added mothur.h and fixed includes in many files

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 1047135f48e6f2f3f23bba3eae5e4b5ff6eb05d4..ac5bd2d2929620357dbc507c49c1d227573b9dfd 100644 (file)
--- 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 43b3e5b535675d433e88cc5d3b9d10f038be7256..ec619cae3a5e373d7cd482c4bc25667e552a6687 100644 (file)
--- 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 c11989289197661f164564024cdc8d7f0eafc768..8c935af9cac59cf8be4723eb5d1bbc3aac37cfab 100644 (file)
--- 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 5bd009989aec5b42f6be23c00eef35fc51157d66..81360b4f945ac4c011f6ed5f3a0686e7b04b6516 100644 (file)
--- 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 a6730275c92b35b15c9a2a091894086b0cf60a45..208ccbfe1ba45ba70d152ba4c5ff12b50182d4dc 100644 (file)
--- 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 5dbeb73e2a5e133669f1d5ffd0d61a85731ed9a5..ad41a4506e926dc646066964ccdd11c98fc48826 100644 (file)
--- 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 64362ef61cdfdc18da9cb5b170a88ff9713d93c9..93b56073dee7955dc60d410347da82b4bf6d2dc2 100644 (file)
--- 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 403c23c70950865cf02c4796aaf71e4da4966b3b..af81c39269b46aa69cf4083f22807e0815fdb449 100644 (file)
--- 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 ffc4278f3b690a4b2f4a0f5bf637146bee65ca3b..6e9d5cc3f498c96574d93321ecf2823edb0fa004 100644 (file)
--- 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 6d734e00b5dd1ef8cc3a4239a8c0b10ad18f8acc..e418de83e772dd824d83a6989ba51e1a92b60e06 100644 (file)
--- 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 840eaaccc82c392de096729a5db32d7c72cdf08a..e05f8dffa1cb5d1c13716152773793fc509ad96c 100644 (file)
--- 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 893d0d9cc0b043b5ccd6f37b45add01445e27152..dcfcf435cbb5d896cc41f9e20c07e54ca44c6a4d 100644 (file)
--- 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 69b68a061fb0d8ccb7cf58ec8ca27af1e3f11f27..3c779b9344866cc4729e460cb3d7b6e6c68dc682 100644 (file)
--- 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 153876f9e147e038a72074b490c8028033a308ce..b661d41402fc715b8073266d11c23224ad65a781 100644 (file)
--- 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 426a75728cf615bc9baf8e257b3dcb8bea0ec15c..73058a992a53e3da313cae4ca595c77797058e94 100644 (file)
--- 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 2ccc20a633b882475099132269eb0142cf55adcf..c80bb360533a8b08e819d820d72f431f722c9e1b 100644 (file)
--- 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 f8daae26eff95bf40bab64e26455281244cd8729..17867c8197575725d9361daf514c5431039f7429 100644 (file)
--- 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 e251f0031d5ffa2bc9685702ef76ae0489af8449..5e56479f2851f89e324f8c62dc54250324da7d66 100644 (file)
--- 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 7990d1790586b5980fb31ada11f85b540572858f..c04cd4ed69306116f7eb72e64bf5fd2e01d92015 100644 (file)
--- 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 54465729f5e04c36c6a0e2bed16064a5ea32b9a2..dccb679cd6638d6de391154b328301e4f7c17df9 100644 (file)
--- 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 8b3c0cafb0e6b787d5d408083828ab39757420bc..8bf68578a44330ce9c3c0c595c0200486b5b41c4 100644 (file)
--- 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 8ba2fc6ec3e9507a018084080d6dd6275b1203d1..169974b27f107a00ba2a0f7738d7551160a37c62 100644 (file)
--- 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 3f90cd59a8225f94d94aee928fd5c24fa289e108..b5784210d0b734ccdf34dabf1b98259f2ec73499 100644 (file)
--- 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 393be4e64a4fbef95244f18ca377b6098035b45e..59987a33e6f169c589f608168a12d9e11747c2b7 100644 (file)
--- 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 00c1b51936009de1fb24d5fa227cc40c3c5325dd..b29673529cca9387ed4a5916166180e0a9966ead 100644 (file)
--- 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 baabc21acbd2182398f85a2bcb47cf18f1c757bb..c5a59acae780cc5b404fd7236712de164b3adc88 100644 (file)
--- 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 ae4c4db2409cfd96d8e044531605d5176329f3ff..d3797acc32e2accb8a3cda94660a40019c970bf4 100644 (file)
--- 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 63dde60900ec5220817283a24981fc9db81b87f7..a7ca17fc34297c58869f0d578f52ec70e1fc3367 100644 (file)
--- 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 295fe9944e86dee8298e85a7f818e5656c9ee08d..7953f9f945b61efb8bc23154ce84130f536d3bb1 100644 (file)
--- 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 31a63b67adad73bd7e46487a4849cee6135f6ede..1bccc34f58fa6fcaf136bab32cd74f5093babda7 100644 (file)
--- 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 de69ca4d94c5e98342c666c7de0a768f61a3b267..d03880d9814fac255613daa381f6d63b4ccfba4a 100644 (file)
--- 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 b6912b3c8bef9803dae6aad648f97a80b3844b5b..1352e94c760469b071a3b56363c932f3be901004 100644 (file)
--- 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 2c2783384c3849c2941509547d2a67b83dee6f9f..5f962a63412ea042904a4ce8397a6ae4da9d3ad6 100644 (file)
--- 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 e15bb91412db24d7b35b9e21cbee671ad1c0231e..a5094f0a862b057c571798180b6c064dc77509bf 100644 (file)
--- 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 3018efed7b94dc4f57b65e5e2b7eaa17f870a526..9005dc0ad450161c580a2ed2dc5074afb8e53912 100644 (file)
--- 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 f4eaca031c8daefa875788bc03f2288973deedf0..801537dac1b76d262fd59161f793c959b78bf73a 100644 (file)
--- 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 2b3f8f5146d7b1c47e8af3845ec9dfdba58fb355..3a91aa6e595393111416cf04b367af0a8ca38e6f 100644 (file)
--- 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 (file)
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 1f2feacff2ebd5eca6d137b23c12cfc416521def..cd9ef4e0381a0a8ec384482b26d1966bb3388763 100644 (file)
--- 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 f3a99fbd3471193d963c5709a593b3e5e18265b7..3d21e322542b29ff0502987444de77f44045f73d 100644 (file)
--- 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 b9cb61a7c6ea3cacbf8f9fd64d3041ffd2c7ec3b..9cbf3d3a59ea69365f1c0543b272149512687332 100644 (file)
--- 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 8732c8a614eed4ce29d882f0abeea13693d81340..333c280278d3cfa97d2a39373932018ba1d4b918 100644 (file)
--- 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 4358762df8da87ad8474e65940c85ed002b52be9..bf8ee5daf24a014728b7ed12698ca744d56d1cd6 100644 (file)
--- 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 e854294834af55cb0cbe97ec035a0e01f78b66a3..bd52fa6a74b66a0700316ebb069519582d0b8733 100644 (file)
--- 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 94ad41607064445a2307e5fcd2298403de8424a5..eec8f09c150efbd947511b898751b87e06d4d68f 100644 (file)
--- 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 82eed70745bc79b7c9fd60b1b6fd5db883e782d4..ae0303cbfeeef2d49c6b6ce5af63d4e5b20f7d70 100644 (file)
--- 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 fd7f3acecf930dbb39c822748c34c7420da19826..d6b7d1225691e9287c94679317fa2ece34caf158 100644 (file)
--- 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 ad6a389c7cf980ee2e1b2912ab8716ccd8a420c7..50e212168893a17cd3f017d2081d3c9e3a43b925 100644 (file)
--- 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 058d7dd2b6e0c0513b0d5c9697c29c68a2da61a3..28be17cf995f18ede3f851579b619862d0c82551 100644 (file)
--- 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 e08f9d769af5aeed6a1a09d275ff9b6643834d84..9d97b809f683125ccc78740197f303f94c3fcf5c 100644 (file)
--- 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 a0afb9607184e4d6e522fe92003047616e07c968..54a6a95024d0fd97f279be2e50f3e31906f308a4 100644 (file)
--- 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 4f38d034f1f14e320da5495ac79a04d4deff16b3..bd4a913d61fb22799c682387b73bd38440b10af0 100644 (file)
--- 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 72dd799ec6d2e419dd843db6288de313fa0b4078..2d981243518004bccb81a0779762b824cf20f4c7 100644 (file)
--- 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 f00369ba8f4116db8d8e5dee015f60fa52f2a432..7bd1ead9dfa9e6cd62d051aa337697350703d9c3 100644 (file)
--- 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 8e7f2903f1f1be4b3f3c0519d3890d9ce04248d3..6cb16b3e4978fd3e8fc88d6efcb892b38769db5c 100644 (file)
--- 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 653a853c5f300de0886205217a6b8d99682627b6..bee4d94a683966e76922269326728ca2e71bd72f 100644 (file)
--- 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 e9424b2be6d534c61dca64195e2272d7782e0aa4..2ee72a15e591374d1df21a4aed7ff2f6a0457cde 100644 (file)
--- 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 4a926b26f17a7002217240156fdf9ae8e936b41f..a7856193a5777d6e3c1cce515549eea3ff325e01 100644 (file)
--- 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 3f64db5fe5e7ec7b01bd4d8b413585580d766cc8..7bc8b051f2f7465ee0dd7c030ffd31ca0569ac2c 100644 (file)
--- 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 32063ef6f3daca1f4586abda0d02497da263933f..e094fb520f7ad26c96cbcfa7226e194bd883f690 100644 (file)
--- 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 8625d8b0f4f370c72f4ec2e8961cd85b6c079888..fd9179ebce0ed7a7b27cd47eb68ac95c06c3dfe8 100644 (file)
--- 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 b3b3e6f5d0381d2354d8113012b13251cdbec7e7..20e2ddb3981df57f471970da64e3631814a6c170 100644 (file)
--- 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 81dd7281893a36667f4314f268fe9571c6bade61..00aef79584951ca468249648bd574ad1c7d42af0 100644 (file)
--- 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 f62248db77da9895e25fcb57f687fcf24922b47d..53fe1b1edd280bd6184766cbdf1d67cc2778cf91 100644 (file)
--- 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 6aeb4ce5ab19a655c832343cb601c715777c2534..a1eff83424b987956f9b9637b19692e883f5dce2 100644 (file)
--- 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 a2b79362e273d3dd8168fb51231b66d381254f34..b35b06d05813f3819cefc2919f5fbb18b4b8c2af 100644 (file)
--- 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 8b6f8faa8695b8acb4a36730519ea6e751df8fb3..7babf1c1f519dc28aa45fab6ec7c378f217499db 100644 (file)
--- 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 3c2697714f4e252a7e2aa0ee06002ba4a8a6fa46..1b0aed227754118eeef8c40c7482642c8778c25c 100644 (file)
--- a/singlelinkage.cpp
+++ b/singlelinkage.cpp
@@ -1,6 +1,6 @@
 
 #include "cluster.hpp"
-#include <exception>
+
 
 /***********************************************************************/
 

diff --git a/sparsematrix.cpp b/sparsematrix.cpp
index 6eaf3ec7d384786fb38ec98669c9db4612593000..0b210c66565324ea85e8fcb4b4dd45634199573e 100644 (file)
--- 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 58aca0d9f2f46900df040c758d1d40747fbcb8bf..bcd78997bc3e2450da6373cc3bb760effdbeb4e1 100644 (file)
--- 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 4c5144c3d2213808ea416f3bf15d95566c6fa21b..4b7e1616e18a99785505a6cbe1c196ce76e2cc99 100644 (file)
--- 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 8a4d2dac76d4a885d17dd0c04195d650bfc4a555..9afe0e405fe994de95008249bf6dc4ae7fbe7f1e 100644 (file)
--- 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 89e610b741128a7607ee50a64d57b9b3089e6b44..90d8960abeeb892f50e259cc3c93df24190a5286 100644 (file)
--- 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 c531b8aafafc03632db7e3e7f52c48a29cdca83c..0e3428d35721d19573153f04a4e19cd693cca6f3 100644 (file)
--- 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 0bc41d9a2bc27db88a40c03bd40278692de88366..133330c46d1e0a75529eeb54aa577c9777f8c180 100644 (file)
--- 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 60fb924278c8df36a405ca363c2584d5ae2fa42a..0dc74eec2fad5ebc157b4fd12e63a7b8b37c967a 100644 (file)
--- 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 799595646268d40dbf64bb118774931ea4ae1098..73532483e96a0e8ea495b983c595435dc9e04ea8 100644 (file)
--- 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 ecf78f58a981e1f95602ed4e10973bcf7695cf14..9fe164298b0c9191674a01b4a4fd72fc4fed37ae 100644 (file)
--- 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 45d3c7cec25d4d80448d32beeaa212a92295d366..1b8b12bf789da9892a78017e7f888e0ad54ace01 100644 (file)
--- 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 8f5009ffc4f0306a5da950e75a541aaa56cfb572..cc6c4900d459828e5fbd2a9336754e589e160266 100644 (file)
--- 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 8906976faa784ca5a124cc402546f34611d11d00..3eea438a0e1ff6d6a1444785a30765a18b3fb71c 100644 (file)
--- 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 9d4cef9337bc3f693b0b1baf5b4e78304e078b57..1534432799d2dfe8a9ef1e52fefe80d9096488dc 100644 (file)
--- 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 1b83b9bf4bab5060e35839b254bb59d45b3ef39e..e59316fca472b419734c0c1e65036b3d2b684b66 100644 (file)
--- 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 a4dd51675445db321b6babad8a51048a11432114..c03c034f41b6308b4945753147abda65cddf48d7 100644 (file)
--- 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.