X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=secondarystructurecommand.cpp;h=c9002cab4a458c1ef9fbb3a2acb85706e01513dc;hb=4169642e8a8d45f71a4a7241ee02f1b1aae29520;hp=c08ee6ab2d512b56c6d39fa2a1290ab12da22bde;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;p=mothur.git

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index c08ee6a..c9002ca 100644
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -10,15 +10,62 @@
 #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; calledHelp = true; 
+		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)  {
 	try {
-		abort = false;
+		abort = false; calledHelp = false;   
 		haderror = 0;
 			
 		//allow user to run help
-		if(option == "help") { help(); abort = true; }
+		if(option == "help") { help(); abort = true; calledHelp = true; }
 		
 		else {
 			//valid paramters for this command
@@ -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 = "";		}
@@ -103,7 +154,7 @@ void AlignCheckCommand::help(){
 int AlignCheckCommand::execute(){
 	try {
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		//get secondary structure info.
 		readMap();
@@ -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;