#include "binsequencecommand.h"
+//**********************************************************************************************************************
+vector<string> BinSeqCommand::getValidParameters(){
+ try {
+ string AlignArray[] = {"fasta","label","name", "group","outputdir","inputdir"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BinSeqCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> BinSeqCommand::getRequiredParameters(){
+ try {
+ string AlignArray[] = {"fasta"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BinSeqCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> BinSeqCommand::getRequiredFiles(){
+ try {
+ string AlignArray[] = {"list"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BinSeqCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+BinSeqCommand::BinSeqCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BinSeqCommand", "BinSeqCommand");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
BinSeqCommand::BinSeqCommand(string option) {
try {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+
//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"){
outputDir = "";
m->openOutputFile(outputFileName, out);
//save to output list of output file names
- outputNames.push_back(outputFileName);
+ outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
m->mothurOut(list->getLabel()); m->mothurOutEndLine();