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

[mothur.git] / removeotulabelscommand.cpp

diff --git a/removeotulabelscommand.cpp b/removeotulabelscommand.cpp
index 77305fb49babaa2640d6a69db0a25e0816ac6785..01d8529dded5e9c7e17bd02724158156566dece7 100644 (file)
--- a/removeotulabelscommand.cpp
+++ b/removeotulabelscommand.cpp
@@ -46,14 +46,36 @@ string RemoveOtuLabelsCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string RemoveOtuLabelsCommand::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 =  "pick.taxonomy"; }
+            else if (type == "otucorr") {  outputFileName =  "pick.corr"; }
+            else if (type == "corraxes") {  outputFileName =  "pick.axes"; }
+            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, "RemoveOtuLabelsCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 RemoveOtuLabelsCommand::RemoveOtuLabelsCommand(){      
        try {
                abort = true; calledHelp = true;
                setParameters();
         vector<string> tempOutNames;
                outputTypes["contaxonomy"] = tempOutNames; 
-        outputTypes["otu.corr"] = tempOutNames;
-        outputTypes["corr.axes"] = tempOutNames;
+        outputTypes["otucorr"] = tempOutNames;
+        outputTypes["corraxes"] = tempOutNames;
        }
        catch(exception& e) {
                m->errorOut(e, "RemoveOtuLabelsCommand", "RemoveOtuLabelsCommand");
@@ -127,8 +149,8 @@ RemoveOtuLabelsCommand::RemoveOtuLabelsCommand(string option)  {
             
             vector<string> tempOutNames;
             outputTypes["contaxonomy"] = tempOutNames; 
-            outputTypes["otu.corr"] = tempOutNames;
-            outputTypes["corr.axes"] = tempOutNames;
+            outputTypes["otucorr"] = tempOutNames;
+            outputTypes["corraxes"] = tempOutNames;
             
                        //check for parameters
             accnosfile = validParameter.validFile(parameters, "accnos", true);
@@ -175,7 +197,7 @@ int RemoveOtuLabelsCommand::execute(){
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
         
         //get labels you want to keep
-               readAccnos();
+               labels = m->readAccnos(accnosfile);
                
                if (m->control_pressed) { return 0; }
                
@@ -204,7 +226,7 @@ int RemoveOtuLabelsCommand::readClassifyOtu(){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(constaxonomyfile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(constaxonomyfile)) + "pick.taxonomy";
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(constaxonomyfile)) + getOutputFileNameTag("constaxonomy");
                ofstream out;
                m->openOutputFile(outputFileName, out);
                
@@ -253,7 +275,7 @@ int RemoveOtuLabelsCommand::readOtuAssociation(){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(otucorrfile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(otucorrfile)) + "pick.corr";
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(otucorrfile)) + getOutputFileNameTag("otucorr");
                ofstream out;
                m->openOutputFile(outputFileName, out);
                
@@ -286,7 +308,7 @@ int RemoveOtuLabelsCommand::readOtuAssociation(){
         out.close();
                
                if (wroteSomething == false) { m->mothurOut("Your file only contains labels from the .accnos file."); m->mothurOutEndLine();  }
-               outputNames.push_back(outputFileName);  outputTypes["otu.corr"].push_back(outputFileName);
+               outputNames.push_back(outputFileName);  outputTypes["otucorr"].push_back(outputFileName);
                
                m->mothurOut("Removed " + toString(removedCount) + " lines from your otu.corr file."); m->mothurOutEndLine();
                
@@ -303,7 +325,7 @@ int RemoveOtuLabelsCommand::readCorrAxes(){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(corraxesfile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(corraxesfile)) + "pick.axes";
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(corraxesfile)) + getOutputFileNameTag("corraxes");
                ofstream out;
                m->openOutputFile(outputFileName, out);
                
@@ -336,7 +358,7 @@ int RemoveOtuLabelsCommand::readCorrAxes(){
         out.close();
                
                if (wroteSomething == false) { m->mothurOut("Your file only contains labels from the .accnos file."); m->mothurOutEndLine();  }
-               outputNames.push_back(outputFileName);  outputTypes["corr.axes"].push_back(outputFileName);
+               outputNames.push_back(outputFileName);  outputTypes["corraxes"].push_back(outputFileName);
                
                m->mothurOut("Removed " + toString(removedCount) + " lines from your corr.axes file."); m->mothurOutEndLine();
                
@@ -348,32 +370,6 @@ int RemoveOtuLabelsCommand::readCorrAxes(){
                exit(1);
        }
 }
-
-//**********************************************************************************************************************
-int RemoveOtuLabelsCommand::readAccnos(){
-       try {
-               
-               ifstream in;
-               m->openInputFile(accnosfile, in);
-               string name;
-               
-               while(!in.eof()){
-                       in >> name;
-            
-                       labels.insert(name);
-                       
-                       m->gobble(in);
-               }
-               in.close();     
-               
-               return 0;
-        
-       }
-       catch(exception& e) {
-               m->errorOut(e, "RemoveOtuLabelsCommand", "readAccnos");
-               exit(1);
-       }
-}
 //**********************************************************************************************************************