changing command name classify.shared to classifyrf.shared

[mothur.git] / deuniqueseqscommand.cpp

diff --git a/deuniqueseqscommand.cpp b/deuniqueseqscommand.cpp
index 7481416f649ddad983877ab02cac08e5668316d1..f72a7c9c7e1264265d4d28e1072e087cf501c288 100644 (file)
--- 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();