Merge remote-tracking branch 'origin/master'

[mothur.git] / sensspeccommand.cpp

diff --git a/sensspeccommand.cpp b/sensspeccommand.cpp
index 55d90bdd2ce1debc857ddb33a47969e0c3f66933..dfb89b927c2de8dd34dcda801fae80d93281cc63 100644 (file)
--- a/sensspeccommand.cpp
+++ b/sensspeccommand.cpp
@@ -12,16 +12,15 @@
 //**********************************************************************************************************************
 vector<string> SensSpecCommand::setParameters(){       
        try {
-               CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
-               CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pphylip);
-               //CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname);
-               CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pcolumn);
-               CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-               CommandParameter pcutoff("cutoff", "Number", "", "-1.00", "", "", "",false,false); parameters.push_back(pcutoff);
-               CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
-               CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","sensspec",false,true,true); parameters.push_back(plist);
+               CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","",false,false); parameters.push_back(pphylip);
+               CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","",false,false); parameters.push_back(pcolumn);
+               CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+               CommandParameter pcutoff("cutoff", "Number", "", "-1.00", "", "", "","",false,false); parameters.push_back(pcutoff);
+               CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);
+               CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard);
+               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 +44,21 @@ string SensSpecCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string SensSpecCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "sensspec") {  pattern = "[filename],sensspec"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "SensSpecCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 SensSpecCommand::SensSpecCommand(){    
        try {
                abort = true; calledHelp = true; 
@@ -116,16 +130,7 @@ SensSpecCommand::SensSpecCommand(string option)  {
                                        path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["column"] = inputDir + it->second;           }
-                               }
-                               
-                               //it = parameters.find("name");
-                               //user has given a template file
-                               //if(it != parameters.end()){ 
-                                       //path = m->hasPath(it->second);
-                                       //if the user has not given a path then, add inputdir. else leave path alone.
-                                       //if (path == "") {     parameters["name"] = inputDir + it->second;             }
-                               //}
-                               
+                               }                               
                        }
                        //check for required parameters
                        listFile = validParameter.validFile(parameters, "list", true);
@@ -176,12 +181,6 @@ SensSpecCommand::SensSpecCommand(string option)  {
                        else if(!m->isTrue(temp))       {       hard = 0;       }
                        else if(m->isTrue(temp))        {       hard = 1;       }
                        
-//                     temp = validParameter.validFile(parameters, "name", true);
-//                     if (temp == "not found")        {       nameFile = "";          }
-//                     else if(temp == "not open")     {       abort = true;           }
-//                     else                                            {       nameFile = temp;        }
-//                     cout << "name:\t" << nameFile << endl;
-
                        temp = validParameter.validFile(parameters, "cutoff", false);           if (temp == "not found") { temp = "-1.00"; }
                        m->mothurConvert(temp, cutoff);  
 //                     cout << cutoff << endl;
@@ -197,7 +196,9 @@ SensSpecCommand::SensSpecCommand(string option)  {
                                else { allLines = 1;  }
                        }
                        
-                       sensSpecFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + "sensspec";
+            map<string, string> variables; 
+            variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listFile));
+                       sensSpecFileName = getOutputFileName("sensspec",variables);
                }
        }
        catch(exception& e) {
@@ -219,7 +220,7 @@ int SensSpecCommand::execute(){
                if (m->control_pressed) { m->mothurRemove(sensSpecFileName); return 0; }
                
                m->mothurOutEndLine();
-               m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+               m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                m->mothurOut(sensSpecFileName); m->mothurOutEndLine();  
                m->mothurOutEndLine();