X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=deuniqueseqscommand.cpp;h=f72a7c9c7e1264265d4d28e1072e087cf501c288;hp=7481416f649ddad983877ab02cac08e5668316d1;hb=615301e57c25e241356a9c2380648d117709458d;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc

diff --git a/deuniqueseqscommand.cpp b/deuniqueseqscommand.cpp
index 7481416..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; 
@@ -147,11 +162,11 @@ 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();