fixed io

[mothur.git] / consensusseqscommand.cpp

diff --git a/consensusseqscommand.cpp b/consensusseqscommand.cpp
index e32867f3737b27bc3b9e929a73f142fe564d48c4..d6158ba3ed3bc147027d54098aa71398182dc2f6 100644 (file)
--- 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;