X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=consensusseqscommand.cpp;h=d6158ba3ed3bc147027d54098aa71398182dc2f6;hb=01f8d2c7d982a6209211f5abbcf2a086fdf60d0a;hp=e32867f3737b27bc3b9e929a73f142fe564d48c4;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/consensusseqscommand.cpp b/consensusseqscommand.cpp
index e32867f..d6158ba 100644
--- a/consensusseqscommand.cpp
+++ b/consensusseqscommand.cpp
@@ -53,6 +53,28 @@ string ConsensusSeqsCommand::getHelpString(){
 		exit(1);
 	}
 }
+//**********************************************************************************************************************
+string ConsensusSeqsCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string outputFileName = "";
+		map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "fasta") {  outputFileName =  "cons.fasta"; }
+            else if (type == "name") {  outputFileName =  "cons.names"; }
+            else if (type == "summary") {  outputFileName =  "cons.summary"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ConsensusSeqsCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
 
 //**********************************************************************************************************************
 ConsensusSeqsCommand::ConsensusSeqsCommand(){	
@@ -142,7 +164,7 @@ ConsensusSeqsCommand::ConsensusSeqsCommand(string option)  {
 			}else { m->setFastaFile(fastafile); }	
 			
 			namefile = validParameter.validFile(parameters, "name", true);
-			if (namefile == "not open") { abort = true; }
+			if (namefile == "not open") { namefile = ""; abort = true; }
 			else if (namefile == "not found") { namefile = ""; }
 			else { m->setNameFile(namefile); }
 			
@@ -159,11 +181,15 @@ ConsensusSeqsCommand::ConsensusSeqsCommand(string option)  {
 			}
 			
 			string temp = validParameter.validFile(parameters, "cutoff", false);  if (temp == "not found") { temp = "100"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
 			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	outputDir = m->hasPath(fastafile);	}
-
+			
+			if (namefile == ""){
+				vector<string> files; files.push_back(fastafile); 
+				parser.getNameFile(files);
+			}
 		}
 	}
 	catch(exception& e) {
@@ -190,7 +216,7 @@ int ConsensusSeqsCommand::execute(){
 		if (listfile == "") {
 			
 			ofstream outSummary;
-			string outputSummaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "cons.summary";
+			string outputSummaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("summary");
 			m->openOutputFile(outputSummaryFile, outSummary);
 			outSummary.setf(ios::fixed, ios::floatfield); outSummary.setf(ios::showpoint);
 			outputNames.push_back(outputSummaryFile); outputTypes["summary"].push_back(outputSummaryFile);
@@ -198,7 +224,7 @@ int ConsensusSeqsCommand::execute(){
 			outSummary << "PositioninAlignment\tA\tT\tG\tC\tGap\tNumberofSeqs\tConsensusBase" << endl;
 			
 			ofstream outFasta;
-			string outputFastaFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "cons.fasta";
+			string outputFastaFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta");
 			m->openOutputFile(outputFastaFile, outFasta);
 			outputNames.push_back(outputFastaFile); outputTypes["fasta"].push_back(outputFastaFile);
 			
@@ -366,18 +392,18 @@ int ConsensusSeqsCommand::processList(ListVector*& list){
 	try{
 		
 		ofstream outSummary;
-		string outputSummaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + ".cons.summary";
+		string outputSummaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + getOutputFileNameTag("summary");
 		m->openOutputFile(outputSummaryFile, outSummary);
 		outSummary.setf(ios::fixed, ios::floatfield); outSummary.setf(ios::showpoint);
 		outputNames.push_back(outputSummaryFile); outputTypes["summary"].push_back(outputSummaryFile);
 		
 		ofstream outName;
-		string outputNameFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + ".cons.names";
+		string outputNameFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + getOutputFileNameTag("name");
 		m->openOutputFile(outputNameFile, outName);
 		outputNames.push_back(outputNameFile); outputTypes["name"].push_back(outputNameFile);
 		
 		ofstream outFasta;
-		string outputFastaFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + ".cons.fasta";
+		string outputFastaFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + getOutputFileNameTag("fasta");
 		m->openOutputFile(outputFastaFile, outFasta);
 		outputNames.push_back(outputFastaFile); outputTypes["fasta"].push_back(outputFastaFile);
 		
@@ -649,38 +675,29 @@ int ConsensusSeqsCommand::readFasta(){
 
 int ConsensusSeqsCommand::readNames(){
 	 try{
-		 
-		 ifstream in;
-		 m->openInputFile(namefile, in);
-		 
-		 string thisname, repnames;
-		 map<string, string>::iterator it;
-		 
-		 bool error = false;
-		 
-		 while(!in.eof()){
-			 
-			 if (m->control_pressed) { break; }
-			 
-			 in >> thisname;		m->gobble(in);		//read from first column
-			 in >> repnames;			//read from second column
-			 
-			 it = nameMap.find(thisname);
+         map<string, string> temp;
+         map<string, string>::iterator it;
+         bool error = false;
+         
+         m->readNames(namefile, temp); //use central buffered read
+         
+         for (map<string, string>::iterator itTemp = temp.begin(); itTemp != temp.end(); itTemp++) {
+             string thisname, repnames;
+             thisname = itTemp->first;
+             repnames = itTemp->second;
+             
+             it = nameMap.find(thisname);
 			 if (it != nameMap.end()) { //then this sequence was in the fastafile
-				 
+				 nameFileMap[thisname] = repnames;	//for later when outputting the new namesFile if the list file is unique
+                 
 				 vector<string> splitRepNames;
 				 m->splitAtComma(repnames, splitRepNames);
 				 
-				 nameFileMap[thisname] = repnames;	//for later when outputting the new namesFile if the list file is unique
 				 for (int i = 0; i < splitRepNames.size(); i++) { nameMap[splitRepNames[i]] = thisname; }
 				 
 			 }else{	m->mothurOut("[ERROR]: " + thisname + " is not in the fasta file, please correct."); m->mothurOutEndLine(); error = true; }
-			 
-			 m->gobble(in);
-		 }
-		 
-		 in.close();
-		 
+         }
+         
 		 if (error) { m->control_pressed = true; }
  
 		 return 0;