X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=splitgroupscommand.cpp;h=3fa7d047b372a1c4335b9446c1b34d2aac9b702a;hb=5bb0453ee6ab8f7e700b5d0c61a84fdc73db4976;hp=6f8788a28daed38deeed9b419b28b699cffb6b55;hpb=cea46f0830d8d1a6dc26e3410fc283d26c355831;p=mothur.git

diff --git a/splitgroupscommand.cpp b/splitgroupscommand.cpp
index 6f8788a..3fa7d04 100644
--- a/splitgroupscommand.cpp
+++ b/splitgroupscommand.cpp
@@ -10,6 +10,55 @@
 #include "splitgroupscommand.h"
 #include "sharedutilities.h"
 
+//**********************************************************************************************************************
+vector<string> SplitGroupCommand::getValidParameters(){	
+	try {
+		string Array[] =  {"name","group","groups","fasta","outputdir","inputdir"}; 
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SplitGroupCommand", "getValidParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> SplitGroupCommand::getRequiredParameters(){	
+	try {
+		string Array[] =  {"fasta","group"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SplitGroupCommand", "getRequiredParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> SplitGroupCommand::getRequiredFiles(){	
+	try {
+		vector<string> myArray;
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SplitGroupCommand", "getRequiredFiles");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+SplitGroupCommand::SplitGroupCommand(){	
+	try {
+		abort = true;
+		//initialize outputTypes
+		vector<string> tempOutNames;
+		outputTypes["fasta"] = tempOutNames;
+		outputTypes["name"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SplitGroupCommand", "SplitGroupCommand");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 SplitGroupCommand::SplitGroupCommand(string option)  {
 	try {
@@ -33,7 +82,12 @@ SplitGroupCommand::SplitGroupCommand(string option)  {
 			for (it = parameters.begin(); it != parameters.end(); it++) { 
 				if (validParameter.isValidParameter(it->first, myArray, it->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 = "";		}
@@ -187,13 +241,13 @@ int SplitGroupCommand::splitFasta() {
 			temp = new ofstream;
 			filehandles[Groups[i]+"fasta"] = temp;
 			m->openOutputFile(filerootFasta + Groups[i] + ".fasta", *(filehandles[Groups[i]+"fasta"]));
-			outputNames.push_back(filerootFasta + Groups[i] + ".fasta");
+			outputNames.push_back(filerootFasta + Groups[i] + ".fasta"); outputTypes["fasta"].push_back(filerootFasta + Groups[i] + ".fasta");
 			
 			if (namefile != "") {
 				temp2 = new ofstream;
 				filehandles[Groups[i]+"name"] = temp2;
 				m->openOutputFile(filerootName + Groups[i] + ".names", *(filehandles[Groups[i]+"name"]));
-				outputNames.push_back(filerootName + Groups[i] + ".names");
+				outputNames.push_back(filerootName + Groups[i] + ".names"); outputTypes["name"].push_back(filerootFasta + Groups[i] + ".names");
 			}
 		}
 			
@@ -267,6 +321,15 @@ int SplitGroupCommand::splitFasta() {
 			(*(filehandles[it3->first])).close();
 			delete it3->second;
 		}
+		
+		vector<string> newOutputNames;
+		//remove blank files
+		for (int i = 0; i < outputNames.size(); i++) {
+			if (m->isBlank(outputNames[i])) {
+				remove(outputNames[i].c_str());
+			}else { newOutputNames.push_back(outputNames[i]); }
+		}
+		outputNames = newOutputNames;
 				
 		return 0;