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

[mothur.git] / clustersplitcommand.cpp

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index 2eee59f6165e28c50f86fd6ab9b1db0920135040..fc0211ee5a5432ef610c6f22696bff74adf0c72b 100644 (file)
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -77,6 +77,29 @@ string ClusterSplitCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string ClusterSplitCommand::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 == "list") {  outputFileName =  "list"; }
+            else if (type == "rabund") {  outputFileName =  "rabund"; }
+            else if (type == "sabund") {  outputFileName =  "sabund"; }
+            else if (type == "column") {  outputFileName =  "dist"; }
+            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, "ClusterSplitCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 ClusterSplitCommand::ClusterSplitCommand(){    
        try {
                abort = true; calledHelp = true; 
@@ -750,14 +773,17 @@ int ClusterSplitCommand::mergeLists(vector<string> listNames, map<float, int> us
                if (outputDir == "") { outputDir += m->hasPath(distfile); }
                fileroot = outputDir + m->getRootName(m->getSimpleName(distfile));
                
-               m->openOutputFile(fileroot+ tag + ".sabund",    outSabund);
-               m->openOutputFile(fileroot+ tag + ".rabund",    outRabund);
-               m->openOutputFile(fileroot+ tag + ".list",              outList);
-                               
-               outputNames.push_back(fileroot+ tag + ".sabund");  outputTypes["list"].push_back(fileroot+ tag + ".list");
-               outputNames.push_back(fileroot+ tag + ".rabund");  outputTypes["rabund"].push_back(fileroot+ tag + ".rabund");
-               outputNames.push_back(fileroot+ tag + ".list");    outputTypes["sabund"].push_back(fileroot+ tag + ".sabund");
+        string sabundFileName = fileroot+ tag + "." + getOutputFileNameTag("sabund");
+        string rabundFileName = fileroot+ tag + "." + getOutputFileNameTag("rabund");
+        string listFileName = fileroot+ tag + "." + getOutputFileNameTag("list");
+        
+               m->openOutputFile(sabundFileName,       outSabund);
+               m->openOutputFile(rabundFileName,       outRabund);
+               m->openOutputFile(listFileName, outList);
                
+               outputNames.push_back(sabundFileName); outputTypes["sabund"].push_back(sabundFileName);
+               outputNames.push_back(rabundFileName); outputTypes["rabund"].push_back(rabundFileName);
+               outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName);               
                map<float, int>::iterator itLabel;
 
                //for each label needed
@@ -1331,7 +1357,7 @@ int ClusterSplitCommand::createMergedDistanceFile(vector< map<string, string> >
                
                string thisOutputDir = outputDir;
                if (outputDir == "") { thisOutputDir = m->hasPath(fastafile); }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "dist";
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("column");
                m->mothurRemove(outputFileName);