added citation function to commands

diff --git a/aligncommand.cpp b/aligncommand.cpp
index a75f9d0f944947f8d941731c0322444e68d40682..95604fc4ff4f738dc780de23b01ab65d4f473fe7 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -103,6 +103,7 @@ AlignCommand::AlignCommand(string option)  {
        
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true;}
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/aligncommand.h b/aligncommand.h
index ef5a92e4b8aad04651ded1ed8caf58dc58c16b30..1e1ebdc71188644f62dda2f1c2dbcb0d5226b29a 100644 (file)
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -27,6 +27,7 @@ public:
        string getCommandName()                 { return "align.seqs";                  }
        string getCommandCategory()             { return "Sequence Processing"; }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Align.seqs"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/amovacommand.cpp b/amovacommand.cpp
index f1e5f61197475b43d52d7dac46dab04cc7f657c2..ad5823b15e108396ee1b0e0977167c8e4f1fbb22 100644 (file)
--- a/amovacommand.cpp
+++ b/amovacommand.cpp
@@ -50,7 +50,6 @@ string AmovaCommand::getHelpString(){
                exit(1);
        }
 }
-
 //**********************************************************************************************************************
 AmovaCommand::AmovaCommand(){  
        try {
@@ -71,6 +70,7 @@ AmovaCommand::AmovaCommand(string option) {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/amovacommand.h b/amovacommand.h
index f50df46f70a3c6cce602ba8eeb5a4987c6dd2c95..ff82ac65f2d24ff122240d75fb326db2e03ff0c2 100644 (file)
--- a/amovacommand.h
+++ b/amovacommand.h
@@ -24,6 +24,7 @@ public:
        string getCommandName()                 { return "amova";                                       }
        string getCommandCategory()             { return "Hypothesis Testing";          }
        string getHelpString(); 
+       string getCitation() { return "Referenced: Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46. http://www.mothur.org/wiki/Amova"; }
        
        int execute();
        void help() { m->mothurOut(getHelpString()); }

diff --git a/anosimcommand.cpp b/anosimcommand.cpp
index 2ee691ea9cb0db6f3a98ff299d0a1f9c6f60bbaf..6f9e53839200ce251b0f607f0b776e075a4dffd4 100644 (file)
--- a/anosimcommand.cpp
+++ b/anosimcommand.cpp
@@ -71,6 +71,7 @@ AnosimCommand::AnosimCommand(string option) {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/anosimcommand.h b/anosimcommand.h
index 7bc5655702df0048aa8d6a476972d7456923d659..aad676ab17d04ef25a9f6be2faa685d3ae580fc4 100644 (file)
--- a/anosimcommand.h
+++ b/anosimcommand.h
@@ -26,6 +26,7 @@ public:
        string getCommandName()                 { return "anosim";                                      }
        string getCommandCategory()             { return "Hypothesis Testing";          }
        string getHelpString(); 
+       string getCitation() { return "Referenced: Clarke, K. R. (1993). Non-parametric multivariate analysis of changes in community structure. _Australian Journal of Ecology_ 18, 117-143. http://www.mothur.org/wiki/Anosim"; }
        
        int execute();
        void help() { m->mothurOut(getHelpString()); }

diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp
index 34965f624cc789e830783302f4ccd36993e28ea4..c4ef741f80c22bc784df4e6916f4a214fb2feacd 100644 (file)
--- a/binsequencecommand.cpp
+++ b/binsequencecommand.cpp
@@ -71,6 +71,7 @@ BinSeqCommand::BinSeqCommand(string option) {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/binsequencecommand.h b/binsequencecommand.h
index fe83f20f59b0e6f4db7d765f9b1aa5dc17618252..7456a2628f42969f66422d3e194b20508276dcea 100644 (file)
--- a/binsequencecommand.h
+++ b/binsequencecommand.h
@@ -28,6 +28,8 @@ public:
        string getCommandName()                 { return "bin.seqs";                    }
        string getCommandCategory()             { return "Sequence Processing"; }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Bin.seqs"; }
+
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }          

diff --git a/bootstrapsharedcommand.cpp b/bootstrapsharedcommand.cpp
index 7f7683bd4f3c779203d3e2944885ad65a4369bc9..cc0cfb63f37c4adad6c4965f9e419f0733100ef3 100644 (file)
--- a/bootstrapsharedcommand.cpp
+++ b/bootstrapsharedcommand.cpp
@@ -78,6 +78,7 @@ BootSharedCommand::BootSharedCommand(string option) {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/bootstrapsharedcommand.h b/bootstrapsharedcommand.h
index 50297b8f5e6f2170cf85487de23ca43c3138ccea..78b5c310f21dc75504e491327ef6f0e5dc4e5eb1 100644 (file)
--- a/bootstrapsharedcommand.h
+++ b/bootstrapsharedcommand.h
@@ -31,6 +31,8 @@ public:
        string getCommandName()                 { return "bootstrap.shared";    }
        string getCommandCategory()             { return "Hidden";                              }
        string getHelpString(); 
+       string getCitation() { return "no citation"; }
+
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/catchallcommand.cpp b/catchallcommand.cpp
index 1e89cdcca0d5230867356d37f8c6404a98639da6..29f2220dcc512d7a5db58bfee3c3767418ff7aa7 100644 (file)
--- a/catchallcommand.cpp
+++ b/catchallcommand.cpp
@@ -72,6 +72,7 @@ CatchAllCommand::CatchAllCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/catchallcommand.h b/catchallcommand.h
index a1c9d0e2e8b1d6806a7c84c45419f297110f5320..c9fe28590e5d5b2082f1d7f1bf04daf4316090ef 100644 (file)
--- a/catchallcommand.h
+++ b/catchallcommand.h
@@ -32,7 +32,8 @@ public:
        string getCommandName()                 { return "catchall";                    }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
-       
+       string getCitation() { return "http://www.northeastern.edu/catchall/index.html http://www.mothur.org/wiki/Catchall"; }
+
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
        

diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp
index 1fcb4fc2956023801d72b9242429b544715bc247..7a62d5bb447c3c20d155b15a5edf5f6b71b19b37 100644 (file)
--- a/chimerabellerophoncommand.cpp
+++ b/chimerabellerophoncommand.cpp
@@ -77,6 +77,7 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        

diff --git a/chimerabellerophoncommand.h b/chimerabellerophoncommand.h
index 867d3618888e37079ed7e61cc44e5a869924ab04..b048459acc058e0287dfb6b8d0744f8afc92d3e7 100644 (file)
--- a/chimerabellerophoncommand.h
+++ b/chimerabellerophoncommand.h
@@ -27,6 +27,8 @@ public:
        string getCommandName()                 { return "chimera.bellerophon"; }
        string getCommandCategory()             { return "Sequence Processing"; }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Chimera.bellerophon"; }
+
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp
index d9dfe16d68340a53468845daeab06bc5fdc3728a..df4e67db118462e1115857331c7adcc4551a272c 100644 (file)
--- a/chimeraccodecommand.cpp
+++ b/chimeraccodecommand.cpp
@@ -82,6 +82,7 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/chimeraccodecommand.h b/chimeraccodecommand.h
index 4f047e169183bc9d9294f1abb6f229015a162496..cedec2f690f6b3c981280d41a0f9bb59777ae015 100644 (file)
--- a/chimeraccodecommand.h
+++ b/chimeraccodecommand.h
@@ -27,6 +27,7 @@ public:
        string getCommandName()                 { return "chimera.ccode";               }
        string getCommandCategory()             { return "Sequence Processing"; }
        string getHelpString(); 
+       string getCitation() { return "Evaluating putative chimeric sequences from PCR-amplified products' paper by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez. http://www.mothur.org/wiki/Chimera.ccode"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index c28934c5c525bbe4954b00181b512876d6cee29e..d82a84a1b86ab5643e0416d8d73091ce16b29e23 100644 (file)
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -81,6 +81,7 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/chimeracheckcommand.h b/chimeracheckcommand.h
index 221d35fe504bea29e6757b35aadd9449703543ab..fbd49da312ab7c5ce015857bb482d2693aafca13 100644 (file)
--- a/chimeracheckcommand.h
+++ b/chimeracheckcommand.h
@@ -28,7 +28,8 @@ public:
        string getCommandName()                 { return "chimera.check";               }
        string getCommandCategory()             { return "Sequence Processing"; }
        string getHelpString(); 
-       
+       string getCitation() { return "CHIMERA_CHECK version 2.7 written by Niels Larsen. http://www.mothur.org/wiki/Chimera.check"; }
+
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
        

diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp
index b11887d8cdddc110490e436777422dc0b0d86105..94c2bf5c1a392a8f12398db3806a503cd099f3bc 100644 (file)
--- a/chimerapintailcommand.cpp
+++ b/chimerapintailcommand.cpp
@@ -86,6 +86,7 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/chimerapintailcommand.h b/chimerapintailcommand.h
index abaef191e2c1ba137f83aad2fb3e7ea46bc0b7de..49912c69a243391311ba08f101f595da3e0c0c97 100644 (file)
--- a/chimerapintailcommand.h
+++ b/chimerapintailcommand.h
@@ -29,6 +29,8 @@ public:
        string getCommandName()                 { return "chimera.pintail";             }
        string getCommandCategory()             { return "Sequence Processing"; }
        string getHelpString(); 
+       string getCitation() { return "At Least 1 in 20 16S rRNA Sequence Records Currently Held in the Public Repositories is Estimated To Contain Substantial Anomalies' paper by Kevin E. Ashelford 1, Nadia A. Chuzhanova 3, John C. Fry 1, Antonia J. Jones 2 and Andrew J. Weightman 1. http://www.mothur.org/wiki/Chimera.pintail"; }
+
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }          

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index 8835290a8a0208fec200a4d0620d3760f3e837ae..097664efc2640af01a0b10cfa3bcd9efcc46d5e3 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -112,6 +112,7 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index e5ffeb69c860aab7d08e60d134d6baacae4033f4..8d2a4280c0e0c5a53eedf76192413b5fae19cb83 100644 (file)
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -26,6 +26,8 @@ public:
        string getCommandName()                 { return "chimera.slayer";              }
        string getCommandCategory()             { return "Sequence Processing"; }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Chimera.slayer"; }
+
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }          

diff --git a/chopseqscommand.cpp b/chopseqscommand.cpp
index cbc55ef56e4deb762db35e23899127ebd224e255..0e500d4982d372c95436b99e1ead81cb3c02a9c5 100644 (file)
--- a/chopseqscommand.cpp
+++ b/chopseqscommand.cpp
@@ -73,6 +73,7 @@ ChopSeqsCommand::ChopSeqsCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/chopseqscommand.h b/chopseqscommand.h
index 92544ee30cb69df2f04b95a4e9f7c99c748e835e..31b495b20a7305d2552a770b67f9f2f812a90b1a 100644 (file)
--- a/chopseqscommand.h
+++ b/chopseqscommand.h
@@ -26,7 +26,8 @@ class ChopSeqsCommand : public Command {
                string getCommandName()                 { return "chop.seqs";           }
                string getCommandCategory()             { return "Sequence Processing"; }
                string getHelpString(); 
-       
+               string getCitation() { return "http://www.mothur.org/wiki/Chops.seqs"; }
+
                int execute(); 
                void help() { m->mothurOut(getHelpString()); }          
        

diff --git a/classify.cpp b/classify.cpp
index 8ea9e4bcf050ce505b3913e4038fc75e1b052272..925dedacbf0edee93af4d89b4cf6386169b6cfc0 100644 (file)
--- a/classify.cpp
+++ b/classify.cpp
@@ -62,7 +62,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                        //create database
                        if(method == "kmer")                    {       database = new KmerDB(tempFile, kmerSize);                      }
                        else if(method == "suffix")             {       database = new SuffixDB(numSeqs);                                                               }
-                       else if(method == "blast")              {       database = new BlastDB(gapOpen, gapExtend, match, misMatch);    }
+                       else if(method == "blast")              {       database = new BlastDB(tempFile.substr(0,tempFile.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch);   }
                        else if(method == "distance")   {       database = new DistanceDB();    }
                        else {
                                m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8."); m->mothurOutEndLine();

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index 5ac7e2c4bd618dac3ce498a0a883ca6722980311..eaf8cc206cebfe6eb1a60b40ff7042ede86ef6bd 100644 (file)
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -87,7 +87,8 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
                //allow user to run help
                if (option == "help") { 
                        help(); abort = true; calledHelp = true;
-               } else {
+               }else if(option == "citation") { citation(); abort = true; calledHelp = true;} 
+               else {
                        vector<string> myArray = setParameters();
                        
                        OptionParser parser(option);

diff --git a/classifyotucommand.h b/classifyotucommand.h
index 7f15c71c1847421abb88c3202d96e8ca7015837a..c38a7c97111b4bd842fb7038a6faaf2acedc5d53 100644 (file)
--- a/classifyotucommand.h
+++ b/classifyotucommand.h
@@ -26,6 +26,8 @@ public:
        string getCommandName()                 { return "classify.otu";                }
        string getCommandCategory()             { return "Phylotype Analysis";  }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Classify.otu"; }
+
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 9d5a625308f8970888833ec7e74ec4b2e2ec32dd..0d5ef61bbf939ce103d38f2ef36473abb01d3efa 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -106,6 +106,7 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index 115360f7d5c3015130b0beef8a704f7669a382b5..b813d40223a383dfb1e5c8734ded39f4e0b0e2a5 100644 (file)
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -35,6 +35,8 @@ public:
        string getCommandName()                 { return "classify.seqs";               }
        string getCommandCategory()             { return "Phylotype Analysis";  }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Classify.seqs"; }
+
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index afb215932958e273093726a3b71a398faabc4dc2..04dbc79aa15d3c4b6913a2e8131283b849dd90b9 100644 (file)
--- a/clearcutcommand.cpp
+++ b/clearcutcommand.cpp
@@ -108,6 +108,7 @@ ClearcutCommand::ClearcutCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/clearcutcommand.h b/clearcutcommand.h
index 89fa1ab81b8c36f552439da56af1f3706bfe19db..702fd7e14cb80dc57fd62cb0a738bdf3c6fd2bbd 100644 (file)
--- a/clearcutcommand.h
+++ b/clearcutcommand.h
@@ -31,6 +31,7 @@ public:
        string getCommandName()                 { return "clearcut";                    }
        string getCommandCategory()             { return "Hypothesis Testing";  }
        string getHelpString(); 
+       string getCitation() { return "The clearcut program written by Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho. http://www.mothur.org/wiki/Clearcut"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 25ab61b9f7068f7d5a36df3bd2e4596fd0905078..16348c8d324a962ca336c82a2ad303f156cde9e3 100644 (file)
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -75,6 +75,7 @@ ClusterCommand::ClusterCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/clustercommand.h b/clustercommand.h
index bda61403ced8b4b7051edd69d22623c14184bc54..23f728755aadb4c4f878e299790ed8669790034a 100644 (file)
--- a/clustercommand.h
+++ b/clustercommand.h
@@ -35,6 +35,7 @@ public:
        string getCommandName()                 { return "cluster";             }
        string getCommandCategory()             { return "Clustering";  }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Cluster"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/clusterdoturcommand.cpp b/clusterdoturcommand.cpp
index 2b7b02b63a3a97d683d16a01b4514c5aa2671626..9f51a8cfd07d83887010f2612831f2eb72e323a7 100644 (file)
--- a/clusterdoturcommand.cpp
+++ b/clusterdoturcommand.cpp
@@ -72,6 +72,7 @@ ClusterDoturCommand::ClusterDoturCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/clusterdoturcommand.h b/clusterdoturcommand.h
index f435a9879c992d3dd5a0739f6db1d8b016b9b8b5..e76332cbd9f7c82afed60ddfc48f84c0489798bb 100644 (file)
--- a/clusterdoturcommand.h
+++ b/clusterdoturcommand.h
@@ -28,6 +28,7 @@ public:
        string getCommandName()                 { return "cluster.classic";             }
        string getCommandCategory()             { return "Clustering";                  }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Cluster.classic"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/clusterfragmentscommand.cpp b/clusterfragmentscommand.cpp
index c51a96a0f7de2cd8f10950e7724678b8c01fa71a..2e37e7caedc35b67609e7c27e263261abd6f88f9 100644 (file)
--- a/clusterfragmentscommand.cpp
+++ b/clusterfragmentscommand.cpp
@@ -87,6 +87,7 @@ ClusterFragmentsCommand::ClusterFragmentsCommand(string option) {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/clusterfragmentscommand.h b/clusterfragmentscommand.h
index 882ab332f1cf8f2dae29ce3436373ebeca4c5b4a..2b0294782550a1da8885bbcd73aa10a046b7376b 100644 (file)
--- a/clusterfragmentscommand.h
+++ b/clusterfragmentscommand.h
@@ -38,6 +38,7 @@ public:
        string getCommandName()                 { return "cluster.fragments";           }
        string getCommandCategory()             { return "Sequence Processing";         }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Cluster.fragments"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index a695a6a750eefc5620e83bb5b9a294b9921495fc..bdc8075342de2f484238c4810ee4da5babb0356c 100644 (file)
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -105,6 +105,7 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/clustersplitcommand.h b/clustersplitcommand.h
index bdefb420de685f6c790deae1589a737ec75c2543..1485613431944edb5daee6e71978af897818cba1 100644 (file)
--- a/clustersplitcommand.h
+++ b/clustersplitcommand.h
@@ -29,6 +29,7 @@ public:
        string getCommandName()                 { return "cluster.split";               }
        string getCommandCategory()             { return "Clustering";                  }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Cluster.split"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/collectcommand.cpp b/collectcommand.cpp
index 5549fd121dfca80e5cd4a406084f68803875dc58..952131436cdb111a142970f3310b4283a1be7123 100644 (file)
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -124,7 +124,8 @@ CollectCommand::CollectCommand(string option)  {
                allLines = 1;
                
                //allow user to run help
-               if(option == "help") { help(); abort = true; }
+               if(option == "help") { help(); calledHelp = true; abort = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/collectcommand.h b/collectcommand.h
index c53152030c4d89807611efb623b50e2d3aaafbfe..d250126551f88a74bcdc7afebde65763e424aab7 100644 (file)
--- a/collectcommand.h
+++ b/collectcommand.h
@@ -37,6 +37,7 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "collect.single";                      }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getCitation() { return "http://www.mothur.org/wiki/Collect.single"; }
        string getHelpString(); 
        
        int execute(); 

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 3a2875afb62b882e9e8654eecb19e2caab5c9673..b9b3606cd9318dd1fe1f3d32834dfc9c29e451f6 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -157,6 +157,7 @@ CollectSharedCommand::CollectSharedCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/collectsharedcommand.h b/collectsharedcommand.h
index d7f2f8f3d946208cee976595bf6d8113811e7094..a10fd554a2f6e062bdecd37eb7e357d6de5283e6 100644 (file)
--- a/collectsharedcommand.h
+++ b/collectsharedcommand.h
@@ -30,6 +30,7 @@ public:
        string getCommandName()                 { return "collect.shared";                      }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Collect.shared"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/command.hpp b/command.hpp
index fd80ad1e9fc786fece31e00525476c453c6c2344..6a1a4deea6c1df252a627fa827bb33a8f49b439c 100644 (file)
--- a/command.hpp
+++ b/command.hpp
@@ -29,6 +29,7 @@ class Command {
                virtual string getCommandName() = 0;
                virtual string getCommandCategory() = 0;
                virtual string getHelpString() = 0;
+               virtual string getCitation() = 0;
                
                virtual map<string, vector<string> > getOutputFiles() { return outputTypes; }
                virtual vector<string> setParameters() = 0; //to fill parameters
@@ -36,6 +37,7 @@ class Command {
        
                virtual int execute() = 0;
                virtual void help() = 0;
+               void citation() { m->mothurOut(getCitation()); }
                virtual ~Command() { }
        
        protected:

diff --git a/consensuscommand.cpp b/consensuscommand.cpp
index 940f840dbc28e74c661bb11b103c737afe821aba..e522b098f0703d6909f1906c3039fb4459e99854 100644 (file)
--- a/consensuscommand.cpp
+++ b/consensuscommand.cpp
@@ -82,6 +82,7 @@ int ConcensusCommand::execute(){
                
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
+               
                m->mothurOut("This command is not currently in use."); m->mothurOutEndLine();
        /*      
                t = globaldata->gTree;

diff --git a/consensuscommand.h b/consensuscommand.h
index 6bd5d3e0edffe82be92d116fcacfe1c0c94a3173..fdad93a5efa8a9aee8493d32c37f016bdc21f4f0 100644 (file)
--- a/consensuscommand.h
+++ b/consensuscommand.h
@@ -25,6 +25,7 @@ public:
        string getCommandName()                 { return "concensus";   }
        string getCommandCategory()             { return "Hidden";              }
        string getHelpString(); 
+       string getCitation() { return "no citation"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/consensusseqscommand.cpp b/consensusseqscommand.cpp
index f1c766d3a270fea328c76f05d1c8d4c606c9df27..e81627df1be2e26b2c40d6322416d96d9bdcf893 100644 (file)
--- a/consensusseqscommand.cpp
+++ b/consensusseqscommand.cpp
@@ -75,6 +75,7 @@ ConsensusSeqsCommand::ConsensusSeqsCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        

diff --git a/consensusseqscommand.h b/consensusseqscommand.h
index 07a4c0816020ee0c9678f81dbdafe108c0f0f92d..226b4c959bf25f9c0629a556755641809401baa4 100644 (file)
--- a/consensusseqscommand.h
+++ b/consensusseqscommand.h
@@ -24,6 +24,7 @@ public:
        string getCommandName()                 { return "consensus.seqs";              }
        string getCommandCategory()             { return "Sequence Processing"; }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Consensus.seqs"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/corraxescommand.cpp b/corraxescommand.cpp
index ae91a24c108c16196fb67b508c62011c8cff1b63..791ec4978fd82d2fb692723fc105dfd5b6c041f0 100644 (file)
--- a/corraxescommand.cpp
+++ b/corraxescommand.cpp
@@ -74,6 +74,7 @@ CorrAxesCommand::CorrAxesCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/corraxescommand.h b/corraxescommand.h
index 5f04c6a754393bda843abdf057e0f47763fd21cf..f4a3dfe83b13fe004239b3db4b4b110c11052c02 100644 (file)
--- a/corraxescommand.h
+++ b/corraxescommand.h
@@ -25,6 +25,7 @@ public:
        string getCommandName()                 { return "corr.axes";                           }
        string getCommandCategory()             { return "Hypothesis Testing";          }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Corr.axes"; }
        
        int execute();
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index 33e51ffdff96a570d2a91d85590b3a2111ddcf63..df97fd88ad471ba97daaa593233d4177f1fe21a2 100644 (file)
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -64,6 +64,7 @@ DeconvoluteCommand::DeconvoluteCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/deconvolutecommand.h b/deconvolutecommand.h
index 8a1cb87cb87f62b9c5dc1a0c4073d13675fe105e..21a008190fdc168a9259c1abe4f8461c99fc87cd 100644 (file)
--- a/deconvolutecommand.h
+++ b/deconvolutecommand.h
@@ -27,6 +27,7 @@ public:
        string getCommandName()                 { return "unique.seqs";         }
        string getCommandCategory()             { return "Sequence Processing";         }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Unique.seqs"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/degapseqscommand.cpp b/degapseqscommand.cpp
index c90064f190af3421a2f3f6ebc673b1265a1f202a..940672c1bef7f6ab2004a9b374011cd1f8420e85 100644 (file)
--- a/degapseqscommand.cpp
+++ b/degapseqscommand.cpp
@@ -65,6 +65,7 @@ DegapSeqsCommand::DegapSeqsCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/degapseqscommand.h b/degapseqscommand.h
index db93b02a299aae60666b1993469f7e00cdc31a58..0bf0a5759ec163cc1b0f87fd693913cd02a8a127 100644 (file)
--- a/degapseqscommand.h
+++ b/degapseqscommand.h
@@ -23,6 +23,7 @@ public:
        string getCommandName()                 { return "degap.seqs";          }
        string getCommandCategory()             { return "Sequence Processing";         }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Degap.seqs"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/deuniqueseqscommand.cpp b/deuniqueseqscommand.cpp
index 24438824a0ba70225f9ae435065d4c55fa631084..aed53037c152ded2b13e00b1dfbf30ff739d341d 100644 (file)
--- a/deuniqueseqscommand.cpp
+++ b/deuniqueseqscommand.cpp
@@ -64,6 +64,7 @@ DeUniqueSeqsCommand::DeUniqueSeqsCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/deuniqueseqscommand.h b/deuniqueseqscommand.h
index 96ed29bd6aaa0f5a717d5164aa7a5a3e538dbaaf..a8edea2fab447cea46b5a2aa0bcd69fbdec27f0d 100644 (file)
--- a/deuniqueseqscommand.h
+++ b/deuniqueseqscommand.h
@@ -24,6 +24,7 @@ public:
        string getCommandName()                 { return "deunique.seqs";               }
        string getCommandCategory()             { return "Sequence Processing";         }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Deunique.seqs"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/distancecommand.cpp b/distancecommand.cpp
index 1be3552ee3d5f637f2cf17edda02695375400809..34206a9460bf21eac543ee3d91031f8fe4af96ad 100644 (file)
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -85,6 +85,7 @@ DistanceCommand::DistanceCommand(string option) {
                                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/distancecommand.h b/distancecommand.h
index 23cc6a580a16756d5b30420cb825b5d43d21ae83..71eac7d24a63ec27a4e918c3e57484e391a89889 100644 (file)
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -28,6 +28,7 @@ public:
        string getCommandName()                 { return "dist.seqs";                   }
        string getCommandCategory()             { return "Sequence Processing"; }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Dist.seqs"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 613dfda1dbbfcc74bea7e218fff53850c366fd7c..167dd3ce835f071e70c187ba9507fb2931a2e548 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -78,6 +78,7 @@ FilterSeqsCommand::FilterSeqsCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 75e7895c6ef2d4a532dfae9d37ea4fc035243b75..809c6eb69b427f8466cb97d60322e7a27b6d53ed 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -25,6 +25,7 @@ public:
        string getCommandName()                 { return "filter.seqs";                 }\r
        string getCommandCategory()             { return "Sequence Processing"; }\r
        string getHelpString(); \r
+       string getCitation() { return "http://www.mothur.org/wiki/Filter.seqs"; }\r
        \r
        int execute(); \r
        void help() { m->mothurOut(getHelpString()); }  \r

diff --git a/getcommandinfocommand.cpp b/getcommandinfocommand.cpp
index 7ca245369136a19da6ec607d0055a1b0351d2cc7..e75897f6bae4bf45142ec7fd8cf643fcb4e483c0 100644 (file)
--- a/getcommandinfocommand.cpp
+++ b/getcommandinfocommand.cpp
@@ -45,6 +45,7 @@ GetCommandInfoCommand::GetCommandInfoCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/getcommandinfocommand.h b/getcommandinfocommand.h
index 4c5b3ab60f7c1fea8d75f7e228c6539536afd877..c67a4eded0536e11177cd3db392efe2fa3ae7364 100644 (file)
--- a/getcommandinfocommand.h
+++ b/getcommandinfocommand.h
@@ -28,6 +28,7 @@ public:
        string getCommandName()                 { return "get.commandinfo";             }
        string getCommandCategory()             { return "Hidden";                              }
        string getHelpString(); 
+       string getCitation() { return "no citation"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/getcurrentcommand.cpp b/getcurrentcommand.cpp
index 5f5235647d28168d4ca187189d5911266a24c71a..12dcc82ff6a1bfb1a105d3d6deac903e855cea9b 100644 (file)
--- a/getcurrentcommand.cpp
+++ b/getcurrentcommand.cpp
@@ -59,6 +59,7 @@ GetCurrentCommand::GetCurrentCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/getcurrentcommand.h b/getcurrentcommand.h
index aa4f8f4f4e488fdb87474b0ceebd52ac25cd4f98..bfa9168dcd81347afe271062f224763fdcb56ce1 100644 (file)
--- a/getcurrentcommand.h
+++ b/getcurrentcommand.h
@@ -23,6 +23,7 @@ class GetCurrentCommand : public Command {
                string getCommandName()                 { return "get.current"; }
                string getCommandCategory()             { return "General";             }
                string getHelpString(); 
+               string getCitation() { return "http://www.mothur.org/wiki/Get.current"; }
        
                int execute(); 
                void help() { m->mothurOut(getHelpString()); }  

diff --git a/getgroupcommand.cpp b/getgroupcommand.cpp
index 6b76bf2d74a1c3443111dade5d7ceaad7a1c75a2..b39fb645154f97252e7d928c9862cde01553ab6b 100644 (file)
--- a/getgroupcommand.cpp
+++ b/getgroupcommand.cpp
@@ -62,6 +62,7 @@ GetgroupCommand::GetgroupCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/getgroupcommand.h b/getgroupcommand.h
index 79dd8057216ec17fcd706d5a6a480c461161a458..a539834177b63a51929d52299c68779a27046fba 100644 (file)
--- a/getgroupcommand.h
+++ b/getgroupcommand.h
@@ -22,6 +22,7 @@ public:
        string getCommandName()                 { return "get.group";                           }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Get.group"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/getgroupscommand.cpp b/getgroupscommand.cpp
index c7f96ec4fba8a42dba043bf4796f42307537c953..e38ac9bc3c683eff7b0915b7fa450d1858b793fe 100644 (file)
--- a/getgroupscommand.cpp
+++ b/getgroupscommand.cpp
@@ -78,6 +78,7 @@ GetGroupsCommand::GetGroupsCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/getgroupscommand.h b/getgroupscommand.h
index 955de627ccb6f4952c6ed3a1444ee2b4d5397187..fda603c1fd46323a3af168cd7ba32777a1fbf5a9 100644 (file)
--- a/getgroupscommand.h
+++ b/getgroupscommand.h
@@ -26,6 +26,7 @@ public:
        string getCommandName()                 { return "get.groups";                          }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Get.groups"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/getlabelcommand.cpp b/getlabelcommand.cpp
index 381a9508a0222e3bbec90930215513b7048a9770..aba8e8a128f6299feabfee18a8118384974fa206 100644 (file)
--- a/getlabelcommand.cpp
+++ b/getlabelcommand.cpp
@@ -62,6 +62,7 @@ GetlabelCommand::GetlabelCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/getlabelcommand.h b/getlabelcommand.h
index 606daf42ab685a4070d8aa54c21a839cdda91773..71645704592d6bebdc4cca894d43d3b13732fed8 100644 (file)
--- a/getlabelcommand.h
+++ b/getlabelcommand.h
@@ -25,6 +25,7 @@ public:
        string getCommandName()                 { return "get.label";                           }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Get.label"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/getlineagecommand.cpp b/getlineagecommand.cpp
index dd00c0368c3e8167f26667d40af1925f184feb32..c6671d1721c691f4a3fdf0e6faba5eb890fe6e1e 100644 (file)
--- a/getlineagecommand.cpp
+++ b/getlineagecommand.cpp
@@ -83,6 +83,7 @@ GetLineageCommand::GetLineageCommand(string option)  {
                                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/getlineagecommand.h b/getlineagecommand.h
index 6375b9483fb335bafde123f3e99e4620c2614234..d62c50f55d253b7e3fd15790e2a6d4b21cb35b8f 100644 (file)
--- a/getlineagecommand.h
+++ b/getlineagecommand.h
@@ -24,6 +24,7 @@ class GetLineageCommand : public Command {
                string getCommandName()                 { return "get.lineage";                         }
                string getCommandCategory()             { return "Phylotype Analysis";          }
                string getHelpString(); 
+               string getCitation() { return "http://www.mothur.org/wiki/Get.lineage"; }
        
                int execute(); 
                void help() { m->mothurOut(getHelpString()); }  

diff --git a/getlistcountcommand.cpp b/getlistcountcommand.cpp
index eb9c980075a069b1e0f08f6f01fc64e4f1a6b358..4dc20634c1e53d774348559447c736f736ff4e69 100644 (file)
--- a/getlistcountcommand.cpp
+++ b/getlistcountcommand.cpp
@@ -69,6 +69,7 @@ GetListCountCommand::GetListCountCommand(string option)  {
                                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/getlistcountcommand.h b/getlistcountcommand.h
index 40ff7d0636f38158eea14fd7523618ab2e107188..a0b5f092247cc6c1a702fb47afc7c2b499542efb 100644 (file)
--- a/getlistcountcommand.h
+++ b/getlistcountcommand.h
@@ -25,7 +25,7 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "get.otulist";                         }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
-       
+       string getCitation() { return "http://www.mothur.org/wiki/Get.otulist"; }
        string getHelpString(); 
        
        int execute(); 

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 06a633e446d907cb7e6a5a5caa615e901a8c37c7..ce4b8950c3f1946054c7b24c82445a9ea1bc1cec 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -117,6 +117,7 @@ GetOTURepCommand::GetOTURepCommand(string option)  {
                //allow user to run help
                if (option == "help") { 
                        help(); abort = true; calledHelp = true;
+               }else if(option == "citation") { citation(); abort = true; calledHelp = true;
                } else {
                        vector<string> myArray = setParameters();
                        

diff --git a/getoturepcommand.h b/getoturepcommand.h
index d8f8f0905ba3c3e8c09dfb8ec83ec34f817db89e..179a1b3becb27091fbe5fc6e78d1b1f91a70e10d 100644 (file)
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -44,6 +44,7 @@ public:
        string getCommandName()                 { return "get.oturep";                          }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Get.oturep"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/getotuscommand.cpp b/getotuscommand.cpp
index b39b4ab74ef178bb1a3dd2029549c69b2bda4be6..681deb7646540d663560ed68d5da61deadea0f44 100644 (file)
--- a/getotuscommand.cpp
+++ b/getotuscommand.cpp
@@ -75,6 +75,7 @@ GetOtusCommand::GetOtusCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/getotuscommand.h b/getotuscommand.h
index 34562fe7cf8f426048e5f1e71d568039bef1a117..30f4f3cb0b18aedb2a28348f41f720e967ea1d01 100644 (file)
--- a/getotuscommand.h
+++ b/getotuscommand.h
@@ -28,6 +28,7 @@ public:
        string getCommandName()                 { return "get.otus";                            }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Get.otus"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp
index 2f49a3b37181603f88065629ddc73f5194be49d9..f886c2369a87d757532b68456af89753f72bb9c6 100644 (file)
--- a/getrabundcommand.cpp
+++ b/getrabundcommand.cpp
@@ -69,6 +69,7 @@ GetRAbundCommand::GetRAbundCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/getrabundcommand.h b/getrabundcommand.h
index dd0cefc89457cb114596c988c35b6be59c650547..81a5d910b53c84db70c560255ce2b508c4361f33 100644 (file)
--- a/getrabundcommand.h
+++ b/getrabundcommand.h
@@ -26,6 +26,7 @@ public:
        string getCommandName()                 { return "get.rabund";                          }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Get.rabund"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/getrelabundcommand.cpp b/getrelabundcommand.cpp
index 74ec992a001e16a91d131a376944165aca1b4622..91384fab4e71bb37c865c1c037e829d2581e3a1a 100644 (file)
--- a/getrelabundcommand.cpp
+++ b/getrelabundcommand.cpp
@@ -69,6 +69,7 @@ GetRelAbundCommand::GetRelAbundCommand(string option) {
                                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/getrelabundcommand.h b/getrelabundcommand.h
index ab1896f5b3c470d393453da29297814d697ca825..0df0e7d981f27b638c4bfd09d745ca9cbc9481bc 100644 (file)
--- a/getrelabundcommand.h
+++ b/getrelabundcommand.h
@@ -26,6 +26,7 @@ public:
        string getCommandName()                 { return "get.relabund";                        }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Get.relabund"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp
index 820868416b7bfc9bebcc27c8f73c24c6ddb7bbb4..3f6413606193afed8b5e2b7f6e89d77c20ef4ce4 100644 (file)
--- a/getsabundcommand.cpp
+++ b/getsabundcommand.cpp
@@ -67,6 +67,7 @@ GetSAbundCommand::GetSAbundCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/getsabundcommand.h b/getsabundcommand.h
index d17574f57a8b33e3a0625ae056d604859736e036..da998f563ba4f9b5a1726f821a8e96dfbfa6209a 100644 (file)
--- a/getsabundcommand.h
+++ b/getsabundcommand.h
@@ -25,6 +25,7 @@ public:
        string getCommandName()                 { return "get.sabund";                          }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Get.sabund"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index 04c3bd325edf89638503cdcb49c2842c75ed1d17..ad9698b695815cc77459cc85d2cca1ec7cd24f67 100644 (file)
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -81,6 +81,7 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/getseqscommand.h b/getseqscommand.h
index 07d13d6703426e1990fab1a1bc9afdb82124c801..4fef8e795be355d23d1348f2ed323e225092b0f9 100644 (file)
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -24,6 +24,7 @@ class GetSeqsCommand : public Command {
                string getCommandName()                 { return "get.seqs";                            }
                string getCommandCategory()             { return "Sequence Processing";         }
                string getHelpString(); 
+               string getCitation() { return "http://www.mothur.org/wiki/Get.seqs"; }
        
                int execute(); 
                void help() { m->mothurOut(getHelpString()); }  

diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp
index f627aedef1223caf64b4eca8a37f06217315c2b6..99687701436dc5ffac7e71a444d97b42f4b6815a 100644 (file)
--- a/getsharedotucommand.cpp
+++ b/getsharedotucommand.cpp
@@ -82,6 +82,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/getsharedotucommand.h b/getsharedotucommand.h
index 27a57b0242a92c95f694a941b4e2c05ed465c384..d7ffef3c74b965967dd6f68d7a6914183ec2253f 100644 (file)
--- a/getsharedotucommand.h
+++ b/getsharedotucommand.h
@@ -29,6 +29,7 @@ class GetSharedOTUCommand : public Command {
                string getCommandCategory()             { return "OTU-Based Approaches";        }
                string getRequiredCommand()             { return "none";                                        }
                string getHelpString(); 
+               string getCitation() { return "http://www.mothur.org/wiki/Get.sharedseqs"; }
        
                int execute(); 
                void help() { m->mothurOut(getHelpString()); }  

diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index 12f1f9e0b33904639cca446f0b0d698e9f64f625..3e99473bb6d742cd759c6a5a3eed55373df58549 100644 (file)
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -74,6 +74,7 @@ HClusterCommand::HClusterCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/hclustercommand.h b/hclustercommand.h
index 9241e94c35441e1b0d09d3bddae9a76d8f6c4cc6..f27837a312bd0b10eca4108352a95003e5ae2be4 100644 (file)
--- a/hclustercommand.h
+++ b/hclustercommand.h
@@ -39,6 +39,7 @@ public:
        string getCommandName()                 { return "hcluster";    }
        string getCommandCategory()             { return "Clustering";  }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Hcluster"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp
index 2da1d245eb8a0241b50aad874388fe83b5be72c8..cf5140a1c7a03db5603cd2358ea7797ea80701f6 100644 (file)
--- a/heatmapcommand.cpp
+++ b/heatmapcommand.cpp
@@ -83,6 +83,7 @@ HeatMapCommand::HeatMapCommand(string option) {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/heatmapcommand.h b/heatmapcommand.h
index 6fb5ff073fb5dea3b2a7237c114142ec0f3b184b..3bb979108948ac712b4758296b34ed3aba8e7c52 100644 (file)
--- a/heatmapcommand.h
+++ b/heatmapcommand.h
@@ -29,6 +29,7 @@ public:
        string getCommandName()                 { return "heatmap.bin";                         }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Heatmap.bin"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/heatmapsimcommand.cpp b/heatmapsimcommand.cpp
index 0d3bc33e2e406e1a811598fee620a92f3cedc3e2..0de3ffc4416f3d8e2318c64ef1a3a3cce240ed7d 100644 (file)
--- a/heatmapsimcommand.cpp
+++ b/heatmapsimcommand.cpp
@@ -92,6 +92,7 @@ HeatMapSimCommand::HeatMapSimCommand(string option)  {
                        
                //allow user to run help
                if(option == "help") {  help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/heatmapsimcommand.h b/heatmapsimcommand.h
index dbaa6840b4513ca085da696c485e5b73e74f37b9..ba5a240c8ade230de7433413cefe1dcfdf930402 100644 (file)
--- a/heatmapsimcommand.h
+++ b/heatmapsimcommand.h
@@ -27,6 +27,7 @@ public:
        string getCommandName()                 { return "heatmap.sim";                         }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Heatmap.sim"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/helpcommand.h b/helpcommand.h
index 46393c020c0a0074525b3df80eb7dade0f8cfa3b..c542899fce02b3d9781f553d55054e876bb3b94e 100644 (file)
--- a/helpcommand.h
+++ b/helpcommand.h
@@ -25,6 +25,7 @@ public:
        string getCommandName()                 { return "help";                }
        string getCommandCategory()             { return "Hidden";              }
        string getHelpString() { return "For more information about a specific command type 'commandName(help)' i.e. 'cluster(help)'"; }        
+       string getCitation() { return "no citation"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/homovacommand.cpp b/homovacommand.cpp
index f9d259d2e817d9d4458dc4b54adc218aea6ab5b3..a8d2786f085ef584ba5f18069dfea2c5a51da572 100644 (file)
--- a/homovacommand.cpp
+++ b/homovacommand.cpp
@@ -72,6 +72,7 @@ HomovaCommand::HomovaCommand(string option) {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/homovacommand.h b/homovacommand.h
index ec7a793bc25082fe12bf1fc768a72e0209d6b96a..8b31cc5a65aeedfc63412c5bc200faf6ce8fb603 100644 (file)
--- a/homovacommand.h
+++ b/homovacommand.h
@@ -27,6 +27,7 @@ public:
        string getCommandName()                 { return "homova";                                      }
        string getCommandCategory()             { return "Hypothesis Testing";          }
        string getHelpString(); 
+       string getCitation() { return "Stewart CN, Excoffier L (1996). Assessing population genetic structure and variability with RAPD data: Application to Vaccinium macrocarpon (American Cranberry). J Evol Biol 9: 153-71. http://www.mothur.org/wiki/Homova"; }
        
        int execute();
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/indicatorcommand.cpp b/indicatorcommand.cpp
index c25e4fa13b4b7cc8eaf7f320d66b1806a3bf194d..ac7efcf5a40846dd8fcf6a2166dbc773f18d2b34 100644 (file)
--- a/indicatorcommand.cpp
+++ b/indicatorcommand.cpp
@@ -74,6 +74,7 @@ IndicatorCommand::IndicatorCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/indicatorcommand.h b/indicatorcommand.h
index 05db05c414de9e0917c68050aebc655afe3aa846..9c8c6d437470588be099c656d89942ab8d78cc61 100644 (file)
--- a/indicatorcommand.h
+++ b/indicatorcommand.h
@@ -27,6 +27,7 @@ public:
        string getCommandName()                 { return "indicator";                           }
        string getCommandCategory()             { return "Hypothesis Testing";          }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Indicator"; }
        
        int execute();
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/libshuffcommand.cpp b/libshuffcommand.cpp
index c827b524649fefe49545aa8769401d781ff016c1..02104142c753b626f245f256e910c4ed3351e6bb 100644 (file)
--- a/libshuffcommand.cpp
+++ b/libshuffcommand.cpp
@@ -86,6 +86,7 @@ LibShuffCommand::LibShuffCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/libshuffcommand.h b/libshuffcommand.h
index 97fcd1cce71290949fde06e96086ab0cc48db70b..25b128157b7fb6ba9a3382542cf353bd2ab74473 100644 (file)
--- a/libshuffcommand.h
+++ b/libshuffcommand.h
@@ -27,6 +27,7 @@ public:
        string getCommandName()                 { return "libshuff";                            }
        string getCommandCategory()             { return "Hypothesis Testing";          }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Libshuff"; }
        
        int execute();
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index d60470cdebcc70114afcb79cc08edbb333816292..902ac87286e302977d2fe555754a632487e6e43b 100644 (file)
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -71,7 +71,7 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
-               
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                else {
                        vector<string> myArray = setParameters();
                        

diff --git a/listseqscommand.h b/listseqscommand.h
index be53d750ac0691938e314c883d689715bc8d11c7..ea48430e9e0876c1034c344d5688fd64bc0c2bde 100644 (file)
--- a/listseqscommand.h
+++ b/listseqscommand.h
@@ -24,6 +24,7 @@ class ListSeqsCommand : public Command {
                string getCommandName()                 { return "list.seqs";                           }
                string getCommandCategory()             { return "Sequence Processing";         }
                string getHelpString(); 
+               string getCitation() { return "http://www.mothur.org/wiki/List.seqs"; }
        
                int execute(); 
                void help() { m->mothurOut(getHelpString()); }  

diff --git a/makefastqcommand.cpp b/makefastqcommand.cpp
index b4c0e8c04d85357ff9bbe2de8008ced7d70186c9..2dd45a542665c71a1221adca4eed77d9c1bb65f5 100644 (file)
--- a/makefastqcommand.cpp
+++ b/makefastqcommand.cpp
@@ -65,6 +65,7 @@ MakeFastQCommand::MakeFastQCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/makefastqcommand.h b/makefastqcommand.h
index 946c990047fe8ad65f2fb332deb6e072534fc932..085654fc28900a871e83a61dffdc26b4f8300bfc 100644 (file)
--- a/makefastqcommand.h
+++ b/makefastqcommand.h
@@ -25,6 +25,7 @@ public:
        string getCommandName()                 { return "make.fastq";                          }
        string getCommandCategory()             { return "Sequence Processing";         }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Make.fastq"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/makegroupcommand.cpp b/makegroupcommand.cpp
index 7ca4aa64d28f9ec23bcc93c37e42c753ef6a8137..e7704642874d050a3de7625a28ed3fae390fe653 100644 (file)
--- a/makegroupcommand.cpp
+++ b/makegroupcommand.cpp
@@ -69,6 +69,7 @@ MakeGroupCommand::MakeGroupCommand(string option)  {
        
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/makegroupcommand.h b/makegroupcommand.h
index 1206938205b6fec35b5252e75f21d7d45af5522b..f5fb3583f13b09b4f4cc4f70709eca3ffeec388e 100644 (file)
--- a/makegroupcommand.h
+++ b/makegroupcommand.h
@@ -23,6 +23,7 @@ public:
        string getCommandName()                 { return "make.group";  }
        string getCommandCategory()             { return "General";             }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Make.group"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/mantelcommand.cpp b/mantelcommand.cpp
index 0c0163b538a747ca5b9b4eb82ef57a06ca302b91..c3ab352a0119ad3aad7ee0959b7c387522a642d1 100644 (file)
--- a/mantelcommand.cpp
+++ b/mantelcommand.cpp
@@ -69,6 +69,7 @@ MantelCommand::MantelCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/mantelcommand.h b/mantelcommand.h
index 224265bc3539a53e16b322847772b8fe2cdbc280..1a6f27b523e24dc0e6d702649eea33dad995a876 100644 (file)
--- a/mantelcommand.h
+++ b/mantelcommand.h
@@ -23,6 +23,7 @@ public:
        string getCommandName()                 { return "mantel";                                      }
        string getCommandCategory()             { return "Hypothesis Testing";          }
        string getHelpString(); 
+       string getCitation() { return "Sokal, R. R., & Rohlf, F. J. (1995). Biometry, 3rd edn. New York: Freeman. http://www.mothur.org/wiki/Mantel"; }
        
        int execute();
        void help() { m->mothurOut(getHelpString()); }

diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index 5dfba366b1247956a2b2c655a8bf790b902e9ba1..4ea8f021d3046a3f25be73b201869a73b98898ce 100644 (file)
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -115,6 +115,7 @@ MatrixOutputCommand::MatrixOutputCommand(string option)  {
                                
                //allow user to run help
                if(option == "help") {  help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index 2871d5e31511572ad30fd9a19f28e50ae4c8bb67..2c403aa1570895546ea1cbeb8e6c2e46d406c7e3 100644 (file)
--- a/matrixoutputcommand.h
+++ b/matrixoutputcommand.h
@@ -32,6 +32,7 @@ public:
        string getCommandName()                 { return "dist.shared";                         }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Dist.shared"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/mergefilecommand.cpp b/mergefilecommand.cpp
index cece52d9cd06b78950f5b197c19d2e9574b7daa8..c944e3bc8774aaa9ccffb712cdda823741c7d2e3 100644 (file)
--- a/mergefilecommand.cpp
+++ b/mergefilecommand.cpp
@@ -64,7 +64,7 @@ MergeFileCommand::MergeFileCommand(string option)  {
                if(option == "help") {
                        help();
                        abort = true; calledHelp = true;
-               }
+               }else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                else {
                        vector<string> myArray = setParameters();
                        

diff --git a/mergefilecommand.h b/mergefilecommand.h
index 1ecc3cb6e24f72b99c5e4d9ddb0850e1cc16e082..1e56f73a865079f7dca0ccab91f3fd6f0ddfcbef 100644 (file)
--- a/mergefilecommand.h
+++ b/mergefilecommand.h
@@ -23,6 +23,7 @@ public:
        string getCommandName()                 { return "merge.files"; }
        string getCommandCategory()             { return "General";             }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Merge.files"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/mergegroupscommand.cpp b/mergegroupscommand.cpp
index cb990e467f49afddfd56a2106ee7c47c12d0bd7e..df74ade901634cc2cbfaa5a06877354a819e2ee2 100644 (file)
--- a/mergegroupscommand.cpp
+++ b/mergegroupscommand.cpp
@@ -73,6 +73,7 @@ MergeGroupsCommand::MergeGroupsCommand(string option) {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/mergegroupscommand.h b/mergegroupscommand.h
index 827f5a32762ce7f6d3c11fd0735e64f5e729e7fd..dfd65adf1fdc9f7c6c84491f0714eff5cfd3888c 100644 (file)
--- a/mergegroupscommand.h
+++ b/mergegroupscommand.h
@@ -25,6 +25,7 @@ public:
        string getCommandName()                 { return "merge.groups";        }
        string getCommandCategory()             { return "General";                     }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Merge.groups"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/metastatscommand.cpp b/metastatscommand.cpp
index f637eec8b5821e45bbeae41a5282481a809a272b..99a3043995b429bf4661a776f25f050262905412 100644 (file)
--- a/metastatscommand.cpp
+++ b/metastatscommand.cpp
@@ -83,6 +83,7 @@ MetaStatsCommand::MetaStatsCommand(string option) {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/metastatscommand.h b/metastatscommand.h
index 1380444dc25e4b0ade5afc240acb2c942b6abd57..491e0761a35712638782fe8efb13cd6427d6b7f2 100644 (file)
--- a/metastatscommand.h
+++ b/metastatscommand.h
@@ -25,6 +25,7 @@ public:
        string getCommandName()                 { return "metastats";                           }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "White, J.R., Nagarajan, N. & Pop, M. Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 5, e1000352 (2009). http://www.mothur.org/wiki/Metastats"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index 945d116c035d663eff0a3bc2317fda9ba643b908..5a790afd45bbfcc2c92d23827aa58a184f257cee 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -82,6 +82,7 @@ MGClusterCommand::MGClusterCommand(string option) {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/mgclustercommand.h b/mgclustercommand.h
index c23534f9dfd375cb34cc8c85963d17e8dbfee23d..d5c784e27a28bb27e6b7cbdadbb8b94e25b199b5 100644 (file)
--- a/mgclustercommand.h
+++ b/mgclustercommand.h
@@ -32,6 +32,7 @@ public:
        string getCommandName()                 { return "mgcluster";   }
        string getCommandCategory()             { return "Clustering";  }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Mgcluster"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/nmdscommand.cpp b/nmdscommand.cpp
index 3f8e34249c3d15c94709262fd252db1b525c820a..4567dbba1e7b0b16e88f496307ef3cb7ff3a8650 100644 (file)
--- a/nmdscommand.cpp
+++ b/nmdscommand.cpp
@@ -77,6 +77,7 @@ NMDSCommand::NMDSCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/nmdscommand.h b/nmdscommand.h
index 861e8eaf95eb79a02c4e918a732f13c19f3ce845..f099f95a4c0baadc0d50747cac5cd18e6972439f 100644 (file)
--- a/nmdscommand.h
+++ b/nmdscommand.h
@@ -38,6 +38,7 @@ public:
        string getCommandName()                 { return "nmds";                                        }
        string getCommandCategory()             { return "Hypothesis Testing";          }
        string getHelpString(); 
+       string getCitation() { return "Non-metric multidimensional scaling function using the majorization algorithm from Borg & Groenen 1997, Modern Multidimensional Scaling. http://www.mothur.org/wiki/Nmds"; }
        
        int execute();
        void help() { m->mothurOut(getHelpString()); }

diff --git a/nocommands.h b/nocommands.h
index 12bfc4dffc6082ab35cc405b5ab03b522391b02d..b7fa6f19fb10d4178d826158a4b19606c81a0e8b 100644 (file)
--- a/nocommands.h
+++ b/nocommands.h
@@ -25,6 +25,7 @@ public:
        string getCommandName()                 { return "NoCommand";   }
        string getCommandCategory()             { return "Hidden";              }
        string getHelpString() { return "No Command"; } 
+       string getCitation() { return "no citation"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/normalizesharedcommand.cpp b/normalizesharedcommand.cpp
index 5f3cacbf194a36205b35f9772aac17cdae4352c2..718eeb131397ecbe99702a1a38b20d3e8e7bc04d 100644 (file)
--- a/normalizesharedcommand.cpp
+++ b/normalizesharedcommand.cpp
@@ -77,6 +77,7 @@ NormalizeSharedCommand::NormalizeSharedCommand(string option) {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/normalizesharedcommand.h b/normalizesharedcommand.h
index 26bc0e4ca542de7a7c56cf2299918ce0f2819e70..6332fd7fe1f36f19cd232cde99d9c6629fc00ca5 100644 (file)
--- a/normalizesharedcommand.h
+++ b/normalizesharedcommand.h
@@ -25,6 +25,7 @@ public:
        string getCommandName()                 { return "normalize.shared";            }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Normalize.shared"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp
index edfdaea6a1a5c02b1a8b0c96b10768be4770b1a5..cc5703223c7db32f31a2bf6db21d256145100f06 100644 (file)
--- a/otuhierarchycommand.cpp
+++ b/otuhierarchycommand.cpp
@@ -67,6 +67,7 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option) {
                
                //allow user to run help
                if(option == "help") {  help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/otuhierarchycommand.h b/otuhierarchycommand.h
index b82ee7606cdafba5c3f392546cb82858eb8aad8b..342b5aa52804dda54bea8da6e8c1b4276d089290 100644 (file)
--- a/otuhierarchycommand.h
+++ b/otuhierarchycommand.h
@@ -25,6 +25,7 @@ public:
        string getCommandName()                 { return "otu.hierarchy";                       }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Otu.hierarchy"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index 1aa133f38c379fd40c495d2c2a844de292c17f51..db032516e69e631147dbe3f2179a99a53ea2a1e2 100644 (file)
--- a/pairwiseseqscommand.cpp
+++ b/pairwiseseqscommand.cpp
@@ -99,6 +99,7 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option)  {
        
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/pairwiseseqscommand.h b/pairwiseseqscommand.h
index 52ba63db10adf51e10e6440e5df7b92b78c4c894..69785186caa063419a06a7dc73054344ebcfeae9 100644 (file)
--- a/pairwiseseqscommand.h
+++ b/pairwiseseqscommand.h
@@ -29,6 +29,7 @@ public:
        string getCommandName()                 { return "pairwise.seqs";               }
        string getCommandCategory()             { return "Sequence Processing"; }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Pairwise.seqs"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp
index 75d6fa01be65bcccf8f176bfd29dcce843efc0e3..1033ba5d5dd3a64b001e2e8bc120b792df02e824 100644 (file)
--- a/parsefastaqcommand.cpp
+++ b/parsefastaqcommand.cpp
@@ -62,6 +62,7 @@ ParseFastaQCommand::ParseFastaQCommand(string option){
                abort = false; calledHelp = false;   
                
                if(option == "help") {  help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/parsefastaqcommand.h b/parsefastaqcommand.h
index fe77cf08f34e3760734fb7b70568c4db09d603a2..dfafca6fee21c9f5493437fe37007669c3fc4ac7 100644 (file)
--- a/parsefastaqcommand.h
+++ b/parsefastaqcommand.h
@@ -24,6 +24,7 @@ public:
        string getCommandName()                 { return "parse.fastq";         }
        string getCommandCategory()             { return "Sequence Processing"; }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Parse.fastq"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }          

diff --git a/parselistscommand.cpp b/parselistscommand.cpp
index c79eb63c31b576359f8b6bf270bea83ba25028d2..b791be7efcbffa74c7aa2e7f325cc4e8d39e00fb 100644 (file)
--- a/parselistscommand.cpp
+++ b/parselistscommand.cpp
@@ -66,6 +66,7 @@ ParseListCommand::ParseListCommand(string option)  {
                        
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/parselistscommand.h b/parselistscommand.h
index 065c499ade25c46fb18ef3746fc5c08687c232d6..9489b9b29108ed13969352c6ed1fe3a994e7f326 100644 (file)
--- a/parselistscommand.h
+++ b/parselistscommand.h
@@ -27,6 +27,7 @@ public:
        string getCommandName()                 { return "parse.list";                          }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Parse.list"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index 1be4697a4f3fde882fa08985a8a1e01072110596..403b2b86d9addf1f9291e7f87fac63ef1755c002 100644 (file)
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -74,6 +74,7 @@ ParsimonyCommand::ParsimonyCommand(string option)  {
                        
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/parsimonycommand.h b/parsimonycommand.h
index 274cac4e94f46b51aca95695f9fc4d7a4ba9c981..30c8332c8285466c7571c4ca275977e47f3469fe 100644 (file)
--- a/parsimonycommand.h
+++ b/parsimonycommand.h
@@ -29,6 +29,7 @@ public:
        string getCommandName()                 { return "parsimony";                           }
        string getCommandCategory()             { return "Hypothesis Testing";          }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Parsimony"; }
        
        int execute();
        void help() { m->mothurOut(getHelpString()); }

diff --git a/pcacommand.cpp b/pcacommand.cpp
index 6e2cce79736a9f01edbaa44bd31e145921850a30..e273e5fe7079ffab790ccf5498e69675a0fafeef 100644 (file)
--- a/pcacommand.cpp
+++ b/pcacommand.cpp
@@ -70,6 +70,7 @@ PCACommand::PCACommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/pcacommand.h b/pcacommand.h
index 379cf6e654bb72b9e5a871ea93d1c230fe819809..9b4a881cb181823a58fcfa9c7962ca561e394346 100644 (file)
--- a/pcacommand.h
+++ b/pcacommand.h
@@ -26,6 +26,7 @@ public:
        string getCommandName()                 { return "pca";                                 }
        string getCommandCategory()             { return "Hypothesis Testing";  }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Pca"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/pcoacommand.cpp b/pcoacommand.cpp
index 607256bc108d33f1b1b869bd3250c49900f385c6..5d917372e5f88a5a45b762efc57ab388d80a4ebc 100644 (file)
--- a/pcoacommand.cpp
+++ b/pcoacommand.cpp
@@ -69,6 +69,7 @@ PCOACommand::PCOACommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/pcoacommand.h b/pcoacommand.h
index ea4d2b381e8c5b60a3d7006e51d128dda72081bb..d9aa270320999d4e5f35e68b1525746ec78e3ae4 100644 (file)
--- a/pcoacommand.h
+++ b/pcoacommand.h
@@ -26,6 +26,7 @@ public:
        string getCommandName()                 { return "pcoa";                                        }
        string getCommandCategory()             { return "Hypothesis Testing";          }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Pcoa"; }
        
        int execute();
        void help() { m->mothurOut(getHelpString()); }

diff --git a/phylodiversitycommand.cpp b/phylodiversitycommand.cpp
index d15899c2f2f853ba9529c9b65f74ce67885c8a63..bf502abe715baadd43112377c374ba218414d3d8 100644 (file)
--- a/phylodiversitycommand.cpp
+++ b/phylodiversitycommand.cpp
@@ -84,6 +84,7 @@ PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();;

diff --git a/phylodiversitycommand.h b/phylodiversitycommand.h
index df04b35d66f1c0dc36893074f6c840711395c49b..1be0e07a7c01398dce1cfd1f091269bbc68fbeca 100644 (file)
--- a/phylodiversitycommand.h
+++ b/phylodiversitycommand.h
@@ -27,6 +27,7 @@ class PhyloDiversityCommand : public Command {
                string getCommandName()                 { return "phylo.diversity";                     }
                string getCommandCategory()             { return "Hypothesis Testing";          }
                string getHelpString(); 
+               string getCitation() { return "http://www.mothur.org/wiki/Phylo.diversity"; }
        
                int execute();
                void help() { m->mothurOut(getHelpString()); }

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index 70f2b2f4e93df4af17aabdd804103a99ef696cf6..c03fcc1ac133572fc7d821816edadc0b1fc32ecb 100644 (file)
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -76,6 +76,7 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/phylotypecommand.h b/phylotypecommand.h
index 30a578221f09042817534b51f91d8e33f3125c6c..a0411308e01121af1a56a68dd28218b421598cbc 100644 (file)
--- a/phylotypecommand.h
+++ b/phylotypecommand.h
@@ -27,6 +27,7 @@ public:
        string getCommandName()                 { return "phylotype";           }
        string getCommandCategory()             { return "Clustering";          }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Phylotype"; }
        
        int execute();
        void help() { m->mothurOut(getHelpString()); }

diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index d1309edde7631d2c8edb0f54c67be9cf02e671d2..7a9d53089cd1b59b7fd278936c28e3f231bea005 100644 (file)
--- a/pipelinepdscommand.cpp
+++ b/pipelinepdscommand.cpp
@@ -94,6 +94,7 @@ PipelineCommand::PipelineCommand(string option) {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/pipelinepdscommand.h b/pipelinepdscommand.h
index 13695a6ec9a178918ab74242d9a2f05a89b9ead7..c4b4646881f5c1b6bfbd9a682bda765a70c4193f 100644 (file)
--- a/pipelinepdscommand.h
+++ b/pipelinepdscommand.h
@@ -27,6 +27,7 @@ public:
        string getCommandName()                 { return "pipeline.pds";        }
        string getCommandCategory()             { return "Hidden";                      }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Pipeline.pds"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index 9f96ebd43a836bf699aa5ae1fff55f8752ad748a..9299a6c6fc26e222869d515eb3fc362d0671bced 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -73,6 +73,7 @@ PreClusterCommand::PreClusterCommand(string option) {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/preclustercommand.h b/preclustercommand.h
index d8ee57de9424e623d0455e0327e6f636ce569135..8302fedc78717b73a642d28f08d8a173ad2fc77b 100644 (file)
--- a/preclustercommand.h
+++ b/preclustercommand.h
@@ -38,6 +38,7 @@ public:
        string getCommandName()                 { return "pre.cluster";                         }
        string getCommandCategory()             { return "Sequence Processing";         }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Pre.cluster"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/quitcommand.cpp b/quitcommand.cpp
index 85e8b526c455cfb5ee8c4ca50b64daec92dd6c24..2c302e9e6b4f195c7d4acb1df97fd6110ea02ad5 100644 (file)
--- a/quitcommand.cpp
+++ b/quitcommand.cpp
@@ -15,6 +15,7 @@ QuitCommand::QuitCommand(string option) {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 
 }
 //**********************************************************************************************************************

diff --git a/quitcommand.h b/quitcommand.h
index e24bb775aa89ec31f7db5135ecb9952d570a2fb9..f1929bf3b861926a893615f12a8e36c8e8f326d8 100644 (file)
--- a/quitcommand.h
+++ b/quitcommand.h
@@ -27,6 +27,7 @@ public:
        string getCommandName()                 { return "quit";                }
        string getCommandCategory()             { return "Hidden";              }
        string getHelpString() { return "The quit command will terminate mothur and should be in the following format: quit() or quit. \n"; }   
+       string getCitation() { return "no citation"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index 7f2a1d2e752ce54d971845acdfa8848c4bada8a1..1c04bc4384fb632db099867821b6ffb3b4d79e95 100644 (file)
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -107,7 +107,8 @@ RareFactCommand::RareFactCommand(string option)  {
                allLines = 1;
                                                
                //allow user to run help
-               if(option == "help") { abort = true; calledHelp = true; }
+               if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/rarefactcommand.h b/rarefactcommand.h
index 67ab70ce2caede69c32fc8a61f6fe258d2133e80..58e6819bf07ef6d63d6fbf8f4bb92a2f154bf163 100644 (file)
--- a/rarefactcommand.h
+++ b/rarefactcommand.h
@@ -27,6 +27,7 @@ public:
        string getCommandName()                 { return "rarefaction.single";          }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Rarefaction.single"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index fb5527a03faa02c913e48a583e0a32705932ec45..0292cba70c536b38049dc943957127ec9a0cb95f 100644 (file)
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -81,6 +81,7 @@ RareFactSharedCommand::RareFactSharedCommand(string option)  {
                                
                //allow user to run help
                if(option == "help") {  help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/rarefactsharedcommand.h b/rarefactsharedcommand.h
index 8219e613b3c71d657deb31deb8a948f501dc6e52..54d0495fdc8a1ac5063c8c01ff24970cea2b02fb 100644 (file)
--- a/rarefactsharedcommand.h
+++ b/rarefactsharedcommand.h
@@ -26,6 +26,7 @@ public:
        string getCommandName()                 { return "rarefaction.shared";          }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Rarefaction.shared"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/readdistcommand.cpp b/readdistcommand.cpp
index d3cbbb1ff22335b346cb5c01ac90b8dd7c560149..8dadc7e705c8fe78a9f4b47a3ed1479607745390 100644 (file)
--- a/readdistcommand.cpp
+++ b/readdistcommand.cpp
@@ -19,6 +19,7 @@ ReadDistCommand::ReadDistCommand(string option) {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        /*//valid paramters for this command

diff --git a/readdistcommand.h b/readdistcommand.h
index 8c248cd0af21ff65cb6eab139f11e56f6bc74e83..eaa4484bc6c9e2fd90acf8b50c2c17b2675aabef 100644 (file)
--- a/readdistcommand.h
+++ b/readdistcommand.h
@@ -32,6 +32,7 @@ public:
        string getCommandName()                 { return "read.dist";   }
        string getCommandCategory()             { return "Hidden";      }
        string getHelpString() { return "This command is no longer available. You can provide your distance files directly to the downstream commands like cluster."; } 
+       string getCitation() { return "http://www.mothur.org/wiki/Read.dist"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/readotucommand.cpp b/readotucommand.cpp
index 19c936e4ec4fd069849ac413721f7501f4fbc3ad..f39e8df2c382f02451848ca41ec6edb23e07aa49 100644 (file)
--- a/readotucommand.cpp
+++ b/readotucommand.cpp
@@ -32,6 +32,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        /*

diff --git a/readotucommand.h b/readotucommand.h
index 6b3d1e0ed3ec709181f78ee8428db2ff273c88d1..0f6644bdb4b8b0126f5ace2b5f11f9e505f44094 100644 (file)
--- a/readotucommand.h
+++ b/readotucommand.h
@@ -24,6 +24,7 @@ public:
        string getCommandName()                 { return "read.otu";    }
        string getCommandCategory()             { return "Hidden";      }
        string getHelpString() { return "This command is no longer available. You can provide your files directly to the downstream commands like collect.shared."; }   
+       string getCitation() { return "http://www.mothur.org/wiki/Read.otu"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/readtreecommand.cpp b/readtreecommand.cpp
index c476f5a89928cf131593178b40eb50d60130a7bd..7660643f062df6413e2d0b5fa846ebb798a0301f 100644 (file)
--- a/readtreecommand.cpp
+++ b/readtreecommand.cpp
@@ -17,6 +17,7 @@ ReadTreeCommand::ReadTreeCommand(string option)  {
                                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        /*

diff --git a/readtreecommand.h b/readtreecommand.h
index 25e08252dd29c0eab2f5c985805408b3c83e10e3..70d3c6e27d8cdd135483e7f4c3c1e5ee57df067c 100644 (file)
--- a/readtreecommand.h
+++ b/readtreecommand.h
@@ -25,6 +25,7 @@ public:
        string getCommandName()                 { return "read.tree";   }
        string getCommandCategory()             { return "Hidden";      }
        string getHelpString() { return "This command is no longer available. You can provide your files directly to the downstream commands like unifrac.unweighted."; }       
+       string getCitation() { return "http://www.mothur.org/wiki/Read.tree"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp
index e0943cf0cb52f2c2ba3faf7fe8a5e2add7281597..5a70b27456e782ddba0ab0c2a133ad1d9831a540 100644 (file)
--- a/removegroupscommand.cpp
+++ b/removegroupscommand.cpp
@@ -79,6 +79,7 @@ RemoveGroupsCommand::RemoveGroupsCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/removegroupscommand.h b/removegroupscommand.h
index 955d94d5090b5fc6caf4ba2a937261a173a3eb91..ce352ca58c93e1b73adeee2c384418dd877af895 100644 (file)
--- a/removegroupscommand.h
+++ b/removegroupscommand.h
@@ -26,6 +26,7 @@ public:
        string getCommandName()                 { return "remove.groups";                       }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Remove.groups"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/removelineagecommand.cpp b/removelineagecommand.cpp
index cf26ea07385360e9b5180b68b901970f6fc4a732..22453a46078a7e99b33c07351722913fbb88f854 100644 (file)
--- a/removelineagecommand.cpp
+++ b/removelineagecommand.cpp
@@ -84,6 +84,7 @@ RemoveLineageCommand::RemoveLineageCommand(string option)  {
                                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();       

diff --git a/removelineagecommand.h b/removelineagecommand.h
index 9fdca48db66da3e0ddf5c603949c7380e61155b0..124f6e309f4b5e6a5842f88da7fdcaabbbf22eac 100644 (file)
--- a/removelineagecommand.h
+++ b/removelineagecommand.h
@@ -24,6 +24,7 @@ class RemoveLineageCommand : public Command {
                string getCommandName()                 { return "remove.lineage";                      }
                string getCommandCategory()             { return "Phylotype Analysis";          }
                string getHelpString(); 
+               string getCitation() { return "http://www.mothur.org/wiki/Remove.lineage"; }
        
                int execute(); 
                void help() { m->mothurOut(getHelpString()); }  

diff --git a/removeotuscommand.cpp b/removeotuscommand.cpp
index 6c8cf6a76561c151eead8d4ac151c286ba0283ad..30f337bf7fffc90bcdf7d9ebb8cc97611c6ebd29 100644 (file)
--- a/removeotuscommand.cpp
+++ b/removeotuscommand.cpp
@@ -75,6 +75,7 @@ RemoveOtusCommand::RemoveOtusCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/removeotuscommand.h b/removeotuscommand.h
index 801eedc6b598820dc101ad73d505e43b87f8f926..cb017b450e78123ea2cd32bbbf93675cd1bc15b5 100644 (file)
--- a/removeotuscommand.h
+++ b/removeotuscommand.h
@@ -26,6 +26,7 @@ public:
        string getCommandName()                 { return "remove.otus";                         }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Remove.otus"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/removerarecommand.cpp b/removerarecommand.cpp
index e46aa09f9e338ddd49305758504288f7dc65aa5e..cd0b602113f496af4a1db27850e882ae04d29077 100644 (file)
--- a/removerarecommand.cpp
+++ b/removerarecommand.cpp
@@ -83,6 +83,7 @@ RemoveRareCommand::RemoveRareCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/removerarecommand.h b/removerarecommand.h
index fa22f7a53e6c5149af4c1c1a51504cfb77e9b04e..2ab1272efbef88fdb008f903cf02a7d66ed3215a 100644 (file)
--- a/removerarecommand.h
+++ b/removerarecommand.h
@@ -27,6 +27,7 @@ public:
        string getCommandName()                 { return "remove.rare";                         }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Remove.rare"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index 832bb9e70dd6d7addf6cc364b384a8b3de100417..c7dd5c227622cb3fe0cbf764ff266fdbdea21271 100644 (file)
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -81,6 +81,7 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/removeseqscommand.h b/removeseqscommand.h
index d99151ec022dfdafcfa2327998466549cbcb3eda..b89a509c5f76971d9df9de9a3fd4e9113a70b816 100644 (file)
--- a/removeseqscommand.h
+++ b/removeseqscommand.h
@@ -24,6 +24,7 @@ class RemoveSeqsCommand : public Command {
                string getCommandName()                 { return "remove.seqs";                         }
                string getCommandCategory()             { return "Sequence Processing";         }
                string getHelpString(); 
+               string getCitation() { return "http://www.mothur.org/wiki/Remove.seqs"; }
        
                int execute(); 
                void help() { m->mothurOut(getHelpString()); }  

diff --git a/reversecommand.cpp b/reversecommand.cpp
index 0a2e9380ebd71a5deae50725d3b36c2d10b52c4e..17924c9669b6b5338d15824b2920410fcf305af4 100644 (file)
--- a/reversecommand.cpp
+++ b/reversecommand.cpp
@@ -66,6 +66,7 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/reversecommand.h b/reversecommand.h
index 0d1da8801adc5a2b5e5bfe9cf81ef58789de534c..2e4719a52ada1949236bca5f42d450e7f2eb168d 100644 (file)
--- a/reversecommand.h
+++ b/reversecommand.h
@@ -22,6 +22,7 @@ public:
        string getCommandName()                 { return "reverse.seqs";                        }
        string getCommandCategory()             { return "Sequence Processing";         }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Reverse.seqs"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 7318f9060cdbf5fa2aa5d23205163c1dfecc048a..b68a8cc8ea0042d53222da781770627c58ff3966 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -94,6 +94,7 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/screenseqscommand.h b/screenseqscommand.h
index 602326c42e2ff75afbeb8050479cf7e188b8b634..b165bba2f2f343a8a20a4b07cb2290a43fd13c32 100644 (file)
--- a/screenseqscommand.h
+++ b/screenseqscommand.h
@@ -23,6 +23,7 @@ public:
        string getCommandName()                 { return "screen.seqs";                         }
        string getCommandCategory()             { return "Sequence Processing";         }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Screen.seqs"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index d33805e42b2ac77233b919ced26627d36caf82aa..2b84cc365d4796363bd3e4c5612abb246cfc5aab 100644 (file)
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -66,6 +66,7 @@ AlignCheckCommand::AlignCheckCommand(string option)  {
                        
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index 2e04936a8eea682d1f8511de11a16a601c9e9d1c..daee85a37fd4e13df952ea363da36227dde85143 100644 (file)
--- a/secondarystructurecommand.h
+++ b/secondarystructurecommand.h
@@ -40,6 +40,7 @@ class AlignCheckCommand : public Command {
                string getCommandName()                 { return "align.check";                         }
                string getCommandCategory()             { return "Sequence Processing";         }
                string getHelpString(); 
+               string getCitation() { return "http://www.mothur.org/wiki/Align.check"; }
        
                int execute(); 
                void help() { m->mothurOut(getHelpString()); }  

diff --git a/sensspeccommand.cpp b/sensspeccommand.cpp
index 3eb422e54c1943b71c59e719ce840cbf9675448a..213a2ca99da988257a46ba8e91cb5e4123b5bb0e 100644 (file)
--- a/sensspeccommand.cpp
+++ b/sensspeccommand.cpp
@@ -66,6 +66,7 @@ SensSpecCommand::SensSpecCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        string temp;

diff --git a/sensspeccommand.h b/sensspeccommand.h
index c690d5704652b3b68635614e4cf0b6e65050278e..b2833bf70fc71c24dc76c0d71910b181fc09aa3c 100644 (file)
--- a/sensspeccommand.h
+++ b/sensspeccommand.h
@@ -25,6 +25,7 @@ public:
        string getCommandName()                 { return "sens.spec";                           }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Sens.spec"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 392f5877d9099308593d0cba26a8ff7baddd1d3b..2bb0e57566e59b39a04ce4b4968086894bf64355 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -78,6 +78,7 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        string temp;

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index 19fcd4731d22edc39383003b62c796242b7a4363..a47f182e1157fc8c76e247451a520b7b696f530f 100644 (file)
--- a/seqerrorcommand.h
+++ b/seqerrorcommand.h
@@ -49,6 +49,7 @@ public:
        string getCommandName()                 { return "seq.error";                           }
        string getCommandCategory()             { return "Sequence Processing";         }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Seq.error"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index 2f3638d2ae8bfc9f051c60520c3bf9429afc9a45..1ca79b1b7c738f10f8a23b1d2fe7ca353e0dcd09 100644 (file)
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -66,6 +66,7 @@ SeqSummaryCommand::SeqSummaryCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/seqsummarycommand.h b/seqsummarycommand.h
index 623c3c1e8f400f4262414a5cf546143d698840e7..4bf6759dcda1d4eccda99658780a1e9d819bcece 100644 (file)
--- a/seqsummarycommand.h
+++ b/seqsummarycommand.h
@@ -23,6 +23,7 @@ public:
        string getCommandName()                 { return "summary.seqs";                        }
        string getCommandCategory()             { return "Sequence Processing";         }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Summary.seqs"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }          

diff --git a/setcurrentcommand.cpp b/setcurrentcommand.cpp
index 75d1f943e37a157f66d82987a74b527a0bc5cec3..5582abd03d6220da752943278cad50f4bceb1a76 100644 (file)
--- a/setcurrentcommand.cpp
+++ b/setcurrentcommand.cpp
@@ -83,6 +83,7 @@ SetCurrentCommand::SetCurrentCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        //valid paramters for this command

diff --git a/setcurrentcommand.h b/setcurrentcommand.h
index 4ce90a2b1111b2feb428feaad96570c2a1363825..e942e60b436acbd5ad9a014ddc8176c899e14806 100644 (file)
--- a/setcurrentcommand.h
+++ b/setcurrentcommand.h
@@ -24,6 +24,7 @@ public:
        string getCommandName()                 { return "set.current"; }
        string getCommandCategory()             { return "General";             }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Set.current"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/setdircommand.cpp b/setdircommand.cpp
index 3135b8133c851e5fe58a13ee32e29da05da90216..ff1e2fe0709cf7e4d6549cc11a227ff9dc355e3f 100644 (file)
--- a/setdircommand.cpp
+++ b/setdircommand.cpp
@@ -59,6 +59,7 @@ SetDirectoryCommand::SetDirectoryCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/setdircommand.h b/setdircommand.h
index 0d12e05be43ce8ec055fa5a9bdc39dad62f9bca2..625c83b63d40c6674490fe00b510cd2780449d08 100644 (file)
--- a/setdircommand.h
+++ b/setdircommand.h
@@ -26,6 +26,7 @@ public:
        string getCommandName()                 { return "set.dir";             }
        string getCommandCategory()             { return "General";             }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Set.dir"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/setlogfilecommand.cpp b/setlogfilecommand.cpp
index 88c792c8b4b485bb8019a45fcac8c09f420511d6..576a37c11a26a656d34a9af69972dc4c3a329233 100644 (file)
--- a/setlogfilecommand.cpp
+++ b/setlogfilecommand.cpp
@@ -51,6 +51,7 @@ SetLogFileCommand::SetLogFileCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/setlogfilecommand.h b/setlogfilecommand.h
index ed08180c7a4429a5a484f143e84e42271e12be36..d187c0732cf6dfc676fcdc6ba6b4d57cef0c6dae 100644 (file)
--- a/setlogfilecommand.h
+++ b/setlogfilecommand.h
@@ -26,6 +26,7 @@ public:
        string getCommandName()                 { return "set.logfile";         }
        string getCommandCategory()             { return "General";                     }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Set.logfile"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 8c50247c6845867ff9f99f62760d81300d433779..765dc78e68a2ac12034853c008055b87d58abc03 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -82,6 +82,7 @@ SffInfoCommand::SffInfoCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        //valid paramters for this command

diff --git a/sffinfocommand.h b/sffinfocommand.h
index 0e242afa2f3eab6e53b1d8927c1658aecee97fc6..abfaa4b8a088713278a9384c08909f9eaaad70d2 100644 (file)
--- a/sffinfocommand.h
+++ b/sffinfocommand.h
@@ -70,6 +70,7 @@ public:
        string getCommandName()                 { return "sffinfo";                                     }
        string getCommandCategory()             { return "Sequence Processing";         }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Sffinfo"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index cb4b4e6ced702b08d2b1dda3668f376a82e1e624..54b06fc1fd3a89c3b9012bd6ebf47e597866707f 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -73,6 +73,7 @@ SharedCommand::SharedCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        

diff --git a/sharedcommand.h b/sharedcommand.h
index f1e7c48cd71ee7ff1984e43cb7bb5676a3ee42a5..add6ee8d4a6ebdfd86d6a08d750c7fe88cc3bd35 100644 (file)
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -31,6 +31,7 @@ public:
        string getCommandName()                 { return "make.shared";                         }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Make.shared"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 74669ed0d9dba0425c81e74852482a62e4f29b46..0977cfb2f0db4d4df43ff731628c82c8d918047f 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -98,6 +98,7 @@ ShhherCommand::ShhherCommand(string option) {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/shhhercommand.h b/shhhercommand.h
index 8d29d86e0ec606379e471a363dbe33af34336d8e..dba4d68917e9027edc8d8888de82b2e6938e9256 100644 (file)
--- a/shhhercommand.h
+++ b/shhhercommand.h
@@ -25,6 +25,7 @@ public:
        string getCommandName()                 { return "shhh.seqs";   }
        string getCommandCategory()             { return "Hidden";              }
        string getHelpString(); 
+       string getCitation() { return "no citation"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }          

diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp
index 9c514a9371ae37a24114c3eacf59424733040cfc..ba59dfe66e1b333f88317542e3a17844ac6d558e 100644 (file)
--- a/splitabundcommand.cpp
+++ b/splitabundcommand.cpp
@@ -82,7 +82,7 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
                        
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
-               
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                else {
                        vector<string> myArray = setParameters();
                        

diff --git a/splitabundcommand.h b/splitabundcommand.h
index c883a690d9846febec2059b4d88ea1393ea2f52c..444b55edf9fb7d5f3f126e3f96a3214aa6a167dc 100644 (file)
--- a/splitabundcommand.h
+++ b/splitabundcommand.h
@@ -36,6 +36,7 @@ public:
        string getCommandName()                 { return "split.abund";                         }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Split.abund"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/splitgroupscommand.cpp b/splitgroupscommand.cpp
index c21243431875e4940cc9e75256eb5e3829584792..220c7cc680b1729880001c5bf94ad1fc284a85e9 100644 (file)
--- a/splitgroupscommand.cpp
+++ b/splitgroupscommand.cpp
@@ -70,6 +70,7 @@ SplitGroupCommand::SplitGroupCommand(string option)  {
                        
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/splitgroupscommand.h b/splitgroupscommand.h
index 6705ba98e3ab9ebd165429260828632eca43ede4..a9a6343084c0982b1be2c6a8688a60cb45804375 100644 (file)
--- a/splitgroupscommand.h
+++ b/splitgroupscommand.h
@@ -31,6 +31,7 @@ public:
        string getCommandName()                 { return "split.group";                         }
        string getCommandCategory()             { return "Sequence Processing";         }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Split.group"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp
index 73c1e5c76c48db67f0676ebb4a409aa0660b241d..66ea7e91df86eb1bc5b2b55c23b08dc852fa135a 100644 (file)
--- a/subsamplecommand.cpp
+++ b/subsamplecommand.cpp
@@ -88,6 +88,7 @@ SubSampleCommand::SubSampleCommand(string option) {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/subsamplecommand.h b/subsamplecommand.h
index 6716903105f2fc25d018b77d977d6fa57875a148..5656dab49e7ac7d58665369e58c1950c17b93542 100644 (file)
--- a/subsamplecommand.h
+++ b/subsamplecommand.h
@@ -29,6 +29,7 @@ public:
        string getCommandName()                 { return "sub.sample";  }
        string getCommandCategory()             { return "General";             }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Sub.sample"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/summarycommand.cpp b/summarycommand.cpp
index 6f4bb454ba57c8fba0c4b501038679d5e48e6a61..076c5ebd055259f81afa75c6953be2e13936d064 100644 (file)
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -102,6 +102,7 @@ SummaryCommand::SummaryCommand(string option)  {
                                
                //allow user to run help
                if(option == "help") {  help();  abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/summarycommand.h b/summarycommand.h
index 5535237c98f97d32cacf3f967cb2501199a76473..e79f3e103bb0cd8295aad188950db2d527cf23a2 100644 (file)
--- a/summarycommand.h
+++ b/summarycommand.h
@@ -26,6 +26,7 @@ public:
        string getCommandName()                 { return "summary.single";                      }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Summary.single"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index 13a77ed31b19ae8b87006ea36ba5a53839365ebe..4cc32e320bc063e52e6ee821331cc91a182bc03e 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -119,6 +119,7 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
                                
                //allow user to run help
                if(option == "help") {  help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/summarysharedcommand.h b/summarysharedcommand.h
index 3d177e7a71967225011f6077a6597b4ac3b2486c..a66027ac8c408685563314f548ae540c87de01c6 100644 (file)
--- a/summarysharedcommand.h
+++ b/summarysharedcommand.h
@@ -27,6 +27,7 @@ public:
        string getCommandName()                 { return "summary.shared";                      }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Summary.shared"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/systemcommand.cpp b/systemcommand.cpp
index 6a1e3555f80ffd3f6f5a1565296faf4072995629..129ed8012fe92aafe37ec8946a2f3367d3da79ce 100644 (file)
--- a/systemcommand.cpp
+++ b/systemcommand.cpp
@@ -30,6 +30,7 @@ SystemCommand::SystemCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/systemcommand.h b/systemcommand.h
index 8c959cfb52302df67651a4196ea533751ad596a1..3c22773f2d9e70417c6dc3fef6a58181a16440f0 100644 (file)
--- a/systemcommand.h
+++ b/systemcommand.h
@@ -25,6 +25,7 @@ class SystemCommand : public Command {
                string getCommandName()                 { return "system";              }
                string getCommandCategory()             { return "General";             }
                string getHelpString(); 
+               string getCitation() { return "http://www.mothur.org/wiki/System"; }
        
                int execute(); 
                void help() { m->mothurOut(getHelpString()); }  

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 5d7df3440439c469f3311073d2237b87272e79e6..b5849d3a0d23f49951161ab3c0bde4abd9af86d1 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -125,6 +125,7 @@ TreeGroupCommand::TreeGroupCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/treegroupscommand.h b/treegroupscommand.h
index 6bb35f26056ea14873b3b8d76773c207ab83243b..a52d3b189354f910c3b92cf65a24aeac4a137c68 100644 (file)
--- a/treegroupscommand.h
+++ b/treegroupscommand.h
@@ -40,6 +40,7 @@ public:
        string getCommandName()                 { return "tree.shared";                         }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Tree.shared"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index bb0fa0475d2bfbb344d025ae493a95c557712592..05ed31ebd880af06984fa87cba97349df3f5e8c4 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -81,6 +81,7 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                                                

diff --git a/trimflowscommand.h b/trimflowscommand.h
index 0514a53edc62362d3b95118d5d5e501fd2ef0b2e..339845883f2b1c088d7d21eee05ee81c0d618d08 100644 (file)
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -26,6 +26,7 @@ public:
        string getCommandName()                 { return "trim.flows";  }
        string getCommandCategory()             { return "Hidden";              }
        string getHelpString(); 
+       string getCitation() { return "no citation"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index d8a0d1d00aaf58768d887134ffb29aa3d4e5275c..ae37a2a421ab7e81ca0f973e3a10ca2b00bef327 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -116,6 +116,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 2d0eabc1aa5a1504d23d1fc146f525504f3213f9..c5a94839cd82427c193e3e78a71c8e8434636653 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -26,6 +26,7 @@ public:
        string getCommandName()                 { return "trim.seqs";   }
        string getCommandCategory()             { return "Sequence Processing";         }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Trim.seqs"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index a9ca4d01260340fbdc08ccf423c6022f8dd5abbc..8ec2d06e75d3980b42cb9980ca1631a978418429 100644 (file)
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -80,6 +80,7 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
                        
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index f462d51f9b5b7022d61b0a521f2526475350b034..74ba2b2d18ed2642804befa4f1b4dc8b21595e67 100644 (file)
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -28,6 +28,7 @@ class UnifracUnweightedCommand : public Command {
                string getCommandName()                 { return "unifrac.unweighted";          }
                string getCommandCategory()             { return "Hypothesis Testing";          }
                string getHelpString(); 
+               string getCitation() { return "http://www.mothur.org/wiki/Unifrac.unweighted"; }
        
                int execute();
                void help() { m->mothurOut(getHelpString()); }

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index f868129fd2236a3aca06cf27f2e25b2229013ccf..0570945b71d9c8962c46bec2a58525a1e37a5e6f 100644 (file)
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -80,6 +80,7 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
                        
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index 612b64abcfad0804c6981100dc6bdb12ebb5d219..2e2ba3a64f11bf35f7b6ff612bd8b32e6bdd644a 100644 (file)
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -29,6 +29,7 @@ class UnifracWeightedCommand : public Command {
                string getCommandName()                 { return "unifrac.weighted";            }
                string getCommandCategory()             { return "Hypothesis Testing";          }
                string getHelpString(); 
+               string getCitation() { return "http://www.mothur.org/wiki/Unifrac.weighted"; }
        
                int execute();
                void help() { m->mothurOut(getHelpString()); }

diff --git a/venncommand.cpp b/venncommand.cpp
index c6d534e1d8eaae7997c88cd95b700755b211ddb9..fb0560b38d6c5659fc7ae8b88af2160e6b479191 100644 (file)
--- a/venncommand.cpp
+++ b/venncommand.cpp
@@ -87,6 +87,7 @@ VennCommand::VennCommand(string option)  {
                        
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();

diff --git a/venncommand.h b/venncommand.h
index fe0e2a6c1a9a063e9eb08527c64b23703153fed0..47f52015674aa52cd3f137b49d203e78ff1ae70d 100644 (file)
--- a/venncommand.h
+++ b/venncommand.h
@@ -26,6 +26,7 @@ public:
        string getCommandName()                 { return "venn";                                        }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Venn"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }