modifications to commands to add headers to list file.

[mothur.git] / removeotuscommand.cpp

diff --git a/removeotuscommand.cpp b/removeotuscommand.cpp
index 16fd8dce8bab96b030a57effd81d218e122628a5..a840bba6d8d91c94cc34350e944a02aa01613ee8 100644 (file)
--- a/removeotuscommand.cpp
+++ b/removeotuscommand.cpp
@@ -243,6 +243,13 @@ int RemoveOtusCommand::execute(){
 //**********************************************************************************************************************
 int RemoveOtusCommand::readListGroup(){
        try {
+        InputData* input = new InputData(listfile, "list");
+               ListVector* list = input->getListVector();
+               string lastLabel = list->getLabel();
+               
+               //using first label seen if none is provided
+               if (label == "") { label = lastLabel; }
+        
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
                map<string, string> variables; 
@@ -263,13 +270,6 @@ int RemoveOtusCommand::readListGroup(){
                ofstream outGroup;
                m->openOutputFile(outputGroupFileName, outGroup);
                
-               InputData* input = new InputData(listfile, "list");
-               ListVector* list = input->getListVector();
-               string lastLabel = list->getLabel();
-               
-               //using first label seen if none is provided
-               if (label == "") { label = lastLabel; }
-               
                //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
                set<string> labels; labels.insert(label);
                set<string> processedLabels;
@@ -365,6 +365,8 @@ int RemoveOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstr
                
                int numOtus = 0;
                //for each bin
+        vector<string> binLabels = list->getLabels();
+        vector<string> newBinLabels;
                for (int i = 0; i < list->getNumBins(); i++) {
                        if (m->control_pressed) { return 0; }
                        
@@ -400,7 +402,8 @@ int RemoveOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstr
                                
                                if (!removeBin) {
                                        //if there are no sequences from the groups we want to remove in this bin add to new list, output to groupfile
-                                       newList.push_back(binnames);    
+                                       newList.push_back(binnames);
+                    newBinLabels.push_back(binLabels[i]);
                                        outGroup << groupFileOutput;
                                }else {
                                        numOtus++;
@@ -414,7 +417,9 @@ int RemoveOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstr
                //print new listvector
                if (newList.getNumBins() != 0) {
                        wroteSomething = true;
-                       newList.print(out);
+                       newList.setLabels(newBinLabels);
+            newList.printHeaders(out);
+            newList.print(out);
                }
                
                m->mothurOut(newList.getLabel() + " - removed " + toString(numOtus) + " of the " + toString(list->getNumBins()) + " OTUs."); m->mothurOutEndLine();