optimizing classify.seqs calculating of template probabilities.

[mothur.git] / parselistscommand.cpp

diff --git a/parselistscommand.cpp b/parselistscommand.cpp
index 6e4082e0c139b76435aa073cd1f0c7013b85dca3..4e61a58d9e5cb4bc640c544797c87a363580575e 100644 (file)
--- a/parselistscommand.cpp
+++ b/parselistscommand.cpp
@@ -37,7 +37,7 @@ string ParseListCommand::getHelpString(){
                helpString += "The label parameter is used to read specific labels in your input you want to use.\n";
                helpString += "The parse.list command should be used in the following format: parse.list(list=yourListFile, group=yourGroupFile, label=yourLabels).\n";
                helpString += "Example: parse.list(list=abrecovery.fn.list, group=abrecovery.groups, label=0.03).\n";
-               helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -45,6 +45,27 @@ string ParseListCommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string ParseListCommand::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 == "list") {  outputFileName =  "list"; }
+            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, "ParseListCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+
 //**********************************************************************************************************************
 ParseListCommand::ParseListCommand(){  
        try {
@@ -66,6 +87,7 @@ ParseListCommand::ParseListCommand(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();
@@ -122,7 +144,7 @@ ParseListCommand::ParseListCommand(string option)  {
                                        abort = true;
                                                
                                }
-                       }       
+                       }else { m->setListFile(listfile); }     
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }  
@@ -136,6 +158,7 @@ ParseListCommand::ParseListCommand(string option)  {
                                        if (error == 1) { abort = true; }
                                }else { m->mothurOut("No valid current group file. You must provide a group file."); m->mothurOutEndLine();  abort = true; } 
                        }else {  
+                               m->setGroupFile(groupfile);
                                groupMap = new GroupMap(groupfile);
                                
                                int error = groupMap->readMap();
@@ -173,11 +196,12 @@ int ParseListCommand::execute(){
                //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";
+                       string filename = fileroot +  gGroups[i] + "." + getOutputFileNameTag("list");
                        outputNames.push_back(filename); outputTypes["list"].push_back(filename);
                        m->openOutputFile(filename, *temp);
                }
@@ -192,8 +216,9 @@ 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 (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
+                       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;
                }
                
@@ -201,8 +226,8 @@ 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]]; } 
-                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
+                               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;
                        }
                        
@@ -239,10 +264,10 @@ 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++) {  remove(outputNames[i].c_str()); } 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
@@ -260,10 +285,10 @@ 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++) {  remove(outputNames[i].c_str()); } 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
@@ -287,7 +312,7 @@ int ParseListCommand::execute(){
                delete input;
                
                if (m->control_pressed) { 
-                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
+                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
                        return 0;
                }