X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=deuniqueseqscommand.cpp;h=f72a7c9c7e1264265d4d28e1072e087cf501c288;hp=24438824a0ba70225f9ae435065d4c55fa631084;hb=615301e57c25e241356a9c2380648d117709458d;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17

diff --git a/deuniqueseqscommand.cpp b/deuniqueseqscommand.cpp
index 2443882..f72a7c9 100644
--- a/deuniqueseqscommand.cpp
+++ b/deuniqueseqscommand.cpp
@@ -13,10 +13,10 @@
 //**********************************************************************************************************************
 vector<string> DeUniqueSeqsCommand::setParameters(){	
 	try {
-		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
-		CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pname);
-		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","fasta",false,true,true); parameters.push_back(pfasta);
+		CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pname);
+		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);		}
@@ -45,6 +45,21 @@ string DeUniqueSeqsCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string DeUniqueSeqsCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "fasta") {  pattern = "[filename],redundant.fasta"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "DeUniqueSeqsCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 DeUniqueSeqsCommand::DeUniqueSeqsCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -64,6 +79,7 @@ DeUniqueSeqsCommand::DeUniqueSeqsCommand(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 {
 			vector<string> myArray = setParameters();
@@ -113,7 +129,7 @@ DeUniqueSeqsCommand::DeUniqueSeqsCommand(string option)  {
 				fastaFile = m->getFastaFile(); 
 				if (fastaFile != "") { m->mothurOut("Using " + fastaFile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}	
+			}else { m->setFastaFile(fastaFile); }	
 			
 			//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"){	
@@ -127,7 +143,7 @@ DeUniqueSeqsCommand::DeUniqueSeqsCommand(string option)  {
 				nameFile = m->getNameFile(); 
 				if (nameFile != "") { m->mothurOut("Using " + nameFile + " as input file for the name parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current namefile and the name parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}
+			}else { m->setNameFile(nameFile); }
 		}
 
 	}
@@ -146,22 +162,22 @@ int DeUniqueSeqsCommand::execute() {
 		ofstream out;
 		string outFastaFile = m->getRootName(m->getSimpleName(fastaFile));
 		int pos = outFastaFile.find("unique");
-		if (pos != string::npos) {
-			outFastaFile = outputDir + outFastaFile.substr(0, pos) + "redundant" + m->getExtension(fastaFile);
-		}else{
-			outFastaFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "redundant" + m->getExtension(fastaFile);
-		}
+		if (pos != string::npos) { outFastaFile = outputDir + outFastaFile.substr(0, pos); }
+        else { outFastaFile = outputDir + outFastaFile; }
+        map<string, string> variables; 
+        variables["[filename]"] = outFastaFile;
+        outFastaFile = getOutputFileName("fasta", variables);
 		m->openOutputFile(outFastaFile, out);
 		
 		readNamesFile();
-		if (m->control_pressed) {  out.close(); outputTypes.clear(); remove(outFastaFile.c_str()); return 0; }
+		if (m->control_pressed) {  out.close(); outputTypes.clear(); m->mothurRemove(outFastaFile); return 0; }
 		
 		ifstream in;
 		m->openInputFile(fastaFile, in);
 		
 		while (!in.eof()) {
 		
-			if (m->control_pressed) { in.close(); out.close(); outputTypes.clear(); remove(outFastaFile.c_str()); return 0; }
+			if (m->control_pressed) { in.close(); out.close(); outputTypes.clear(); m->mothurRemove(outFastaFile); return 0; }
 			
 			Sequence seq(in); m->gobble(in);
 			
@@ -195,7 +211,7 @@ int DeUniqueSeqsCommand::execute() {
 			}
 		}
 				
-		if (m->control_pressed) { outputTypes.clear(); remove(outFastaFile.c_str()); return 0; }
+		if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outFastaFile); return 0; }
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();