added classify.shared command and random forest files. added count file to pcr.seqs...

[mothur.git] / makegroupcommand.cpp

diff --git a/makegroupcommand.cpp b/makegroupcommand.cpp
index e7704642874d050a3de7625a28ed3fae390fe653..77c2a2911468fe8c0cd123eddce3346b02a4c54c 100644 (file)
--- a/makegroupcommand.cpp
+++ b/makegroupcommand.cpp
@@ -16,6 +16,7 @@ vector<string> MakeGroupCommand::setParameters(){
        try {
                CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
                CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+               CommandParameter poutput("output", "String", "", "", "", "", "",false,false); parameters.push_back(poutput);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
                
@@ -47,6 +48,26 @@ string MakeGroupCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string MakeGroupCommand::getOutputFileNameTag(string type, string inputName=""){       
+       try {
+        string outputFileName = "";
+               map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "group")             {   outputFileName =  "groups";         }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "MakeGroupCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 MakeGroupCommand::MakeGroupCommand(){  
        try {
                abort = true; calledHelp = true; 
@@ -159,13 +180,13 @@ MakeGroupCommand::MakeGroupCommand(string option)  {
                                                        //erase from file list
                                                        fastaFileNames.erase(fastaFileNames.begin()+i);
                                                        i--;
-                                               }else{  filename += m->getRootName(m->getSimpleName(fastaFileNames[i]));  }
+                                               }else{  filename += m->getRootName(m->getSimpleName(fastaFileNames[i]));  m->setFastaFile(fastaFileNames[i]); }
                                        }
                                }
                                
                                //prevent giantic file name
-                               if (fastaFileNames.size() > 3) { filename = outputDir + "merge.groups"; }
-                               else {  filename += "groups";  }
+                               if (fastaFileNames.size() > 3) { filename = outputDir + "merge." + getOutputFileNameTag("group"); }
+                               else {  filename += getOutputFileNameTag("group");  }
                                
                                //make sure there is at least one valid file left
                                if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
@@ -205,7 +226,7 @@ int MakeGroupCommand::execute(){
                
                for (int i = 0; i < fastaFileNames.size(); i++) {
                
-                       if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); return 0; }
+                       if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); return 0; }
                        
                        ifstream in;
                        m->openInputFile(fastaFileNames[i], in);
@@ -214,7 +235,7 @@ int MakeGroupCommand::execute(){
                                
                                Sequence seq(in, "no align"); m->gobble(in);
                                
-                               if (m->control_pressed) { outputTypes.clear();  in.close(); out.close(); remove(filename.c_str()); return 0; }
+                               if (m->control_pressed) { outputTypes.clear();  in.close(); out.close(); m->mothurRemove(filename); return 0; }
                                
                                if (seq.getName() != "") {      out << seq.getName() << '\t' << groupsNames[i] << endl;         }
                        }