X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerabellerophoncommand.cpp;h=1fc87db562bf2994465ee3b9e043f4a961c4e844;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=7a62d5bb447c3c20d155b15a5edf5f6b71b19b37;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp
index 7a62d5b..1fc87db 100644
--- a/chimerabellerophoncommand.cpp
+++ b/chimerabellerophoncommand.cpp
@@ -171,6 +171,8 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option)  {
 							//erase from file list
 							fastaFileNames.erase(fastaFileNames.begin()+i);
 							i--;
+						}else {
+							m->setFastaFile(fastaFileNames[i]);
 						}
 					}
 				}
@@ -191,13 +193,13 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option)  {
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors);
+			m->mothurConvert(temp, processors);
 			
 			temp = validParameter.validFile(parameters, "window", false);			if (temp == "not found") { temp = "0"; }
-			convert(temp, window);
+			m->mothurConvert(temp, window);
 			
 			temp = validParameter.validFile(parameters, "increment", false);		if (temp == "not found") { temp = "25"; }
-			convert(temp, increment);
+			m->mothurConvert(temp, increment);
 		}
 	}
 	catch(exception& e) {
@@ -225,7 +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;
@@ -261,7 +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();