X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=preclustercommand.cpp;h=14409f5a0a6aa86a166f42ff6f99423777237759;hb=6973be461c47c057531f447de22003a30cabc193;hp=a7f211345697a72c18b6fa0aaa1ac40200c46d94;hpb=afcbef163b4f32d0ff25a834cb9af8eef8d06ffa;p=mothur.git

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index a7f2113..14409f5 100644
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -12,13 +12,61 @@
 //**********************************************************************************************************************
 inline bool comparePriority(seqPNode first, seqPNode second) {  return (first.numIdentical > second.numIdentical); }
 //**********************************************************************************************************************
+vector<string> PreClusterCommand::getValidParameters(){	
+	try {
+		string Array[] =  {"fasta", "name", "diffs", "outputdir","inputdir"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PreClusterCommand", "getValidParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+PreClusterCommand::PreClusterCommand(){	
+	try {
+		abort = true; calledHelp = true; 
+		vector<string> tempOutNames;
+		outputTypes["fasta"] = tempOutNames;
+		outputTypes["name"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PreClusterCommand", "PreClusterCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> PreClusterCommand::getRequiredParameters(){	
+	try {
+		string Array[] =  {"fasta"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PreClusterCommand", "getRequiredParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> PreClusterCommand::getRequiredFiles(){	
+	try {
+		vector<string> myArray;
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PreClusterCommand", "getRequiredFiles");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 
 PreClusterCommand::PreClusterCommand(string option) {
 	try {
-		abort = false;
+		abort = false; calledHelp = false;   
 		
 		//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 +84,11 @@ PreClusterCommand::PreClusterCommand(string option) {
 				if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) {  abort = true;  }
 			}
 			
+			//initialize outputTypes
+			vector<string> tempOutNames;
+			outputTypes["fasta"] = tempOutNames;
+			outputTypes["name"] = 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 = "";		}
@@ -113,7 +166,7 @@ void PreClusterCommand::help(){
 int PreClusterCommand::execute(){
 	try {
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		int start = time(NULL);
 		
@@ -189,8 +242,8 @@ int PreClusterCommand::execute(){
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
-		m->mothurOut(newFastaFile); m->mothurOutEndLine();	
-		m->mothurOut(newNamesFile); m->mothurOutEndLine();	
+		m->mothurOut(newFastaFile); m->mothurOutEndLine();	outputNames.push_back(newFastaFile); outputTypes["fasta"].push_back(newFastaFile);
+		m->mothurOut(newNamesFile); m->mothurOutEndLine();	outputNames.push_back(newNamesFile); outputTypes["name"].push_back(newNamesFile);
 		m->mothurOutEndLine();
 
 		return 0;