modifications to commands to add headers to list file.

[mothur.git] / removerarecommand.cpp

diff --git a/removerarecommand.cpp b/removerarecommand.cpp
index c378e41447013ba021935d07e76af3ae029ad1b0..24d5bef750e32e06493f7e91351bbf8af0b3099b 100644 (file)
--- a/removerarecommand.cpp
+++ b/removerarecommand.cpp
@@ -68,7 +68,7 @@ string RemoveRareCommand::getOutputPattern(string type) {
         else if (type == "sabund")    {   pattern = "[filename],pick,[extension]";    }
         else if (type == "group")       {   pattern = "[filename],pick,[extension]";    }
         else if (type == "count")       {   pattern = "[filename],pick,[extension]";    }
-        else if (type == "list")        {   pattern = "[filename],pick,[extension]";    }
+        else if (type == "list")        {   pattern = "[filename],[tag],pick,[extension]";    }
         else if (type == "shared")      {   pattern = "[filename],[tag],pick,[extension]";    }
         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
         
@@ -344,24 +344,7 @@ int RemoveRareCommand::execute(){
 //**********************************************************************************************************************
 int RemoveRareCommand::processList(){
        try {
-               string thisOutputDir = outputDir;
-               if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
-        map<string, string> variables; 
-        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
-        variables["[extension]"] = m->getExtension(listfile);
-               string outputFileName = getOutputFileName("list", variables);
-        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
-        variables["[extension]"] = m->getExtension(groupfile);
-               string outputGroupFileName = getOutputFileName("group", variables);
-        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
-        variables["[extension]"] = m->getExtension(countfile);
-        string outputCountFileName = getOutputFileName("count", variables);
-        
-               ofstream out, outGroup;
-               m->openOutputFile(outputFileName, out);
-               
-               bool wroteSomething = false;
-               
+                               
                //you must provide a label because the names in the listfile need to be consistent
                string thisLabel = "";
                if (allLines) { m->mothurOut("For the listfile you must select one label, using first label in your listfile."); m->mothurOutEndLine(); }
@@ -400,6 +383,26 @@ int RemoveRareCommand::processList(){
                                list = input.getListVector(lastLabel); 
                        }
                }
+        
+        string thisOutputDir = outputDir;
+               if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
+        map<string, string> variables;
+        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
+        variables["[extension]"] = m->getExtension(listfile);
+        variables["[tag]"] = list->getLabel();
+               string outputFileName = getOutputFileName("list", variables);
+        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
+        variables["[extension]"] = m->getExtension(groupfile);
+               string outputGroupFileName = getOutputFileName("group", variables);
+        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
+        variables["[extension]"] = m->getExtension(countfile);
+        string outputCountFileName = getOutputFileName("count", variables);
+        
+               ofstream out, outGroup;
+               m->openOutputFile(outputFileName, out);
+               
+               bool wroteSomething = false;
+
                
                //if groupfile is given then use it
                GroupMap* groupMap;
@@ -420,7 +423,11 @@ int RemoveRareCommand::processList(){
         }
                
                
-               if (list != NULL) {     
+               if (list != NULL) {
+            
+            vector<string> binLabels = list->getLabels();
+            vector<string> newLabels;
+            
                        //make a new list vector
                        ListVector newList;
                        newList.setLabel(list->getLabel());
@@ -479,6 +486,7 @@ int RemoveRareCommand::processList(){
 
                                if (binsize > nseqs) { //keep bin
                                        newList.push_back(saveBinNames);
+                    newLabels.push_back(binLabels[i]);
                                        if (groupfile != "") {  for(int k = 0; k < newGroupFile.size(); k++) { outGroup << newGroupFile[k] << endl; }  }
                     else if (countfile != "") { for(int k = 0; k < newGroupFile.size(); k++) {  ct.remove(newGroupFile[k]); } }  
                                }else {  if (countfile != "") {  for(int k = 0; k < names.size(); k++) {  ct.remove(names[k]); } }  }
@@ -487,7 +495,9 @@ int RemoveRareCommand::processList(){
                        //print new listvector
                        if (newList.getNumBins() != 0) {
                                wroteSomething = true;
-                               newList.print(out);
+                               newList.setLabels(newLabels);
+                newList.printHeaders(out);
+                newList.print(out);
                        }
                }