added code to check path for uchime and catchall executables

[mothur.git] / chimerabellerophoncommand.cpp

diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp
index 1fcb4fc2956023801d72b9242429b544715bc247..c519f91ede4bafbf1802dc813d2679be4a792c17 100644 (file)
--- a/chimerabellerophoncommand.cpp
+++ b/chimerabellerophoncommand.cpp
@@ -15,7 +15,7 @@ vector<string> ChimeraBellerophonCommand::setParameters(){
        try {
                CommandParameter pfasta("fasta", "InputTypes", "", "", "none","none","none",false,true); parameters.push_back(pfasta);
                CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pfilter);
-               CommandParameter pcorrection("filter", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pcorrection);
+               CommandParameter pcorrection("correction", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pcorrection);
                CommandParameter pwindow("window", "Number", "", "0", "", "", "",false,false); parameters.push_back(pwindow);
                CommandParameter pincrement("increment", "Number", "", "25", "", "", "",false,false); parameters.push_back(pincrement);
                CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
@@ -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]);
                                                }
                                        }
                                }
@@ -190,13 +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) {
@@ -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();