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

[mothur.git] / otuassociationcommand.cpp

diff --git a/otuassociationcommand.cpp b/otuassociationcommand.cpp
index 93f46ba1e716f80e321245832eb11eabb2bda733..06f83a4f1a390536a9952d10d413ec22613b89cd 100644 (file)
--- a/otuassociationcommand.cpp
+++ b/otuassociationcommand.cpp
@@ -53,12 +53,32 @@ string OTUAssociationCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string OTUAssociationCommand::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 == "otucorr") {  outputFileName =  "otu.corr"; }
+            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, "OTUAssociationCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 OTUAssociationCommand::OTUAssociationCommand(){        
        try {
                abort = true; calledHelp = true; 
                setParameters();
                vector<string> tempOutNames;
-               outputTypes["otu.corr"] = tempOutNames;
+               outputTypes["otucorr"] = tempOutNames;
        }
        catch(exception& e) {
                m->errorOut(e, "OTUAssociationCommand", "OTUAssociationCommand");
@@ -90,7 +110,7 @@ OTUAssociationCommand::OTUAssociationCommand(string option)  {
                        }
                        
                        vector<string> tempOutNames;
-                       outputTypes["otu.corr"] = tempOutNames;
+                       outputTypes["otucorr"] = 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);              
@@ -306,8 +326,8 @@ int OTUAssociationCommand::processShared(){
 int OTUAssociationCommand::process(vector<SharedRAbundVector*>& lookup){
        try {
                
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + "." + method + ".otu.corr";
-               outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName);
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + "." + method + "." + getOutputFileNameTag("otucorr");
+               outputNames.push_back(outputFileName); outputTypes["otucorr"].push_back(outputFileName);
                
                ofstream out;
                m->openOutputFile(outputFileName, out);
@@ -466,8 +486,8 @@ int OTUAssociationCommand::processRelabund(){
 int OTUAssociationCommand::process(vector<SharedRAbundFloatVector*>& lookup){
        try {
                
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + "." + method + ".otu.corr";
-               outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName);
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + "." + method + "." + getOutputFileNameTag("otucorr");
+               outputNames.push_back(outputFileName); outputTypes["otucorr"].push_back(outputFileName);
                
                ofstream out;
                m->openOutputFile(outputFileName, out);