X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=secondarystructurecommand.cpp;h=36e0f609ca67bd3cd37e7c0d33a98e88cee65e6f;hp=c08ee6ab2d512b56c6d39fa2a1290ab12da22bde;hb=8bc3e5b38c2317a1715f53be22fa96455868c281;hpb=f663afa231c9bc1b5e18e0ea3bdd2b2ee784f5b2

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index c08ee6a..36e0f60 100644
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -10,6 +10,53 @@
 #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 {
+		//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)  {
@@ -36,6 +83,10 @@ 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 = "";		}
@@ -140,7 +191,7 @@ int AlignCheckCommand::execute(){
 		
 		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;