working on make.contigs. fixed trim.seqs filename issue

[mothur.git] / parselistscommand.cpp

diff --git a/parselistscommand.cpp b/parselistscommand.cpp
index 9459294fa49945a00b270c1d98529de0a93c008d..61cb2454b52ee9e05cf1027995906371b5463762 100644 (file)
--- a/parselistscommand.cpp
+++ b/parselistscommand.cpp
@@ -12,11 +12,11 @@
 //**********************************************************************************************************************
 vector<string> ParseListCommand::setParameters(){      
        try {
-               CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
-               CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
-               CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-               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","list",false,true,true); parameters.push_back(plist);
+               CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pgroup);
+               CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+               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);          }
@@ -46,6 +46,21 @@ string ParseListCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string ParseListCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "list") {  pattern = "[filename],[group],list"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "ParseListCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 ParseListCommand::ParseListCommand(){  
        try {
                abort = true; calledHelp = true; 
@@ -170,16 +185,19 @@ int ParseListCommand::execute(){
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                //set fileroot
-               string fileroot = outputDir + m->getRootName(m->getSimpleName(listfile));
+               map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
                
                //fill filehandles with neccessary ofstreams
                int i;
                ofstream* temp;
-               for (i=0; i<groupMap->namesOfGroups.size(); i++) {
+               vector<string> gGroups = groupMap->getNamesOfGroups();
+               for (i=0; i<gGroups.size(); i++) {
                        temp = new ofstream;
-                       filehandles[groupMap->namesOfGroups[i]] = temp;
+                       filehandles[gGroups[i]] = temp;
                        
-                       string filename = fileroot +  groupMap->namesOfGroups[i] + ".list";
+            variables["[group]"] = gGroups[i];
+                       string filename = getOutputFileName("list",variables);
                        outputNames.push_back(filename); outputTypes["list"].push_back(filename);
                        m->openOutputFile(filename, *temp);
                }
@@ -194,7 +212,8 @@ int ParseListCommand::execute(){
                
                if (m->control_pressed) { 
                        delete input; delete list; delete groupMap;
-                       for (i=0; i<groupMap->namesOfGroups.size(); i++) {  (*(filehandles[groupMap->namesOfGroups[i]])).close();  delete filehandles[groupMap->namesOfGroups[i]]; } 
+                       vector<string> gGroups = groupMap->getNamesOfGroups();
+                       for (i=0; i<gGroups.size(); i++) {  (*(filehandles[gGroups[i]])).close();  delete filehandles[gGroups[i]]; } 
                        for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
                        return 0;
                }
@@ -203,7 +222,7 @@ int ParseListCommand::execute(){
                
                        if (m->control_pressed) { 
                                delete input; delete list; delete groupMap;
-                               for (i=0; i<groupMap->namesOfGroups.size(); i++) {  (*(filehandles[groupMap->namesOfGroups[i]])).close();  delete filehandles[groupMap->namesOfGroups[i]]; } 
+                               for (i=0; i<gGroups.size(); i++) {  (*(filehandles[gGroups[i]])).close();  delete filehandles[gGroups[i]]; } 
                                for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
                                return 0;
                        }
@@ -241,10 +260,10 @@ int ParseListCommand::execute(){
                }
                
                if (m->control_pressed) { 
-                               delete input; delete groupMap;
-                               for (i=0; i<groupMap->namesOfGroups.size(); i++) { (*(filehandles[groupMap->namesOfGroups[i]])).close();  delete filehandles[groupMap->namesOfGroups[i]]; } 
-                               for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
-                               return 0;
+                       delete input; delete groupMap;
+                       for (i=0; i<gGroups.size(); i++) {  (*(filehandles[gGroups[i]])).close();  delete filehandles[gGroups[i]]; } 
+                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
+                       return 0;
                }
                
                //output error messages about any remaining user labels
@@ -262,10 +281,10 @@ int ParseListCommand::execute(){
                }
                
                if (m->control_pressed) { 
-                               delete input; delete groupMap;
-                               for (i=0; i<groupMap->namesOfGroups.size(); i++) {  (*(filehandles[groupMap->namesOfGroups[i]])).close();  delete filehandles[groupMap->namesOfGroups[i]]; } 
-                               for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
-                               return 0;
+                       delete input; delete groupMap;
+                       for (i=0; i<gGroups.size(); i++) {  (*(filehandles[gGroups[i]])).close();  delete filehandles[gGroups[i]]; } 
+                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
+                       return 0;
                }
                
                //run last label if you need to