#include "reversecommand.h"
#include "sequence.hpp"
-
+//**********************************************************************************************************************
+vector<string> ReverseSeqsCommand::getValidParameters(){
+ try {
+ string Array[] = {"fasta", "outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReverseSeqsCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ReverseSeqsCommand::ReverseSeqsCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ReverseSeqsCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"fasta"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReverseSeqsCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ReverseSeqsCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReverseSeqsCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//***************************************************************************************************************
ReverseSeqsCommand::ReverseSeqsCommand(string option) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
void ReverseSeqsCommand::help(){
try {
- m->mothurOut("The reverse.seqs command reads a fastafile and ....\n");
+ m->mothurOut("The reverse.seqs command reads a fastafile and outputs a fasta file containing the reverse compliment.\n");
m->mothurOut("The reverse.seqs command parameter is fasta and it is required.\n");
m->mothurOut("The reverse.seqs command should be in the following format: \n");
m->mothurOut("reverse.seqs(fasta=yourFastaFile) \n");
m->mothurOutEndLine();
m->mothurOut("Output File Name: "); m->mothurOutEndLine();
- m->mothurOut(reverseFile); m->mothurOutEndLine();
+ m->mothurOut(reverseFile); m->mothurOutEndLine(); outputNames.push_back(reverseFile); outputTypes["fasta"].push_back(reverseFile);
m->mothurOutEndLine();