#include "inputdata.h"
//**********************************************************************************************************************
-vector<string> ConsensusSeqsCommand::getValidParameters(){
+vector<string> ConsensusSeqsCommand::setParameters(){
try {
- string Array[] = {"fasta", "list", "name", "label","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(plist);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "ConsensusSeqsCommand", "getValidParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-ConsensusSeqsCommand::ConsensusSeqsCommand(){
- try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- outputTypes["name"] = tempOutNames;
- outputTypes["summary"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "ConsensusSeqsCommand", "ConsensusSeqsCommand");
+ m->errorOut(e, "ConsensusSeqsCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> ConsensusSeqsCommand::getRequiredParameters(){
+string ConsensusSeqsCommand::getHelpString(){
try {
- string Array[] = {"fasta", "list"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
+ string helpString = "";
+ helpString += "The consensus.seqs command can be used in 2 ways: create a consensus sequence from a fastafile, or with a listfile create a consensus sequence for each otu. Sequences must be aligned.\n";
+ helpString += "The consensus.seqs command parameters are fasta, list, name and label.\n";
+ helpString += "The fasta parameter allows you to enter the fasta file containing your sequences, and is required, unless you have a valid current fasta file. \n";
+ helpString += "The list parameter allows you to enter a your list file. \n";
+ helpString += "The name parameter allows you to enter a names file associated with the fasta file. \n";
+ helpString += "The label parameter allows you to select what distance levels you would like output files for, and are separated by dashes.\n";
+ helpString += "The consensus.seqs command should be in the following format: \n";
+ helpString += "consensus.seqs(fasta=yourFastaFile, list=yourListFile) \n";
+ helpString += "Example: consensus.seqs(fasta=abrecovery.align, list=abrecovery.fn.list) \n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "ConsensusSeqsCommand", "getRequiredParameters");
+ m->errorOut(e, "ConsensusSeqsCommand", "getHelpString");
exit(1);
}
}
+
//**********************************************************************************************************************
-vector<string> ConsensusSeqsCommand::getRequiredFiles(){
+ConsensusSeqsCommand::ConsensusSeqsCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["summary"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "DegapSeqsCommand", "getRequiredFiles");
+ m->errorOut(e, "ConsensusSeqsCommand", "ConsensusSeqsCommand");
exit(1);
}
}
if(option == "help") { help(); abort = true; calledHelp = true; }
else {
- //valid paramters for this command
- string Array[] = {"fasta","list","name","label", "outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
//check for parameters
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not open") { abort = true; }
- else if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the consensus.seqs command."); m->mothurOutEndLine(); abort = true; }
+ else if (fastafile == "not found") {
+ fastafile = m->getFastaFile();
+ if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { abort = true; }
exit(1);
}
}
-//**********************************************************************************************************************
-
-void ConsensusSeqsCommand::help(){
- try {
- m->mothurOut("The consensus.seqs command can be used in 2 ways: create a consensus sequence from a fastafile, or with a listfile create a consensus sequence for each otu. Sequences must be aligned.\n");
- m->mothurOut("The consensus.seqs command parameters are fasta, list, name and label.\n");
- m->mothurOut("The fasta parameter allows you to enter the fasta file containing your sequences, and is required. \n");
- m->mothurOut("The list parameter allows you to enter a your list file. \n");
- m->mothurOut("The name parameter allows you to enter a names file associated with the fasta file. \n");
- m->mothurOut("The label parameter allows you to select what distance levels you would like output files for, and are separated by dashes.\n");
- m->mothurOut("The consensus.seqs command should be in the following format: \n");
- m->mothurOut("consensus.seqs(fasta=yourFastaFile, list=yourListFile) \n");
- m->mothurOut("Example: consensus.seqs(fasta=abrecovery.align, list=abrecovery.fn.list) \n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "ConsensusSeqsCommand", "help");
- exit(1);
- }
-}
-
-//***************************************************************************************************************
-
-ConsensusSeqsCommand::~ConsensusSeqsCommand(){ /* do nothing */ }
-
//***************************************************************************************************************
int ConsensusSeqsCommand::execute(){
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