fixed order of unifrac commands so that it matches the summary commands

[mothur.git] / chimerabellerophoncommand.cpp

diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp
index 2a38438fdfb4e71b68ac007dde4221a152acd6cf..a504d0b496dec5b23795b546c70b573bc6c0c2ca 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
@@ -42,43 +42,34 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option)  {
                        fastafile = validParameter.validFile(parameters, "fasta", false);
                        if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.bellerophon command."); m->mothurOutEndLine(); abort = true;  }
                        else { 
-                               splitAtDash(fastafile, fastaFileNames);
+                               m->splitAtDash(fastafile, fastaFileNames);
                                
                                //go through files and make sure they are good, if not, then disregard them
                                for (int i = 0; i < fastaFileNames.size(); i++) {
                                        if (inputDir != "") {
-                                               string path = hasPath(fastaFileNames[i]);
+                                               string path = m->hasPath(fastaFileNames[i]);
                                                //if the user has not given a path then, add inputdir. else leave path alone.
                                                if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
                                        }
        
                                        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 = m->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() + m->getSimpleName(fastaFileNames[i]);
+                                                       m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+                                                       ableToOpen = m->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--;
@@ -93,15 +84,15 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option)  {
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  
                                outputDir = ""; 
-                               outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it  
+                               outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it       
                        }
 
                        string temp;
                        temp = validParameter.validFile(parameters, "filter", false);                   if (temp == "not found") { temp = "F"; }
-                       filter = isTrue(temp);
+                       filter = m->isTrue(temp);
                        
                        temp = validParameter.validFile(parameters, "correction", false);               if (temp == "not found") { temp = "T"; }
-                       correction = isTrue(temp);
+                       correction = m->isTrue(temp);
                        
                        temp = validParameter.validFile(parameters, "processors", false);               if (temp == "not found") { temp = "1"; }
                        convert(temp, processors);
@@ -162,8 +153,8 @@ int ChimeraBellerophonCommand::execute(){
                        
                        chimera = new Bellerophon(fastaFileNames[i], filter, correction, window, increment, processors, outputDir);     
                                        
-                       string outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[i])) +  "bellerophon.chimeras";
-                       string accnosFileName = outputDir + getRootName(getSimpleName(fastaFileNames[i])) + "bellerophon.accnos";
+                       string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) +  "bellerophon.chimeras";
+                       string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "bellerophon.accnos";
                        
                        chimera->getChimeras();
                        
@@ -192,10 +183,10 @@ int ChimeraBellerophonCommand::execute(){
                #else
                
                        ofstream out;
-                       openOutputFile(outputFileName, out);
+                       m->openOutputFile(outputFileName, out);
                        
                        ofstream out2;
-                       openOutputFile(accnosFileName, out2);
+                       m->openOutputFile(accnosFileName, out2);
                        
                        numSeqs = chimera->print(out, out2);
                        out.close();