working on chimera.perseus. made removeConfidences function smarter. Fixed bug in...

[mothur.git] / chimerabellerophoncommand.cpp

diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp
index 1fcb4fc2956023801d72b9242429b544715bc247..ac1645dd4e1f4f271cad18240c80814cf87c2b03 100644 (file)
--- a/chimerabellerophoncommand.cpp
+++ b/chimerabellerophoncommand.cpp
@@ -77,6 +77,7 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        
@@ -170,6 +171,8 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option)  {
                                                        //erase from file list
                                                        fastaFileNames.erase(fastaFileNames.begin()+i);
                                                        i--;
+                                               }else {
+                                                       m->setFastaFile(fastaFileNames[i]);
                                                }
                                        }
                                }
@@ -224,7 +227,7 @@ int ChimeraBellerophonCommand::execute(){
                        
                        chimera->getChimeras();
                        
-                       if (m->control_pressed) { delete chimera; for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } outputTypes.clear(); return 0;        }
+                       if (m->control_pressed) { delete chimera; for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } outputTypes.clear(); return 0;        }
                        
                #ifdef USE_MPI
                        MPI_File outMPI;
@@ -260,7 +263,7 @@ int ChimeraBellerophonCommand::execute(){
                        
                #endif
                        
-                       if (m->control_pressed) { remove(accnosFileName.c_str()); remove(outputFileName.c_str()); for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } outputTypes.clear(); delete chimera;  return 0;       }
+                       if (m->control_pressed) { m->mothurRemove(accnosFileName); m->mothurRemove(outputFileName); for (int i = 0; i < outputNames.size(); i++) {      m->mothurRemove(outputNames[i]);        } outputTypes.clear(); delete chimera;  return 0;       }
                        
                        m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();