added load.logfile command. changed summary.single output for subsample=t.

[mothur.git] / classifyotucommand.cpp

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index ef41ee1bab8853f6741938005f775076b60723ab..00ae690214177d94020069986aedbbb0cb118b9e 100644 (file)
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -63,6 +63,27 @@ string ClassifyOtuCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string ClassifyOtuCommand::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 == "constaxonomy") {  outputFileName =  "cons.taxonomy"; }
+            else if (type == "taxsummary") {  outputFileName =  "cons.tax.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, "ClassifyOtuCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 ClassifyOtuCommand::ClassifyOtuCommand(){      
        try {
                abort = true; calledHelp = true; 
@@ -234,10 +255,10 @@ int ClassifyOtuCommand::execute(){
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                //if user gave a namesfile then use it
-               if (namefile != "") {   readNamesFile();        }
+               if (namefile != "") {   m->readNames(namefile, nameMap, true);  }
                
                //read taxonomy file and save in map for easy access in building bin trees
-               readTaxonomyFile();
+               m->readTax(taxfile, taxMap);
                
                if (m->control_pressed) { return 0; }
                
@@ -327,67 +348,6 @@ int ClassifyOtuCommand::execute(){
                exit(1);
        }
 }
-
-//**********************************************************************************************************************
-int ClassifyOtuCommand::readNamesFile() {
-       try {
-               
-               ifstream inNames;
-               m->openInputFile(namefile, inNames);
-               
-               string name, names;
-       
-               while(!inNames.eof()){
-                       inNames >> name;                        //read from first column  A
-                       inNames >> names;               //read from second column  A,B,C,D
-                       m->gobble(inNames);
-                       
-                       //parse names into vector
-                       vector<string> theseNames;
-                       m->splitAtComma(names, theseNames);
-
-                       for (int i = 0; i < theseNames.size(); i++) {  nameMap[theseNames[i]] = name;  }
-                       
-                       if (m->control_pressed) { inNames.close(); nameMap.clear(); return 0; }
-               }
-               inNames.close();
-               
-               return 0;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ClassifyOtuCommand", "readNamesFile");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-int ClassifyOtuCommand::readTaxonomyFile() {
-       try {
-               
-               ifstream in;
-               m->openInputFile(taxfile, in);
-               
-               string name, tax;
-       
-               while(!in.eof()){
-                       in >> name >> tax;              
-                       m->gobble(in);
-                       
-                       //are there confidence scores, if so remove them
-                       if (tax.find_first_of('(') != -1) {  m->removeConfidences(tax); }
-                       
-                       taxMap[name] = tax;
-                       
-                       if (m->control_pressed) { in.close(); taxMap.clear(); return 0; }
-               }
-               in.close();
-               
-               return 0;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ClassifyOtuCommand", "readTaxonomyFile");
-               exit(1);
-       }
-}
 //**********************************************************************************************************************
 vector<string> ClassifyOtuCommand::findConsensusTaxonomy(int bin, ListVector* thisList, int& size, string& conTax) {
        try{
@@ -526,12 +486,12 @@ int ClassifyOtuCommand::process(ListVector* processList) {
                if (outputDir == "") { outputDir += m->hasPath(listfile); }
                                
                ofstream out;
-               string outputFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + ".cons.taxonomy";
+               string outputFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + getOutputFileNameTag("constaxonomy");
                m->openOutputFile(outputFile, out);
                outputNames.push_back(outputFile); outputTypes["constaxonomy"].push_back(outputFile);
                
                ofstream outSum;
-               string outputSumFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + ".cons.tax.summary";
+               string outputSumFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + getOutputFileNameTag("taxsummary");
                m->openOutputFile(outputSumFile, outSum);
                outputNames.push_back(outputSumFile); outputTypes["taxsummary"].push_back(outputSumFile);