#include "deconvolutecommand.h"
//**********************************************************************************************************************
-vector<string> DeconvoluteCommand::getValidParameters(){
+vector<string> DeconvoluteCommand::setParameters(){
try {
- string Array[] = {"fasta", "name","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 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, "DeconvoluteCommand", "getValidParameters");
+ m->errorOut(e, "DeconvoluteCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-DeconvoluteCommand::DeconvoluteCommand(){
+string DeconvoluteCommand::getHelpString(){
try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- outputTypes["name"] = tempOutNames;
+ string helpString = "";
+ helpString += "The unique.seqs command reads a fastafile and creates a namesfile.\n";
+ helpString += "It creates a file where the first column is the groupname and the second column is a list of sequence names who have the same sequence. \n";
+ helpString += "If the sequence is unique the second column will just contain its name. \n";
+ helpString += "The unique.seqs command parameters are fasta and name. fasta is required, unless there is a valid current fasta file.\n";
+ helpString += "The unique.seqs command should be in the following format: \n";
+ helpString += "unique.seqs(fasta=yourFastaFile) \n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
+ m->errorOut(e, "DeconvoluteCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> DeconvoluteCommand::getRequiredParameters(){
- try {
- string Array[] = {"fasta"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "DeconvoluteCommand", "getRequiredParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> DeconvoluteCommand::getRequiredFiles(){
+DeconvoluteCommand::DeconvoluteCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "DeconvoluteCommand", "getRequiredFiles");
+ m->errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
exit(1);
}
}
if(option == "help") { help(); abort = true; calledHelp = true; }
else {
- //valid paramters for this command
- string Array[] = {"fasta", "name","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 required parameters
inFastaName = validParameter.validFile(parameters, "fasta", true);
if (inFastaName == "not open") { abort = true; }
- else if (inFastaName == "not found") { inFastaName = ""; m->mothurOut("fasta is a required parameter for the unique.seqs command."); m->mothurOutEndLine(); abort = true; }
+ else if (inFastaName == "not found") {
+ inFastaName = m->getFastaFile();
+ if (inFastaName != "") { m->mothurOut("Using " + inFastaName + " 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; }
+ }
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
exit(1);
}
}
-//**********************************************************************************************************************
-
-void DeconvoluteCommand::help(){
- try {
- m->mothurOut("The unique.seqs command reads a fastafile and creates a namesfile.\n");
- m->mothurOut("It creates a file where the first column is the groupname and the second column is a list of sequence names who have the same sequence. \n");
- m->mothurOut("If the sequence is unique the second column will just contain its name. \n");
- m->mothurOut("The unique.seqs command parameter is fasta and it is required.\n");
- m->mothurOut("The unique.seqs command should be in the following format: \n");
- m->mothurOut("unique.seqs(fasta=yourFastaFile) \n");
- }
- catch(exception& e) {
- m->errorOut(e, "DeconvoluteCommand", "help");
- exit(1);
- }
-}
-
/**************************************************************************************/
int DeconvoluteCommand::execute() {
try {