changes for 1.16.0

[mothur.git] / splitabundcommand.cpp

diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp
index fb0326a479efbc64d09bf946316355ce8dc44bac..80145bfee4f3bfad04ae5becb2f5198e7a109abb 100644 (file)
--- a/splitabundcommand.cpp
+++ b/splitabundcommand.cpp
@@ -237,28 +237,6 @@ int SplitAbundCommand::execute(){
                
                if (listfile != "") { //you are using a listfile to determine abundance
                        if (outputDir == "") { outputDir = m->hasPath(listfile); }
-               
-                       //remove old files so you can append later....
-                       string fileroot = outputDir + m->getRootName(m->getSimpleName(listfile));
-                       if (Groups.size() == 0) {
-                               remove((fileroot + "rare.list").c_str());
-                               remove((fileroot + "abund.list").c_str());
-                               
-                               outputNames.push_back((fileroot + "rare.list"));
-                               outputNames.push_back((fileroot + "abund.list"));
-                               outputTypes["list"].push_back((fileroot + "rare.list"));
-                               outputTypes["list"].push_back((fileroot + "abund.list"));
-                       }else{
-                               for (int i=0; i<Groups.size(); i++) {
-                                       remove((fileroot + Groups[i] + ".rare.list").c_str());
-                                       remove((fileroot + Groups[i] + ".abund.list").c_str());
-                                       
-                                       outputNames.push_back((fileroot + Groups[i] + ".rare.list"));
-                                       outputNames.push_back((fileroot + Groups[i] + ".abund.list"));
-                                       outputTypes["list"].push_back((fileroot + Groups[i] + ".rare.list"));
-                                       outputTypes["list"].push_back((fileroot + Groups[i] + ".abund.list"));
-                               }
-                       }
                        
                        //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
                        set<string> processedLabels;
@@ -390,9 +368,11 @@ int SplitAbundCommand::splitList(ListVector* thisList) {
                        }
                }//end for
 
-               writeList(thisList);
                
                string tag = thisList->getLabel() + ".";
+               
+               writeList(thisList, tag);
+               
                if (groupfile != "")                            {  parseGroup(tag);             }
                if (accnos)                                                     {  writeAccnos(tag);    }
                if (fastafile != "")                            {  parseFasta(tag);             }
@@ -406,7 +386,7 @@ int SplitAbundCommand::splitList(ListVector* thisList) {
        }
 }
 /**********************************************************************************************************************/
-int SplitAbundCommand::writeList(ListVector* thisList) { 
+int SplitAbundCommand::writeList(ListVector* thisList, string tag) { 
        try {
                
                map<string, ofstream*> filehandles;
@@ -428,13 +408,13 @@ int SplitAbundCommand::writeList(ListVector* thisList) {
                        ofstream aout;
                        ofstream rout;
                        
-                       string rare = outputDir + m->getRootName(m->getSimpleName(listfile))  + "rare.list";
-                       m->openOutputFileAppend(rare, rout);
-                       //outputNames.push_back(rare);
+                       string rare = outputDir + m->getRootName(m->getSimpleName(listfile)) + tag + "rare.list";
+                       m->openOutputFile(rare, rout);
+                       outputNames.push_back(rare); outputTypes["list"].push_back(rare);
                        
-                       string abund = outputDir + m->getRootName(m->getSimpleName(listfile))  + "abund.list";
-                       m->openOutputFileAppend(abund, aout);
-                       //outputNames.push_back(abund);
+                       string abund = outputDir + m->getRootName(m->getSimpleName(listfile)) + tag + "abund.list";
+                       m->openOutputFile(abund, aout);
+                       outputNames.push_back(abund); outputTypes["list"].push_back(abund);
 
                        if (rareNames.size() != 0)      {  rout << thisList->getLabel() << '\t' << numRareBins << '\t';         }
                        if (abundNames.size() != 0) {   aout << thisList->getLabel() << '\t' << numAbundBins << '\t';   }
@@ -470,8 +450,10 @@ int SplitAbundCommand::writeList(ListVector* thisList) {
                                temp2 = new ofstream;
                                filehandles[Groups[i]+".abund"] = temp2;
                                
-                               m->openOutputFileAppend(fileroot + Groups[i] + ".rare.list", *(filehandles[Groups[i]+".rare"]));
-                               m->openOutputFileAppend(fileroot + Groups[i] + ".abund.list", *(filehandles[Groups[i]+".abund"]));
+                               m->openOutputFile(fileroot + Groups[i] + tag + ".rare.list", *(filehandles[Groups[i]+".rare"]));
+                               m->openOutputFile(fileroot + Groups[i] + tag + ".abund.list", *(filehandles[Groups[i]+".abund"]));
+                               outputNames.push_back(fileroot + Groups[i] + tag + ".rare.list"); outputTypes["list"].push_back(fileroot + Groups[i] + tag + ".rare.list");
+                               outputNames.push_back(fileroot + Groups[i] + tag + ".abund.list"); outputTypes["list"].push_back(fileroot + Groups[i] + tag + ".abund.list");
                        }
                        
                        map<string, string> groupVector;