changing command name classify.shared to classifyrf.shared

[mothur.git] / deuniqueseqscommand.cpp

diff --git a/deuniqueseqscommand.cpp b/deuniqueseqscommand.cpp
index 24438824a0ba70225f9ae435065d4c55fa631084..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; 
@@ -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();