X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=makegroupcommand.cpp;h=68b1e84d0e7e6eb811971128d14490832ad390ae;hp=e7704642874d050a3de7625a28ed3fae390fe653;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77

diff --git a/makegroupcommand.cpp b/makegroupcommand.cpp
index e770464..68b1e84 100644
--- a/makegroupcommand.cpp
+++ b/makegroupcommand.cpp
@@ -14,10 +14,11 @@
 //**********************************************************************************************************************
 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 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","group",false,true,true); parameters.push_back(pfasta);
+		CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false,true); 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);
 		
 		vector<string> myArray;
 		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
@@ -47,6 +48,21 @@ string MakeGroupCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string MakeGroupCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "group") {  pattern = "[filename],groups"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "MakeGroupCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 MakeGroupCommand::MakeGroupCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -159,13 +175,15 @@ 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";  }
+                map<string, string> variables; 
+                variables["[filename]"] = filename;
+				if (fastaFileNames.size() > 3) { variables["[filename]"] = outputDir + "merge"; }
+				filename = getOutputFileName("group",variables);  
 				
 				//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 +223,7 @@ 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 +232,7 @@ 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;		}
 			}
@@ -224,7 +242,7 @@ int MakeGroupCommand::execute(){
 		out.close();
 		
 		m->mothurOutEndLine();
-		m->mothurOut("Output File Name: " + filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["group"].push_back(filename); 
+		m->mothurOut("Output File Names: " + filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["group"].push_back(filename); 
 		m->mothurOutEndLine();
 		
 		//set group file as new current groupfile