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

[mothur.git] / readotucommand.cpp

diff --git a/readotucommand.cpp b/readotucommand.cpp
index 8683fc3fa80154729ea5228fcaa38fb03726603a..3d0b94d84fb4ec54fe14e4b07a6adfde21f6f432 100644 (file)
--- a/readotucommand.cpp
+++ b/readotucommand.cpp
@@ -24,8 +24,7 @@ vector<string> ReadOtuCommand::getValidParameters(){
 //**********************************************************************************************************************
 ReadOtuCommand::ReadOtuCommand(){      
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["rabund"] = tempOutNames;
                outputTypes["shared"] = tempOutNames;
@@ -62,11 +61,11 @@ vector<string> ReadOtuCommand::getRequiredFiles(){
 ReadOtuCommand::ReadOtuCommand(string option)  {
        try {
                globaldata = GlobalData::getInstance();
-               abort = false;
+               abort = false; calledHelp = false;   
                allLines = 1;
                
                //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
@@ -290,7 +289,7 @@ ReadOtuCommand::~ReadOtuCommand(){}
 int ReadOtuCommand::execute(){
        try {
        
-               if (abort == true) {    return 0;       }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
        
                if (globaldata->getFormat() == "shared") {
                        
@@ -311,8 +310,22 @@ int ReadOtuCommand::execute(){
                        
                        outputTypes = shared->getOutputFiles();
                        
+                       //set rabund file as new current rabundfile
+                       string current = "";
+                       itTypes = outputTypes.find("rabund");
+                       if (itTypes != outputTypes.end()) {
+                               if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
+                       }
+                       
+                       itTypes = outputTypes.find("shared");
+                       if (itTypes != outputTypes.end()) {
+                               if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
+                       }                       
+                       
                        delete shared;
                }
+               
+                               
                return 0;
        }
        catch(exception& e) {