From: westcott Date: Tue, 10 May 2011 16:44:40 +0000 (+0000) Subject: added citation function to commands X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=e150b0b0664caec517485ee6d69dcdade6dcae77 added citation function to commands --- diff --git a/aligncommand.cpp b/aligncommand.cpp index a75f9d0..95604fc 100644 --- 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 myArray = setParameters(); diff --git a/aligncommand.h b/aligncommand.h index ef5a92e..1e1ebdc 100644 --- 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 f1e5f61..ad5823b 100644 --- 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 myArray = setParameters(); diff --git a/amovacommand.h b/amovacommand.h index f50df46..ff82ac6 100644 --- 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 2ee691e..6f9e538 100644 --- 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 myArray = setParameters(); diff --git a/anosimcommand.h b/anosimcommand.h index 7bc5655..aad676a 100644 --- 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 34965f6..c4ef741 100644 --- 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 myArray = setParameters(); diff --git a/binsequencecommand.h b/binsequencecommand.h index fe83f20..7456a26 100644 --- 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 7f7683b..cc0cfb6 100644 --- 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 myArray = setParameters(); diff --git a/bootstrapsharedcommand.h b/bootstrapsharedcommand.h index 50297b8..78b5c31 100644 --- 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 1e89cdc..29f2220 100644 --- 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 myArray = setParameters(); diff --git a/catchallcommand.h b/catchallcommand.h index a1c9d0e..c9fe285 100644 --- 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 1fcb4fc..7a62d5b 100644 --- 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 867d361..b048459 100644 --- 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 d9dfe16..df4e67d 100644 --- 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 myArray = setParameters(); diff --git a/chimeraccodecommand.h b/chimeraccodecommand.h index 4f047e1..cedec2f 100644 --- 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 c28934c..d82a84a 100644 --- 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 myArray = setParameters(); diff --git a/chimeracheckcommand.h b/chimeracheckcommand.h index 221d35f..fbd49da 100644 --- 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 b11887d..94c2bf5 100644 --- 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 myArray = setParameters(); diff --git a/chimerapintailcommand.h b/chimerapintailcommand.h index abaef19..49912c6 100644 --- 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 8835290..097664e 100644 --- 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 myArray = setParameters(); diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h index e5ffeb6..8d2a428 100644 --- 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 cbc55ef..0e500d4 100644 --- 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 myArray = setParameters(); diff --git a/chopseqscommand.h b/chopseqscommand.h index 92544ee..31b495b 100644 --- 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 8ea9e4b..925deda 100644 --- 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 5ac7e2c..eaf8cc2 100644 --- 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 myArray = setParameters(); OptionParser parser(option); diff --git a/classifyotucommand.h b/classifyotucommand.h index 7f15c71..c38a7c9 100644 --- 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 9d5a625..0d5ef61 100644 --- 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 myArray = setParameters(); diff --git a/classifyseqscommand.h b/classifyseqscommand.h index 115360f..b813d40 100644 --- 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 afb2159..04dbc79 100644 --- 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 myArray = setParameters(); diff --git a/clearcutcommand.h b/clearcutcommand.h index 89fa1ab..702fd7e 100644 --- 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 25ab61b..16348c8 100644 --- 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 myArray = setParameters(); diff --git a/clustercommand.h b/clustercommand.h index bda6140..23f7287 100644 --- 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 2b7b02b..9f51a8c 100644 --- 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 myArray = setParameters(); diff --git a/clusterdoturcommand.h b/clusterdoturcommand.h index f435a98..e76332c 100644 --- 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 c51a96a..2e37e7c 100644 --- 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 myArray = setParameters(); diff --git a/clusterfragmentscommand.h b/clusterfragmentscommand.h index 882ab33..2b02947 100644 --- 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 a695a6a..bdc8075 100644 --- 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 myArray = setParameters(); diff --git a/clustersplitcommand.h b/clustersplitcommand.h index bdefb42..1485613 100644 --- 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 5549fd1..9521314 100644 --- 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 myArray = setParameters(); diff --git a/collectcommand.h b/collectcommand.h index c531520..d250126 100644 --- a/collectcommand.h +++ b/collectcommand.h @@ -37,6 +37,7 @@ public: vector 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 3a2875a..b9b3606 100644 --- 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 myArray = setParameters(); diff --git a/collectsharedcommand.h b/collectsharedcommand.h index d7f2f8f..a10fd55 100644 --- 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 fd80ad1..6a1a4de 100644 --- 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 > getOutputFiles() { return outputTypes; } virtual vector 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 940f840..e522b09 100644 --- 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 6bd5d3e..fdad93a 100644 --- 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 f1c766d..e81627d 100644 --- 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 07a4c08..226b4c9 100644 --- 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 ae91a24..791ec49 100644 --- 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 myArray = setParameters(); diff --git a/corraxescommand.h b/corraxescommand.h index 5f04c6a..f4a3dfe 100644 --- 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 33e51ff..df97fd8 100644 --- 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 myArray = setParameters(); diff --git a/deconvolutecommand.h b/deconvolutecommand.h index 8a1cb87..21a0081 100644 --- 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 c90064f..940672c 100644 --- 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 myArray = setParameters(); diff --git a/degapseqscommand.h b/degapseqscommand.h index db93b02..0bf0a57 100644 --- 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 2443882..aed5303 100644 --- 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 myArray = setParameters(); diff --git a/deuniqueseqscommand.h b/deuniqueseqscommand.h index 96ed29b..a8edea2 100644 --- 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 1be3552..34206a9 100644 --- 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 myArray = setParameters(); diff --git a/distancecommand.h b/distancecommand.h index 23cc6a5..71eac7d 100644 --- 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 613dfda..167dd3c 100644 --- 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 myArray = setParameters(); diff --git a/filterseqscommand.h b/filterseqscommand.h index 75e7895..809c6eb 100644 --- a/filterseqscommand.h +++ b/filterseqscommand.h @@ -25,6 +25,7 @@ public: string getCommandName() { return "filter.seqs"; } string getCommandCategory() { return "Sequence Processing"; } string getHelpString(); + string getCitation() { return "http://www.mothur.org/wiki/Filter.seqs"; } int execute(); void help() { m->mothurOut(getHelpString()); } diff --git a/getcommandinfocommand.cpp b/getcommandinfocommand.cpp index 7ca2453..e75897f 100644 --- 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 myArray = setParameters(); diff --git a/getcommandinfocommand.h b/getcommandinfocommand.h index 4c5b3ab..c67a4ed 100644 --- 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 5f52356..12dcc82 100644 --- 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 myArray = setParameters(); diff --git a/getcurrentcommand.h b/getcurrentcommand.h index aa4f8f4..bfa9168 100644 --- 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 6b76bf2..b39fb64 100644 --- 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 myArray = setParameters(); diff --git a/getgroupcommand.h b/getgroupcommand.h index 79dd805..a539834 100644 --- 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 c7f96ec..e38ac9b 100644 --- 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 myArray = setParameters(); diff --git a/getgroupscommand.h b/getgroupscommand.h index 955de62..fda603c 100644 --- 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 381a950..aba8e8a 100644 --- 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 myArray = setParameters(); diff --git a/getlabelcommand.h b/getlabelcommand.h index 606daf4..7164570 100644 --- 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 dd00c03..c6671d1 100644 --- 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 myArray = setParameters(); diff --git a/getlineagecommand.h b/getlineagecommand.h index 6375b94..d62c50f 100644 --- 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 eb9c980..4dc2063 100644 --- 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 myArray = setParameters(); diff --git a/getlistcountcommand.h b/getlistcountcommand.h index 40ff7d0..a0b5f09 100644 --- a/getlistcountcommand.h +++ b/getlistcountcommand.h @@ -25,7 +25,7 @@ public: vector 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 06a633e..ce4b895 100644 --- 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 myArray = setParameters(); diff --git a/getoturepcommand.h b/getoturepcommand.h index d8f8f09..179a1b3 100644 --- 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 b39b4ab..681deb7 100644 --- 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 myArray = setParameters(); diff --git a/getotuscommand.h b/getotuscommand.h index 34562fe..30f4f3c 100644 --- 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 2f49a3b..f886c23 100644 --- 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 myArray = setParameters(); diff --git a/getrabundcommand.h b/getrabundcommand.h index dd0cefc..81a5d91 100644 --- 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 74ec992..91384fa 100644 --- 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 myArray = setParameters(); diff --git a/getrelabundcommand.h b/getrelabundcommand.h index ab1896f..0df0e7d 100644 --- 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 8208684..3f64136 100644 --- 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 myArray = setParameters(); diff --git a/getsabundcommand.h b/getsabundcommand.h index d17574f..da998f5 100644 --- 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 04c3bd3..ad9698b 100644 --- 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 myArray = setParameters(); diff --git a/getseqscommand.h b/getseqscommand.h index 07d13d6..4fef8e7 100644 --- 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 f627aed..9968770 100644 --- 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 myArray = setParameters(); diff --git a/getsharedotucommand.h b/getsharedotucommand.h index 27a57b0..d7ffef3 100644 --- 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 12f1f9e..3e99473 100644 --- 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 myArray = setParameters(); diff --git a/hclustercommand.h b/hclustercommand.h index 9241e94..f27837a 100644 --- 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 2da1d24..cf5140a 100644 --- 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 myArray = setParameters(); diff --git a/heatmapcommand.h b/heatmapcommand.h index 6fb5ff0..3bb9791 100644 --- 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 0d3bc33..0de3ffc 100644 --- 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 myArray = setParameters(); diff --git a/heatmapsimcommand.h b/heatmapsimcommand.h index dbaa684..ba5a240 100644 --- 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 46393c0..c542899 100644 --- 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 f9d259d..a8d2786 100644 --- 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 myArray = setParameters(); diff --git a/homovacommand.h b/homovacommand.h index ec7a793..8b31cc5 100644 --- 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 c25e4fa..ac7efcf 100644 --- 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 myArray = setParameters(); diff --git a/indicatorcommand.h b/indicatorcommand.h index 05db05c..9c8c6d4 100644 --- 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 c827b52..0210414 100644 --- 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 myArray = setParameters(); diff --git a/libshuffcommand.h b/libshuffcommand.h index 97fcd1c..25b1281 100644 --- 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 d60470c..902ac87 100644 --- 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 myArray = setParameters(); diff --git a/listseqscommand.h b/listseqscommand.h index be53d75..ea48430 100644 --- 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 b4c0e8c..2dd45a5 100644 --- 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 myArray = setParameters(); diff --git a/makefastqcommand.h b/makefastqcommand.h index 946c990..085654f 100644 --- 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 7ca4aa6..e770464 100644 --- 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 myArray = setParameters(); diff --git a/makegroupcommand.h b/makegroupcommand.h index 1206938..f5fb358 100644 --- 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 0c0163b..c3ab352 100644 --- 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 myArray = setParameters(); diff --git a/mantelcommand.h b/mantelcommand.h index 224265b..1a6f27b 100644 --- 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 5dfba36..4ea8f02 100644 --- 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 myArray = setParameters(); diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h index 2871d5e..2c403aa 100644 --- 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 cece52d..c944e3b 100644 --- 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 myArray = setParameters(); diff --git a/mergefilecommand.h b/mergefilecommand.h index 1ecc3cb..1e56f73 100644 --- 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 cb990e4..df74ade 100644 --- 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 myArray = setParameters(); diff --git a/mergegroupscommand.h b/mergegroupscommand.h index 827f5a3..dfd65ad 100644 --- 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 f637eec..99a3043 100644 --- 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 myArray = setParameters(); diff --git a/metastatscommand.h b/metastatscommand.h index 1380444..491e076 100644 --- 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 945d116..5a790af 100644 --- 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 myArray = setParameters(); diff --git a/mgclustercommand.h b/mgclustercommand.h index c23534f..d5c784e 100644 --- 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 3f8e342..4567dbb 100644 --- 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 myArray = setParameters(); diff --git a/nmdscommand.h b/nmdscommand.h index 861e8ea..f099f95 100644 --- 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 12bfc4d..b7fa6f1 100644 --- 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 5f3cacb..718eeb1 100644 --- 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 myArray = setParameters(); diff --git a/normalizesharedcommand.h b/normalizesharedcommand.h index 26bc0e4..6332fd7 100644 --- 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 edfdaea..cc57032 100644 --- 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 myArray = setParameters(); diff --git a/otuhierarchycommand.h b/otuhierarchycommand.h index b82ee76..342b5aa 100644 --- 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 1aa133f..db03251 100644 --- 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 myArray = setParameters(); diff --git a/pairwiseseqscommand.h b/pairwiseseqscommand.h index 52ba63d..6978518 100644 --- 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 75d6fa0..1033ba5 100644 --- 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 myArray = setParameters(); diff --git a/parsefastaqcommand.h b/parsefastaqcommand.h index fe77cf0..dfafca6 100644 --- 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 c79eb63..b791be7 100644 --- 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 myArray = setParameters(); diff --git a/parselistscommand.h b/parselistscommand.h index 065c499..9489b9b 100644 --- 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 1be4697..403b2b8 100644 --- 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 myArray = setParameters(); diff --git a/parsimonycommand.h b/parsimonycommand.h index 274cac4..30c8332 100644 --- 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 6e2cce7..e273e5f 100644 --- 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 myArray = setParameters(); diff --git a/pcacommand.h b/pcacommand.h index 379cf6e..9b4a881 100644 --- 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 607256b..5d91737 100644 --- 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 myArray = setParameters(); diff --git a/pcoacommand.h b/pcoacommand.h index ea4d2b3..d9aa270 100644 --- 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 d15899c..bf502ab 100644 --- 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 myArray = setParameters();; diff --git a/phylodiversitycommand.h b/phylodiversitycommand.h index df04b35..1be0e07 100644 --- 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 70f2b2f..c03fcc1 100644 --- 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 myArray = setParameters(); diff --git a/phylotypecommand.h b/phylotypecommand.h index 30a5782..a041130 100644 --- 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 d1309ed..7a9d530 100644 --- 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 myArray = setParameters(); diff --git a/pipelinepdscommand.h b/pipelinepdscommand.h index 13695a6..c4b4646 100644 --- 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 9f96ebd..9299a6c 100644 --- 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 myArray = setParameters(); diff --git a/preclustercommand.h b/preclustercommand.h index d8ee57d..8302fed 100644 --- 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 85e8b52..2c302e9 100644 --- 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 e24bb77..f1929bf 100644 --- 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 7f2a1d2..1c04bc4 100644 --- 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 myArray = setParameters(); diff --git a/rarefactcommand.h b/rarefactcommand.h index 67ab70c..58e6819 100644 --- 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 fb5527a..0292cba 100644 --- 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 myArray = setParameters(); diff --git a/rarefactsharedcommand.h b/rarefactsharedcommand.h index 8219e61..54d0495 100644 --- 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 d3cbbb1..8dadc7e 100644 --- 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 8c248cd..eaa4484 100644 --- 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 19c936e..f39e8df 100644 --- 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 6b3d1e0..0f6644b 100644 --- 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 c476f5a..7660643 100644 --- 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 25e0825..70d3c6e 100644 --- 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 e0943cf..5a70b27 100644 --- 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 myArray = setParameters(); diff --git a/removegroupscommand.h b/removegroupscommand.h index 955d94d..ce352ca 100644 --- 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 cf26ea0..22453a4 100644 --- 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 myArray = setParameters(); diff --git a/removelineagecommand.h b/removelineagecommand.h index 9fdca48..124f6e3 100644 --- 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 6c8cf6a..30f337b 100644 --- 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 myArray = setParameters(); diff --git a/removeotuscommand.h b/removeotuscommand.h index 801eedc..cb017b4 100644 --- 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 e46aa09..cd0b602 100644 --- 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 myArray = setParameters(); diff --git a/removerarecommand.h b/removerarecommand.h index fa22f7a..2ab1272 100644 --- 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 832bb9e..c7dd5c2 100644 --- 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 myArray = setParameters(); diff --git a/removeseqscommand.h b/removeseqscommand.h index d99151e..b89a509 100644 --- 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 0a2e938..17924c9 100644 --- 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 myArray = setParameters(); diff --git a/reversecommand.h b/reversecommand.h index 0d1da88..2e4719a 100644 --- 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 7318f90..b68a8cc 100644 --- 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 myArray = setParameters(); diff --git a/screenseqscommand.h b/screenseqscommand.h index 602326c..b165bba 100644 --- 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 d33805e..2b84cc3 100644 --- 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 myArray = setParameters(); diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h index 2e04936..daee85a 100644 --- 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 3eb422e..213a2ca 100644 --- 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 c690d57..b2833bf 100644 --- 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 392f587..2bb0e57 100644 --- 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 19fcd47..a47f182 100644 --- 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 2f3638d..1ca79b1 100644 --- 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 myArray = setParameters(); diff --git a/seqsummarycommand.h b/seqsummarycommand.h index 623c3c1..4bf6759 100644 --- 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 75d1f94..5582abd 100644 --- 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 4ce90a2..e942e60 100644 --- 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 3135b81..ff1e2fe 100644 --- 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 myArray = setParameters(); diff --git a/setdircommand.h b/setdircommand.h index 0d12e05..625c83b 100644 --- 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 88c792c..576a37c 100644 --- 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 myArray = setParameters(); diff --git a/setlogfilecommand.h b/setlogfilecommand.h index ed08180..d187c07 100644 --- 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 8c50247..765dc78 100644 --- 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 0e242af..abfaa4b 100644 --- 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 cb4b4e6..54b06fc 100644 --- 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 f1e7c48..add6ee8 100644 --- 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 74669ed..0977cfb 100644 --- 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 myArray = setParameters(); diff --git a/shhhercommand.h b/shhhercommand.h index 8d29d86..dba4d68 100644 --- 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 9c514a9..ba59dfe 100644 --- 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 myArray = setParameters(); diff --git a/splitabundcommand.h b/splitabundcommand.h index c883a69..444b55e 100644 --- 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 c212434..220c7cc 100644 --- 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 myArray = setParameters(); diff --git a/splitgroupscommand.h b/splitgroupscommand.h index 6705ba9..a9a6343 100644 --- 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 73c1e5c..66ea7e9 100644 --- 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 myArray = setParameters(); diff --git a/subsamplecommand.h b/subsamplecommand.h index 6716903..5656dab 100644 --- 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 6f4bb45..076c5eb 100644 --- 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 myArray = setParameters(); diff --git a/summarycommand.h b/summarycommand.h index 5535237..e79f3e1 100644 --- 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 13a77ed..4cc32e3 100644 --- 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 myArray = setParameters(); diff --git a/summarysharedcommand.h b/summarysharedcommand.h index 3d177e7..a66027a 100644 --- 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 6a1e355..129ed80 100644 --- 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 myArray = setParameters(); diff --git a/systemcommand.h b/systemcommand.h index 8c959cf..3c22773 100644 --- 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 5d7df34..b5849d3 100644 --- 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 myArray = setParameters(); diff --git a/treegroupscommand.h b/treegroupscommand.h index 6bb35f2..a52d3b1 100644 --- 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 bb0fa04..05ed31e 100644 --- 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 0514a53..3398458 100644 --- 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 d8a0d1d..ae37a2a 100644 --- 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 myArray = setParameters(); diff --git a/trimseqscommand.h b/trimseqscommand.h index 2d0eabc..c5a9483 100644 --- 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 a9ca4d0..8ec2d06 100644 --- 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 myArray = setParameters(); diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h index f462d51..74ba2b2 100644 --- 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 f868129..0570945 100644 --- 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 myArray = setParameters(); diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h index 612b64a..2e2ba3a 100644 --- 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 c6d534e..fb0560b 100644 --- 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 myArray = setParameters(); diff --git a/venncommand.h b/venncommand.h index fe0e2a6..47f5201 100644 --- 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()); }