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

[mothur.git] / chimerabellerophoncommand.cpp

diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp
index 34096159b4e1379d5e7c61ea6094d8514d48267c..140a94993df3634fec862bd371f7658390b928e6 100644 (file)
--- a/chimerabellerophoncommand.cpp
+++ b/chimerabellerophoncommand.cpp
@@ -48,8 +48,7 @@ vector<string> ChimeraBellerophonCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 ChimeraBellerophonCommand::ChimeraBellerophonCommand(){        
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["chimera"] = tempOutNames;
                outputTypes["accnos"] = tempOutNames;
@@ -62,10 +61,10 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(){
 //***************************************************************************************************************
 ChimeraBellerophonCommand::ChimeraBellerophonCommand(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
@@ -208,7 +207,7 @@ ChimeraBellerophonCommand::~ChimeraBellerophonCommand(){    /*      do nothing      */      }
 int ChimeraBellerophonCommand::execute(){
        try{
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                for (int i = 0; i < fastaFileNames.size(); i++) {
                        
@@ -241,7 +240,7 @@ int ChimeraBellerophonCommand::execute(){
                        MPI_File_open(MPI_COMM_WORLD, FileName, outMode, MPI_INFO_NULL, &outMPI);  //comm, filename, mode, info, filepointer
                        MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
        
-                       numSeqs = chimera->print(outMPI, outMPIAccnos);
+                       numSeqs = chimera->print(outMPI, outMPIAccnos, "");
                        
                        MPI_File_close(&outMPI);
                        MPI_File_close(&outMPIAccnos);
@@ -254,7 +253,7 @@ int ChimeraBellerophonCommand::execute(){
                        ofstream out2;
                        m->openOutputFile(accnosFileName, out2);
                        
-                       numSeqs = chimera->print(out, out2);
+                       numSeqs = chimera->print(out, out2, "");
                        out.close();
                        out2.close(); 
                        
@@ -270,6 +269,13 @@ int ChimeraBellerophonCommand::execute(){
                        delete chimera;
                }
                
+               //set accnos file as new current accnosfile
+               string current = "";
+               itTypes = outputTypes.find("accnos");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
+               }
+               
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }