sabundvector.hpp"
 #include "ordervector.hpp"
 
diff --git a/sharedsabundvector.cpp b/sharedsabundvector.cpp
index 8b6f8fa..7babf1c 100644
--- a/sharedsabundvector.cpp
+++ b/sharedsabundvector.cpp
@@ -9,9 +9,7 @@
 
 #include "sharedsabundvector.h"
 #include "sabundvector.hpp"
-#include "datavector.hpp"
 #include "utilities.hpp"
-#include <exception>
 
 using namespace std;
 
diff --git a/singlelinkage.cpp b/singlelinkage.cpp
index 3c26977..1b0aed2 100644
--- a/singlelinkage.cpp
+++ b/singlelinkage.cpp
@@ -1,6 +1,6 @@
 
 #include "cluster.hpp"
-#include <exception>
+
 
 /***********************************************************************/
 
diff --git a/sparsematrix.cpp b/sparsematrix.cpp
index 6eaf3ec..0b210c6 100644
--- a/sparsematrix.cpp
+++ b/sparsematrix.cpp
@@ -1,10 +1,6 @@
-#include <vector>
-#include <iostream>
-#include <list>
 #include "utilities.hpp"
 #include "sparsematrix.hpp"
 #include "listvector.hpp"
-#include <exception>
 
 using namespace std;
 
diff --git a/sparsematrix.hpp b/sparsematrix.hpp
index 58aca0d..bcd7899 100644
--- a/sparsematrix.hpp
+++ b/sparsematrix.hpp
@@ -2,7 +2,7 @@
 #define SPARSEMATRIX_H
 
 #include "utilities.hpp"
-#include <list>
+#include "mothur.h"
 
 
 class ListVector;
diff --git a/summarycommand.h b/summarycommand.h
index 4c5144c..4b7e161 100644
--- a/summarycommand.h
+++ b/summarycommand.h
@@ -9,9 +9,6 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
 #include "command.hpp"
 #include "sabundvector.hpp"
 #include "inputdata.h"
diff --git a/summarydata.h b/summarydata.h
index 8a4d2da..9afe0e4 100644
--- a/summarydata.h
+++ b/summarydata.h
@@ -1,7 +1,7 @@
 #ifndef SUMMARYDATA_H
 #define SUMMARYDATA_H
 
-#include <set>
+#include "mothur.h"
 #include "sabundvector.hpp"
 #include "display.h"
 #include "observable.h"
diff --git a/summarydisplay.h b/summarydisplay.h
index 89e610b..90d8960 100644
--- a/summarydisplay.h
+++ b/summarydisplay.h
@@ -1,10 +1,7 @@
 #ifndef SUMMARY_H
 #define SUMMARY_H
 
-#include <iostream>
-#include <iomanip>
-#include <fstream>
-#include <string>
+#include "mothur.h"
 #include "display.h"
 
 
diff --git a/summarysharedcommand.h b/summarysharedcommand.h
index c531b8a..0e3428d 100644
--- a/summarysharedcommand.h
+++ b/summarysharedcommand.h
@@ -9,9 +9,7 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
+
 #include "command.hpp"
 #include "sharedrabundvector.h"
 #include "inputdata.h"
diff --git a/treecalculator.h b/treecalculator.h
index 0bc41d9..133330c 100644
--- a/treecalculator.h
+++ b/treecalculator.h
@@ -12,12 +12,7 @@
 
 using namespace std;
 
-#include <vector>
-#include <cmath>
-#include <math.h>
-#include <string>
-#include <map>
-#include <algorithm>
+#include "mothur.h"
 #include "utilities.hpp"
 #include "tree.h"
 
diff --git a/treemap.h b/treemap.h
index 60fb924..0dc74ee 100644
--- a/treemap.h
+++ b/treemap.h
@@ -9,10 +9,7 @@
  *
  */
 
-#include <map>
-#include <string>
-#include <iostream>
-#include <fstream>
+#include "mothur.h"
 #include "utilities.hpp"
 
 /* This class is used by the read.tree command to build the tree container. */
diff --git a/treenode.h b/treenode.h
index 7995956..7353248 100644
--- a/treenode.h
+++ b/treenode.h
@@ -12,12 +12,7 @@
 
 using namespace std;
 
-#include <string>
-#include <iostream>
-#include <fstream>
-#include <iomanip>
-#include <vector>
-#include <map>
+#include "mothur.h"
 
 /* This class represents a node on a tree. */
 
diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index ecf78f5..9fe1642 100644
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -10,11 +10,6 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
-#include <map>
-#include <cmath>
 #include "command.hpp"
 #include "unweighted.h"
 #include "treemap.h"
diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index 45d3c7c..1b8b12b 100644
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -10,11 +10,6 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
-#include <map>
-#include <cmath>
 #include "command.hpp"
 #include "weighted.h"
 #include "treemap.h"
diff --git a/utilities.hpp b/utilities.hpp
index 8f5009f..cc6c490 100644
--- a/utilities.hpp
+++ b/utilities.hpp
@@ -3,14 +3,7 @@
 
 using namespace std;
 
-#include <iostream>
-#include <iomanip>
-#include <fstream>
-#include <sstream>
-#include <cmath>
-#include <vector>
-#include <stdexcept>
-#include <set>
+#include "mothur.h"
 
 typedef unsigned long long ull;
 
diff --git a/uvest.h b/uvest.h
index 8906976..3eea438 100644
--- a/uvest.h
+++ b/uvest.h
@@ -15,11 +15,7 @@ It is used by sharedJAbund and SharedSorensonAbund. */
  
 using namespace std;
 
-#include <vector>
-#include <iostream>
-#include <fstream>
-#include <cmath>
-
+#include "mothur.h"
 #include "sharedrabundvector.h"
 
 typedef vector<double> EstOutput;
diff --git a/validcalculator.h b/validcalculator.h
index 9d4cef9..1534432 100644
--- a/validcalculator.h
+++ b/validcalculator.h
@@ -11,9 +11,7 @@
  */
 using namespace std;
 
-#include <string>
-#include <iostream>
-#include <map>
+#include "mothur.h"
 
 //This class contains a list of all valid calculators in Mothur.  
 //It has a function which will tell you if your calculator is valid for the given parameter.
diff --git a/validcommands.h b/validcommands.h
index 1b83b9b..e59316f 100644
--- a/validcommands.h
+++ b/validcommands.h
@@ -11,9 +11,7 @@
  */
 using namespace std;
 
-#include <string>
-#include <iostream>
-#include <map>
+#include "mothur.h"
 
 //This class contains a list of all valid commands in Mothur.  
 //It has a function which will tell you if your command is valid.
diff --git a/validparameter.h b/validparameter.h
index a4dd516..c03c034 100644
--- a/validparameter.h
+++ b/validparameter.h
@@ -11,9 +11,7 @@
  */
 using namespace std;
 
-#include <iostream>
-#include <string>
-#include <map>
+#include "mothur.h"
 
 //This class contains a list of all valid parameters in Mothur.  
 //It has a function which will tell you if your parameter is valid.
-- 
2.39.2