#include "secondarystructurecommand.h"
#include "sequence.hpp"
+//**********************************************************************************************************************
+vector<string> AlignCheckCommand::getValidParameters(){
+ try {
+ string Array[] = {"fasta","map", "outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AlignCheckCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+AlignCheckCommand::AlignCheckCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["aligncheck"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AlignCheckCommand", "AlignCheckCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> AlignCheckCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"fasta","map"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AlignCheckCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> AlignCheckCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AlignCheckCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
AlignCheckCommand::AlignCheckCommand(string option) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["aligncheck"] = 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 = ""; }
m->mothurOutEndLine();
m->mothurOut("Output File Name: "); m->mothurOutEndLine();
- m->mothurOut(outfile); m->mothurOutEndLine();
+ m->mothurOut(outfile); m->mothurOutEndLine(); outputNames.push_back(outfile); outputTypes["aligncheck"].push_back(outfile);
m->mothurOutEndLine();
return 0;