changed file divide for trim.seqs

[mothur.git] / chimerabellerophoncommand.cpp

diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp
index 2a38438fdfb4e71b68ac007dde4221a152acd6cf..6d0961689d425b1ffd8ba75a86653453e3e72011 100644 (file)
--- a/chimerabellerophoncommand.cpp
+++ b/chimerabellerophoncommand.cpp
@@ -27,7 +27,7 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option)  {
                        OptionParser parser(option);
                        map<string,string> parameters = parser.getParameters();
                        
-                       ValidParameters validParameter;
+                       ValidParameters validParameter("chimera.bellerophon");
                        map<string,string>::iterator it;
                        
                        //check to make sure all parameters are valid for command
@@ -54,31 +54,22 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option)  {
        
                                        int ableToOpen;
                                        ifstream in;
-                                       
-                                       #ifdef USE_MPI  
-                                               int pid;
-                                               MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
-                                               MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-                               
-                                               if (pid == 0) {
-                                       #endif
 
-                                       ableToOpen = openInputFile(fastaFileNames[i], in);
-                                       in.close();
-                                       
-                                       #ifdef USE_MPI  
-                                                       for (int j = 1; j < processors; j++) {
-                                                               MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD); 
-                                                       }
-                                               }else{
-                                                       MPI_Status status;
-                                                       MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+                                       ableToOpen = openInputFile(fastaFileNames[i], in, "noerror");
+                               
+                                       //if you can't open it, try default location
+                                       if (ableToOpen == 1) {
+                                               if (m->getDefaultPath() != "") { //default path is set
+                                                       string tryPath = m->getDefaultPath() + getSimpleName(fastaFileNames[i]);
+                                                       m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+                                                       ableToOpen = openInputFile(tryPath, in, "noerror");
+                                                       fastaFileNames[i] = tryPath;
                                                }
-                                               
-                                       #endif
+                                       }
+                                       in.close();
 
                                        if (ableToOpen == 1) { 
-                                               m->mothurOut(fastaFileNames[i] + " will be disregarded."); m->mothurOutEndLine(); 
+                                               m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); 
                                                //erase from file list
                                                fastaFileNames.erase(fastaFileNames.begin()+i);
                                                i--;