When Pat tried to compile mothur in Ubuntu linux, there were a number of minor proble...

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 0a3c22cd4788a1b5fa21192c64aa5971a7cbcaff..e773981a535e6c8b4d5332e1ce6a87266f1618c4 100644 (file)
--- 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 = "<group>"; };
                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 = "<group>"; };
 /* 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 19188fa3d2269b0bfc6e03ecc44e25d8887910a6..4c4a69de67c1b4ccccf9aa0d4adc33927b2fd6c2 100644 (file)
--- 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 <Carbon/Carbon.h>
 #include "calculator.h"
 
 /***********************************************************************/

diff --git a/bootstrap.h b/bootstrap.h
index 71d2c2602c0980e2b8071bc86b4c79deff9a0200..7c72ca2222eb47d458cb4780c0006faa37a3135a 100644 (file)
--- 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 <Carbon/Carbon.h>
 #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 3a7cfc75eb6e69de6ab072bf363c661013a084c2..548e1a7b3694fe992bc5490999239b3b03cb2975 100644 (file)
--- a/chao1.h
+++ b/chao1.h
@@ -9,7 +9,6 @@
  *
  */
 
-#include <Carbon/Carbon.h>
 #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 1487b3e8985420b096959fdb2737b8ce9f86e7c5..5dbeb73e2a5e133669f1d5ffd0d61a85731ed9a5 100644 (file)
--- a/clustercommand.h
+++ b/clustercommand.h
@@ -9,7 +9,6 @@
  *
  */
 
-#include <Carbon/Carbon.h>
 #include <iostream>
 #include <fstream>
 #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 7f589ce692eab1297cbc059563a5aa5a6a17e9e7..0a922180fe566f0ec7b1f7cf56c2f293f7484125 100644 (file)
--- 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 633f3459f178faeca29f7ba41cb973975482f1d6..b92b35034466d1dd61f29a04d478d620c8bc4ef2 100644 (file)
--- a/collectcommand.h
+++ b/collectcommand.h
@@ -9,7 +9,6 @@
  *
  */
 
-#include <Carbon/Carbon.h>
 #include <iostream>
 #include <fstream>
 #include <vector>
@@ -55,4 +54,4 @@ private:
 
 };
 
-#endif
\ No newline at end of file
+#endif

diff --git a/collectdisplay.h b/collectdisplay.h
index 71275737d24a437f09a97eefa528e7f30ed4a134..367a188dfb8de90c2e464cb70cc4a7b1b826ccfe 100644 (file)
--- 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 e6f62785e221e1321aa21305f0c1b142e4e460e0..403c23c70950865cf02c4796aaf71e4da4966b3b 100644 (file)
--- a/collectorscurvedata.h
+++ b/collectorscurvedata.h
@@ -3,7 +3,7 @@
 
 #include <set>
 #include "sabundvector.hpp"
-#include "sharedRAbundvector.h"
+#include "sharedrabundvector.h"
 #include "display.h"
 #include "observable.h"
 

diff --git a/collectsharedcommand.h b/collectsharedcommand.h
index 3737c11196c48cd7fba5179ee311264f22b0e6ba..6a8f96f1c9115548cc6dca8f7ff13835468ec441 100644 (file)
--- a/collectsharedcommand.h
+++ b/collectsharedcommand.h
@@ -9,7 +9,6 @@
  *
  */
 
-#include <Carbon/Carbon.h>
 #include <iostream>
 #include <fstream>
 #include <vector>
@@ -57,4 +56,4 @@ private:
 
 };
 
-#endif
\ No newline at end of file
+#endif

diff --git a/commandfactory.cpp b/commandfactory.cpp
index ed6aebe7cadcf302c180a553ca5f586486371874..0a065cdf36524ca775649cf2f3e863c02839be38 100644 (file)
--- 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 6b05704c693ec902f5ed4bae6e79233e99f5b1cd..b9b208493f2f6fea9a35055c448b65973ddc6a46 100644 (file)
--- 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 e526e56c72465a33081aae06f97c13fa58abfc6e..f8daae26eff95bf40bab64e26455281244cd8729 100644 (file)
--- 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 e1bc23dfe4e800d74c9116b083b4eecf910e9e5b..1ca98b021214e624215ec897a549e0f14ed47ca3 100644 (file)
--- 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 756f676d5b3363887ebf553c956e194420c097d6..d1e2f82451cc3f5d5e4be6d7496894d6b884e9cc 100644 (file)
--- a/errorchecking.h
+++ b/errorchecking.h
@@ -9,7 +9,6 @@
  *
  */
 
-#include <Carbon/Carbon.h>
 #include <iostream>
 #include <map>
 #include "globaldata.hpp"
@@ -44,4 +43,4 @@ class ErrorCheck {
                vector<string> singleEsimators, sharedEstimators, rareEstimators, summaryEstimators, sharedRareEstimators;
                
 };
-#endif
\ No newline at end of file
+#endif

diff --git a/fastamap.h b/fastamap.h
index 9eab85353063cc434d765719c937e82920e60f4a..864a2d03951a9892919dfbdc8641a156e4ef5134 100644 (file)
--- a/fastamap.h
+++ b/fastamap.h
@@ -51,4 +51,4 @@ private:
        map<string, group>::iterator it;
 };
 
-#endif
\ No newline at end of file
+#endif

diff --git a/fileoutput.cpp b/fileoutput.cpp
index c8df770c8054b42d1bdcf7c654700a284ee2aa8f..2f7639fbbcfec3233f5388e66e2e34637e4d90fe 100644 (file)
--- 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 b7837d2277ed89d17b54d52ea180ac095856ba34..3f90cd59a8225f94d94aee928fd5c24fa289e108 100644 (file)
--- a/fileoutput.h
+++ b/fileoutput.h
@@ -107,4 +107,3 @@ private:
 
 
 #endif
-

diff --git a/groupmap.h b/groupmap.h
index 263fc845b00f535d6d5db76e79d07470851b4481..a3b923cd4da60ce601c58d1553e2a95f6b9f4ab9 100644 (file)
--- a/groupmap.h
+++ b/groupmap.h
@@ -9,7 +9,6 @@
  *
  */
 
-#include <Carbon/Carbon.h>
 #include <map>
 #include <string>
 #include <iostream>
@@ -37,4 +36,4 @@ private:
        map<string, string> groupmap; //sequence name and groupname
 };
 
-#endif
\ No newline at end of file
+#endif

diff --git a/helpcommand.h b/helpcommand.h
index 4ea46280c64f3b527b9b58173e9ff00ceaf4a6e9..6d95d86293c8660d3d514ac5895d4b57dccd68d2 100644 (file)
--- a/helpcommand.h
+++ b/helpcommand.h
@@ -11,7 +11,6 @@
 
 /* This class is designed to aid the user in running mothur. */
 
-#include <Carbon/Carbon.h>
 #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 6d814c584a6c3abd332034c17bfa3b8616db9c0c..abb343e98eb02677006af4316fbc10e4693f3a2a 100644 (file)
--- 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 45f9287b124498ad7bd798b948d88eac71befff0..ec920e0a184231c77dda1cc4ca1626fe42a07f8d 100644 (file)
--- a/jackknife.h
+++ b/jackknife.h
@@ -10,7 +10,6 @@
  *
  */
 
-#include <Carbon/Carbon.h>
 #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 e195f4e089f48afd94d3027470b8bf42b1e165a3..f4eaca031c8daefa875788bc03f2288973deedf0 100644 (file)
--- a/listvector.hpp
+++ b/listvector.hpp
@@ -1,7 +1,6 @@
 #ifndef LIST_H
 #define LIST_H
 
-#include <Carbon/Carbon.h>
 #include "datavector.hpp"
 #include <iostream>
 #include <map>

diff --git a/nocommand.h b/nocommand.h
index ce202e4f2c12b6844b39b0b60ff5bf747093077a..b529392a890483eeb61b5346f6a59ef91add7d9a 100644 (file)
--- a/nocommand.h
+++ b/nocommand.h
@@ -11,7 +11,6 @@
 
 /* This command is run if the user enters an invalid command. */
 
-#include <Carbon/Carbon.h>
 #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 4a633b30526bbe26812bd777dd05e5be74e08f60..9272409a995b3ddff581d796002b44dbdfeaf6ae 100644 (file)
--- 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 <Carbon/Carbon.h>
 #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 73c1070a7ca371cbbea5aa7495814c49146b5d82..4358762df8da87ad8474e65940c85ed002b52be9 100644 (file)
--- a/parselistcommand.h
+++ b/parselistcommand.h
@@ -9,7 +9,6 @@
  *
  */
 
-#include <Carbon/Carbon.h>
 #include <iostream>
 #include <fstream>
 #include <map>
@@ -53,4 +52,4 @@ private:
        string fileroot;
 };
 
-#endif
\ No newline at end of file
+#endif

diff --git a/quitcommand.h b/quitcommand.h
index c54e7f27abfaafcc791b6c0895209a6c7a96393d..7f7b7e23d85ff47db1d60d81d1e1406534eee0ec 100644 (file)
--- a/quitcommand.h
+++ b/quitcommand.h
@@ -9,7 +9,6 @@
  *
  */
 
-#include <Carbon/Carbon.h>
 #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 1079b96708bf8a5fc2f17e54828a22f270493601..99964ec07d4dd9912d1060be4f8a4b0c753822ea 100644 (file)
--- a/rarecalc.h
+++ b/rarecalc.h
@@ -11,8 +11,6 @@
 
 /* This class is not currently used by Mothur */
 
-
-#include <Carbon/Carbon.h>
 #include "calculator.h"
 
 /***********************************************************************/

diff --git a/rarefactcommand.h b/rarefactcommand.h
index b1b706c99c80adf203059e781d8a4d89866f2dfb..0da5f0c20548196ed65d6e200620a8b0d9009d39 100644 (file)
--- a/rarefactcommand.h
+++ b/rarefactcommand.h
@@ -9,7 +9,6 @@
  *
  */
 
-#include <Carbon/Carbon.h>
 #include <iostream>
 #include <fstream>
 #include <vector>
@@ -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 1d877106bda0678fadfd99fff7e17f9766daa841..ab870242000bb0b07f3e28078feba84bcce1de4c 100644 (file)
--- a/rarefactsharedcommand.h
+++ b/rarefactsharedcommand.h
@@ -9,7 +9,6 @@
  *
  */
 
-#include <Carbon/Carbon.h>
 #include <iostream>
 #include <fstream>
 #include <vector>
@@ -54,4 +53,4 @@ private:
 
 };
 
-#endif
\ No newline at end of file
+#endif

diff --git a/readdistcommand.cpp b/readdistcommand.cpp
index 4feddfde47e51b6564e2da9b414009709fade4e8..4cf5c4e368067510ea7462dcd27eff9ac59d47ed 100644 (file)
--- 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 3dfda1ba5cb5960642c0891570290fa9ae0d01a1..4f38d034f1f14e320da5495ac79a04d4deff16b3 100644 (file)
--- a/readdistcommand.h
+++ b/readdistcommand.h
@@ -9,7 +9,6 @@
  *
  */
 
-#include <Carbon/Carbon.h>
 #include <iostream>
 #include <fstream>
 #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 c7e83e4db2e5a3048fcf9144db13c8044eada09c..eeb8cd6e3d910d30e7fde7b6d20947a693d739ed 100644 (file)
--- 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 69741581b7caa06066b8900e1ba712cb23900d8c..f00369ba8f4116db8d8e5dee015f60fa52f2a432 100644 (file)
--- a/readotucommand.h
+++ b/readotucommand.h
@@ -9,7 +9,6 @@
  *
  */
 
-#include <Carbon/Carbon.h>
 #include <iostream>
 #include <fstream>
 #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 9b96861a661a6a794120f2d47899222f3664e33b..47da6d6c81886e84961c5170267d5908199dd135 100644 (file)
--- 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 d363cd6884835558fba84e9ebaad678c4efe21b5..1abef8a179478b9db980ee6c21e6e6b9855a024b 100644 (file)
--- 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 452c0ec7b2fb881d46884832906ebd5053a5e7ae..7cca943274aa929e6bfb5acf29f4c12988b8e965 100644 (file)
--- 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 0810ab015ab93d98a90ec2e742ac7d4f77050722..e9424b2be6d534c61dca64195e2272d7782e0aa4 100644 (file)
--- a/readtreecommand.h
+++ b/readtreecommand.h
@@ -10,7 +10,6 @@
  *
  */
 
-#include <Carbon/Carbon.h>
 #include <iostream>
 #include <fstream>
 #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 223bc90adf00529da4639e9e0701b393d610d478..e594c09d496c5e1e3b8cee3fd636a99d010246e3 100644 (file)
--- a/shannon.h
+++ b/shannon.h
@@ -13,7 +13,6 @@
 It is a child of the calculator class. */
 
 
-#include <Carbon/Carbon.h>
 #include "calculator.h"
 
 /***********************************************************************/

diff --git a/shared.h b/shared.h
index 0607c13974f4a089505f1bca7221413305e504f6..8625d8b0f4f370c72f4ec2e8961cd85b6c079888 100644 (file)
--- a/shared.h
+++ b/shared.h
@@ -12,7 +12,6 @@
  
 using namespace std;
 
-#include <Carbon/Carbon.h>
 #include <iostream>
 #include <fstream>
 #include <iomanip>
@@ -37,4 +36,4 @@ class Shared {
                vector< map<string, SharedRAbundVector*> > 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 fead251ba0ced3ab338bf735b53e46bc0715d2b2..c73f153fc501e2a005a276012f9cc172434e477a 100644 (file)
--- 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 <Carbon/Carbon.h>
 #include "calculator.h"
 
 /***********************************************************************/
@@ -29,5 +27,5 @@ private:
 };
 
 /***********************************************************************/
-#endif
 
+#endif

diff --git a/sharedchao1.cpp b/sharedchao1.cpp
index 0536528e38a55402fbafcf5b1d13ad1ecdfa47ec..824115f0f856e47278f7f06c6c2d64b40f3c09a0 100644 (file)
--- 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 86f718fdaae07b85e8f9d796af51b3b0761b4524..bba43424276ff52bd2492a2ae4118b6638cab96e 100644 (file)
--- a/sharedchao1.h
+++ b/sharedchao1.h
@@ -13,7 +13,6 @@
 It is a child of the calculator class. */
 
 
-#include <Carbon/Carbon.h>
 #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 318fe9820e0444c444cd0bcb73f1e1559e763a37..b3b3e6f5d0381d2354d8113012b13251cdbec7e7 100644 (file)
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -9,7 +9,6 @@
  *
  */
 
-#include <Carbon/Carbon.h>
 #include <iostream>
 #include <fstream>
 #include <map>
@@ -48,4 +47,4 @@ private:
 
 };
 
-#endif
\ No newline at end of file
+#endif

diff --git a/sharedjabund.cpp b/sharedjabund.cpp
index 9cd938e5fb022f222423c4ee5ff457abde19eeaf..1c0b6ed37ace1f3042eee85769280168f13d78ce 100644 (file)
--- 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 cba2d980a9f331b3070ec6285ea7902d9818d482..426f2042f35d590fa146bac0c239360ce51d1aae 100644 (file)
--- a/sharedjabund.h
+++ b/sharedjabund.h
@@ -13,7 +13,6 @@
 It is a child of the calculator class. */
 
 
-#include <Carbon/Carbon.h>
 #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 52591f5b8cf05f707857e771a299e6cb9ecd41aa..6557a0f16b8d4eab412d82616e8d74cb99374b86 100644 (file)
--- 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 c35abffc9d8ded2f9f092d9b8ef37d8770ae2f6c..301518bc5eefa191b8d56a6e3045b2c3ce7badde 100644 (file)
--- 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 <Carbon/Carbon.h>
 #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 ba62e3355085a726f989885e0354594d4a053713..5a3b6b83781d397756e1c7f3db06795378525f15 100644 (file)
--- 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 19f36f958e1d87f5235bf75756a7dde96e971a23..405e68c65fee05eb84be835639e6fe547cc68dea 100644 (file)
--- a/sharedjest.h
+++ b/sharedjest.h
@@ -13,11 +13,8 @@
 It is a child of the calculator class. */
 
 
-#include <Carbon/Carbon.h>
 #include "calculator.h"
 
-
-
 /***********************************************************************/
 
 class SharedJest : public Calculator  {

diff --git a/sharedlistvector.h b/sharedlistvector.h
index 492997eee0ea238a1909c44baf262950442d0d95..f62248db77da9895e25fcb57f687fcf24922b47d 100644 (file)
--- a/sharedlistvector.h
+++ b/sharedlistvector.h
@@ -10,7 +10,6 @@
  *
  */
 
-#include <Carbon/Carbon.h>
 #include "datavector.hpp"
 #include "groupmap.h"
 #include "globaldata.hpp"
@@ -69,4 +68,3 @@ private:
 };
 
 #endif
-

diff --git a/sharedordervector.h b/sharedordervector.h
index f925964e72b7bf7173945b7c04299bbfba1d2fdc..b1b4a653dd51fb0280a5ea1189d690cf090614a4 100644 (file)
--- a/sharedordervector.h
+++ b/sharedordervector.h
@@ -25,7 +25,6 @@ struct individual {
                int abundance;
 };
 
-#include <Carbon/Carbon.h>
 #include "sabundvector.hpp"
 #include "rabundvector.hpp"
 #include "sharedrabundvector.h"

diff --git a/sharedrabundvector.h b/sharedrabundvector.h
index b69bc30657a1667665709df1d21653c05d574b3a..5547f89dabeafdf59554e4c8d2144e5375b38fe8 100644 (file)
--- a/sharedrabundvector.h
+++ b/sharedrabundvector.h
@@ -10,7 +10,6 @@
  *
  */
 
-#include <Carbon/Carbon.h>
 #include "datavector.hpp"
 #include "sharedordervector.h"
 #include "sharedsabundvector.h"

diff --git a/sharedsabundvector.h b/sharedsabundvector.h
index 60b9364e471a0df8b295b23ea62b66e8a37bca47..64b89835157090b3274303694fe59e7f079b34e4 100644 (file)
--- a/sharedsabundvector.h
+++ b/sharedsabundvector.h
@@ -11,8 +11,6 @@
  *
  */
 
-
-#include <Carbon/Carbon.h>
 #include "datavector.hpp"
 #include "rabundvector.hpp"
 #include "ordervector.hpp"

diff --git a/sharedsobs.h b/sharedsobs.h
index 3a7037e17a5eff4d8ec7240a51005940138e075a..a4c5b9bd92e43eb3497eaea24f3a660f2e0c396a 100644 (file)
--- a/sharedsobs.h
+++ b/sharedsobs.h
@@ -13,7 +13,6 @@
 It is a child of the calculator class. */
 
 
-#include <Carbon/Carbon.h>
 #include "calculator.h"
 
 /***********************************************************************/

diff --git a/sharedsorabund.h b/sharedsorabund.h
index 7fd6434839e647ab79f2092d860175330a0bd817..e1ca45abc8a681001edbd6f860f2c632cc297a8d 100644 (file)
--- a/sharedsorabund.h
+++ b/sharedsorabund.h
@@ -13,7 +13,6 @@
 It is a child of the calculator class. */
 
 
-#include <Carbon/Carbon.h>
 #include "calculator.h"
 
 /***********************************************************************/

diff --git a/sharedsorclass.h b/sharedsorclass.h
index d8702fff4d1f891c009d9d5a475d8aee5a3d95d7..7a5e282421fafeb74b8aa10d5958557c409e78b1 100644 (file)
--- a/sharedsorclass.h
+++ b/sharedsorclass.h
@@ -13,7 +13,6 @@
 It is a child of the calculator class. */
 
 
-#include <Carbon/Carbon.h>
 #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 1795f66bf39222e8232e343213f03ac8ee247a2a..1589ccc88ded7362314c294699f34c04d329d738 100644 (file)
--- a/sharedsorest.h
+++ b/sharedsorest.h
@@ -13,7 +13,6 @@
 It is a child of the calculator class. */
 
 
-#include <Carbon/Carbon.h>
 #include "calculator.h"
 
 /***********************************************************************/

diff --git a/sharedthetan.cpp b/sharedthetan.cpp
index 329368994d8e1895e2e60fbecc106eaab0c6dc5b..3c97d89bb648baa6807b17cf43ee260b6d05f6f3 100644 (file)
--- 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 b6f2c87b4deb7d38db5f1d19a47e1fd806d7f218..02b9f87327974fe56897a5130f4be0b8ec50a2fc 100644 (file)
--- a/sharedthetan.h
+++ b/sharedthetan.h
@@ -13,7 +13,6 @@
 It is a child of the calculator class. */
 
 
-#include <Carbon/Carbon.h>
 #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 9c69fb1fc15539736a9d56df381cc4eb05b236c7..c3c00005d3d6a9b89211cb16994758c7d21f8788 100644 (file)
--- a/sharedthetayc.h
+++ b/sharedthetayc.h
@@ -13,7 +13,6 @@
 It is a child of the calculator class. */
 
 
-#include <Carbon/Carbon.h>
 #include "calculator.h"
 
 /***********************************************************************/
@@ -29,5 +28,6 @@ private:
 };
 
 /***********************************************************************/
- #endif
+
+#endif
 

diff --git a/simpson.h b/simpson.h
index 968d5a152a3625429c89af509a13a949604d5759..66f4c1328aa93a2db4b4979bb80713d8ad0361d9 100644 (file)
--- a/simpson.h
+++ b/simpson.h
@@ -13,7 +13,6 @@
 It is a child of the calculator class. */
 
 
-#include <Carbon/Carbon.h>
 #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 3162f708a3acb0877c0c2638f4a61b8d2107e040..c2136b5e493dc7b81d5b1d2dd4564e0bad9c6b7a 100644 (file)
--- 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 <Carbon/Carbon.h>
 #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 1f24cd433f5db9b4f6d5e9512294449529cafc58..c03a6c61b34cef50b064593e346518d4ad741083 100644 (file)
--- a/summarycommand.h
+++ b/summarycommand.h
@@ -9,7 +9,6 @@
  *
  */
 
-#include <Carbon/Carbon.h>
 #include <iostream>
 #include <fstream>
 #include <vector>
@@ -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 42e6e197da20cc1d0e07c26b98fa9fecc4b7281c..89e610b741128a7607ee50a64d57b9b3089e6b44 100644 (file)
--- 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 24ce04b8f278e0a4dd938831a8fe9a434dc047f5..9ce3b69b65fab19c845b9344f9fe192d70e88ae0 100644 (file)
--- a/summarysharedcommand.h
+++ b/summarysharedcommand.h
@@ -9,7 +9,6 @@
  *
  */
 
-#include <Carbon/Carbon.h>
 #include <iostream>
 #include <fstream>
 #include <vector>
@@ -62,4 +61,4 @@ private:
 
 };
 
-#endif
\ No newline at end of file
+#endif

diff --git a/tree.h b/tree.h
index 63c7d5f5cdc2a170e2eef909565842dcbf1fcef2..872283dc95cccd5ba8cc3ea7faef058048bc4418 100644 (file)
--- 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 58379da96ee0be5110f36d8ab022be04aea6e4f2..6fb853682e7c468c2ef5227eb48b9688317a61bb 100644 (file)
--- 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 20bbcfee7090f0aad18e9eee8324358a2f69c5ba..d9617f5455e03f0f5fc702fffaf3516335351b15 100644 (file)
--- a/treemap.h
+++ b/treemap.h
@@ -9,7 +9,6 @@
  *
  */
 
-#include <Carbon/Carbon.h>
 #include <map>
 #include <string>
 #include <iostream>
@@ -48,4 +47,4 @@ private:
        map<string, GroupIndex> treemap; //sequence name and groupname
 };
 
-#endif
\ No newline at end of file
+#endif

diff --git a/treenode.cpp b/treenode.cpp
index 6cd99f9bbb7234e1276d6c292474ac692bb0eff4..b31fefd43a2806f19dc691b51ee802fe996a5385 100644 (file)
--- 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 d17e7b3054df4ff8eb042a7f99dfdeaed579a456..8bd055931be0ead0d8dc8a2c08d9f8e9ba637aba 100644 (file)
--- 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 7c7ac6f540be38e2f151568034737a01d16d5d8c..8906976faa784ca5a124cc402546f34611d11d00 100644 (file)
--- a/uvest.h
+++ b/uvest.h
@@ -15,10 +15,11 @@ It is used by sharedJAbund and SharedSorensonAbund. */
  
 using namespace std;
 
-#include <Carbon/Carbon.h>
 #include <vector>
 #include <iostream>
 #include <fstream>
+#include <cmath>
+
 #include "sharedrabundvector.h"
 
 typedef vector<double> EstOutput;
@@ -30,4 +31,4 @@ class UVEst {
 };
 /***********************************************************************/
 
-#endif
\ No newline at end of file
+#endif

diff --git a/validcalculator.h b/validcalculator.h
index 36a1174b813dc1d9581a927982e0e0182534e2e9..b23c24f0b287d926d68090c25533007b3a86dca9 100644 (file)
--- 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 <Carbon/Carbon.h>
 #include <string>
 #include <iostream>
 #include <map>
@@ -37,6 +39,6 @@ class ValidCalculators {
                void initialSharedRarefact();
                void initialSummary();
                void initialSharedSummary();
-               
-               
 };
+
+#endif

diff --git a/validcommands.cpp b/validcommands.cpp
index 3a72a2ba3eb64c6c23a5ae7ebdf7b4b4a5cd8ad7..734e0ce697a5dff86261ef2451d2fbcdd323b0a0 100644 (file)
--- 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 658d5e4fccbc6455d7f3a8e6b247baab2ed5295b..19554979d087cf82dc25027e0e441b883424e305 100644 (file)
--- 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 <Carbon/Carbon.h>
 #include <string>
 #include <iostream>
 #include <map>
@@ -26,4 +28,6 @@ class ValidCommands {
        private:
                map<string, string> commands;
 
-};
\ No newline at end of file
+};
+
+#endif

diff --git a/validparameter.cpp b/validparameter.cpp
index 70287c907b0d92e92c43780299603b3a05b09f02..1f6e1ef550a9e8ed7b6677a1636e3e7980d2015c 100644 (file)
--- 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 d3fb2b7071fc79ab875ad3f696a4d8c90cf8fde7..e0477aab0e9c1f39ffa19c836ef960de2c0e2bfa 100644 (file)
--- 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 <Carbon/Carbon.h>
 #include <iostream>
 #include <string>
 #include <map>
@@ -27,4 +29,6 @@ class ValidParameters {
        private:
                map<string, string> parameters;
 
-};
\ No newline at end of file
+};
+
+#endif