X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimerabellerophoncommand.cpp;h=bb119e41c8e5b40dd681793c43c10f4c6f7e6c61;hp=0031acb15b750823bb8cb3afed79d79f9a07d399;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=220dc345e493cddc569521111ce32ac4d965ab7f

diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp
index 0031acb..bb119e4 100644
--- a/chimerabellerophoncommand.cpp
+++ b/chimerabellerophoncommand.cpp
@@ -13,14 +13,14 @@
 //**********************************************************************************************************************
 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 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);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter pfasta("fasta", "InputTypes", "", "", "none","none","none","chimera-accnos",false,true,true); parameters.push_back(pfasta);
+		CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pfilter);
+		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,true); parameters.push_back(pprocessors);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
 		
 		vector<string> myArray;
 		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
@@ -57,6 +57,22 @@ string ChimeraBellerophonCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string ChimeraBellerophonCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "chimera") {  pattern = "[filename],bellerophon.chimeras"; } 
+        else if (type == "accnos") {  pattern = "[filename],bellerophon.accnos"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "ChimeraBellerophonCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 ChimeraBellerophonCommand::ChimeraBellerophonCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -193,13 +209,13 @@ 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) {
@@ -221,13 +237,15 @@ 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";
+			if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]);  }//if user entered a file with a path then preserve it	
+            map<string, string> variables; 
+            variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i]));
+			string outputFileName = getOutputFileName("chimera", variables);
+			string accnosFileName = getOutputFileName("accnos", variables);
 			
 			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;
@@ -263,7 +281,7 @@ 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();