X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerabellerophoncommand.cpp;h=82400112bc8770ca2ded637853028d86e6aede99;hb=529ec122f7cac4af987e121d150b878d7c7a0d5d;hp=1fcb4fc2956023801d72b9242429b544715bc247;hpb=86c838c428a9e7d26f902f5492738241fa72c4e7;p=mothur.git

diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp
index 1fcb4fc..8240011 100644
--- 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);
@@ -57,6 +57,27 @@ string ChimeraBellerophonCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string ChimeraBellerophonCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string outputFileName = "";
+		map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "chimera") {  outputFileName =  "bellerophon.chimeras"; }
+            else if (type == "accnos") {  outputFileName =  "bellerophon.accnos"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ChimeraBellerophonCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 ChimeraBellerophonCommand::ChimeraBellerophonCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -77,6 +98,7 @@ 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 +192,8 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option)  {
 							//erase from file list
 							fastaFileNames.erase(fastaFileNames.begin()+i);
 							i--;
+						}else {
+							m->setFastaFile(fastaFileNames[i]);
 						}
 					}
 				}
@@ -190,13 +214,13 @@ 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) {
@@ -219,12 +243,12 @@ int ChimeraBellerophonCommand::execute(){
 			chimera = new Bellerophon(fastaFileNames[i], filter, correction, window, increment, processors, outputDir);	
 			
 			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";
+			string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) +  getOutputFileNameTag("chimera");
+			string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) +  getOutputFileNameTag("accnos");
 			
 			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 +284,7 @@ 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();