fixed clearcut version bug, added group count output to get.groups and remove.groups

[mothur.git] / removeotuscommand.cpp

diff --git a/removeotuscommand.cpp b/removeotuscommand.cpp
index 0e7d302ecc065c00a364dfe8e58b0b6e46750a6a..f1ef4ac5a80c7e2782843349d1433680b38bda45 100644 (file)
--- a/removeotuscommand.cpp
+++ b/removeotuscommand.cpp
@@ -27,8 +27,7 @@ vector<string> RemoveOtusCommand::getValidParameters(){
 //**********************************************************************************************************************
 RemoveOtusCommand::RemoveOtusCommand(){        
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["group"] = tempOutNames;
                outputTypes["list"] = tempOutNames;
@@ -64,10 +63,10 @@ vector<string> RemoveOtusCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 RemoveOtusCommand::RemoveOtusCommand(string option)  {
        try {
-               abort = false;
+               abort = false; calledHelp = false;   
                
                //allow user to run help
-               if(option == "help") { help(); abort = true; }
+               if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
                        //valid paramters for this command
@@ -182,7 +181,7 @@ void RemoveOtusCommand::help(){
 int RemoveOtusCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                groupMap = new GroupMap(groupfile);
                groupMap->readMap();
@@ -208,6 +207,18 @@ int RemoveOtusCommand::execute(){
                        m->mothurOut("Output File names: "); m->mothurOutEndLine();
                        for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
                        m->mothurOutEndLine();
+                       
+                       //set fasta file as new current fastafile
+                       string current = "";
+                       itTypes = outputTypes.find("group");
+                       if (itTypes != outputTypes.end()) {
+                               if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
+                       }
+                       
+                       itTypes = outputTypes.find("list");
+                       if (itTypes != outputTypes.end()) {
+                               if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
+                       }
                }
                
                return 0;               
@@ -388,6 +399,7 @@ int RemoveOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstr
                
                m->mothurOut(newList.getLabel() + " - removed " + toString(numOtus) + " of the " + toString(list->getNumBins()) + " OTUs."); m->mothurOutEndLine();
                
+               return 0;
                
        }
        catch(exception& e) {