X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerabellerophoncommand.cpp;h=5972c62f028100b71b9007785af7c9d4600aaeb4;hb=f663afa231c9bc1b5e18e0ea3bdd2b2ee784f5b2;hp=d7f60e7901322b44d3548db5200bce9d723407e9;hpb=52ea8f3a52c05331b9bd7519ae0b518bda233d05;p=mothur.git

diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp
index d7f60e7..5972c62 100644
--- 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--;
@@ -91,17 +82,14 @@ 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 = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	outputDir = "";	}
 
 			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);
@@ -161,10 +149,10 @@ int ChimeraBellerophonCommand::execute(){
 			int start = time(NULL);	
 			
 			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";
-			bool hasAccnos = true;
+			
+			if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]);  }//if user entered a file with a path then preserve it		
+			string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) +  "bellerophon.chimeras";
+			string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "bellerophon.accnos";
 			
 			chimera->getChimeras();
 			
@@ -193,10 +181,10 @@ 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();
@@ -206,13 +194,10 @@ int ChimeraBellerophonCommand::execute(){
 			
 			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());	} delete chimera;	return 0;	}
 			
-			//delete accnos file if its blank 
-			if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
-			
 			m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences.");	m->mothurOutEndLine(); m->mothurOutEndLine();
 			
 			outputNames.push_back(outputFileName);
-			if (hasAccnos) {  outputNames.push_back(accnosFileName);  }
+			outputNames.push_back(accnosFileName);
 			
 			delete chimera;
 		}