X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=parsesffcommand.cpp;h=c636ec99221d874ec6b497e2ae3965fd353c8dc0;hp=03d8e96d44308c6a07eaba10344d8fce860e3943;hb=8bc3e5b38c2317a1715f53be22fa96455868c281;hpb=f663afa231c9bc1b5e18e0ea3bdd2b2ee784f5b2

diff --git a/parsesffcommand.cpp b/parsesffcommand.cpp
index 03d8e96..c636ec9 100644
--- a/parsesffcommand.cpp
+++ b/parsesffcommand.cpp
@@ -10,6 +10,53 @@
 #include "parsesffcommand.h"
 #include "sequence.hpp"
 
+//**********************************************************************************************************************
+vector<string> ParseSFFCommand::getValidParameters(){	
+	try {
+		string Array[] =  {"sff", "oligos", "minlength", "outputdir", "inputdir"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ParseSFFCommand", "getValidParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+ParseSFFCommand::ParseSFFCommand(){	
+	try {
+		//initialize outputTypes
+		vector<string> tempOutNames;
+		outputTypes["flow"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ParseSFFCommand", "ParseSFFCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> ParseSFFCommand::getRequiredParameters(){	
+	try {
+		string Array[] =  {"sff"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ParseSFFCommand", "getRequiredParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> ParseSFFCommand::getRequiredFiles(){	
+	try {
+		vector<string> myArray;
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ParseSFFCommand", "getRequiredFiles");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 
 ParseSFFCommand::ParseSFFCommand(string option){
@@ -36,6 +83,10 @@ ParseSFFCommand::ParseSFFCommand(string option){
 				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
 			
+			//initialize outputTypes
+			vector<string> tempOutNames;
+			outputTypes["flow"] = 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 = "";		}
@@ -115,7 +166,7 @@ int ParseSFFCommand::execute(){
 		}
 		else{
 			flowFileNames.push_back(new ofstream((outputDir + m->getRootName(m->getSimpleName(sffFile)) + "flow").c_str(), ios::ate));
-			outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(sffFile)) + "flow"));
+			outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(sffFile)) + "flow")); outputTypes["flow"].push_back((outputDir + m->getRootName(m->getSimpleName(sffFile)) + "flow"));
 		}
 		
 		for(int i=0;i<flowFileNames.size();i++){
@@ -124,7 +175,7 @@ int ParseSFFCommand::execute(){
 			*flowFileNames[i] << setprecision(2);
 		}			
 		
-		if (m->control_pressed) { for(int i=0;i<flowFileNames.size();i++){	flowFileNames[i]->close();  } return 0; }
+		if (m->control_pressed) { outputTypes.clear(); for(int i=0;i<flowFileNames.size();i++){	flowFileNames[i]->close();  } return 0; }
 		
 //		ofstream fastaFile;
 //		m->openOutputFile(m->getRootName(sffFile) + "fasta", fastaFile);
@@ -151,7 +202,7 @@ int ParseSFFCommand::execute(){
 		
 		for(int i=0;i<numReads;i++){
 			
-			if (m->control_pressed) { for(int i=0;i<flowFileNames.size();i++){	flowFileNames[i]->close();  } return 0; }
+			if (m->control_pressed) { outputTypes.clear(); for(int i=0;i<flowFileNames.size();i++){	flowFileNames[i]->close();  } return 0; }
 			
 			inSFF >> seqName;
 			seqName = seqName.substr(1);
@@ -282,6 +333,7 @@ void ParseSFFCommand::getOligos(vector<ofstream*>& outSFFFlowVec){
 					
 					outSFFFlowVec.push_back(new ofstream((outputDir + m->getRootName(m->getSimpleName(sffFile)) + group + ".flow").c_str(), ios::ate));
 					outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(sffFile)) + group + "flow"));
+					outputTypes["flow"].push_back((outputDir + m->getRootName(m->getSimpleName(sffFile)) + group + "flow"));
 				}
 			}
 			m->gobble(inOligos);