added pipeline commands which involved change to command factory and command class...

[mothur.git] / parselistscommand.cpp

diff --git a/parselistscommand.cpp b/parselistscommand.cpp
index 4b24236e3497ab67f2be5299163798a9f43e8667..84d91048b181ddf19fc3f2c3977541e2ccebd2bd 100644 (file)
--- a/parselistscommand.cpp
+++ b/parselistscommand.cpp
@@ -9,6 +9,54 @@
 
 #include "parselistscommand.h"
 
+//**********************************************************************************************************************
+vector<string> ParseListCommand::getValidParameters(){ 
+       try {
+               string Array[] =  {"list","group", "label", "outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ParseListCommand", "getValidParameters");
+               exit(1);
+       }
+}
+
+//**********************************************************************************************************************
+ParseListCommand::ParseListCommand(){  
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["list"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ParseListCommand", "ParseListCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ParseListCommand::getRequiredParameters(){      
+       try {
+               string Array[] =  {"list","group"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ParseListCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ParseListCommand::getRequiredFiles(){   
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ParseListCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 ParseListCommand::ParseListCommand(string option)  {
        try {
@@ -33,7 +81,11 @@ ParseListCommand::ParseListCommand(string option)  {
                        for (it = parameters.begin(); it != parameters.end(); it++) { 
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
-                                               
+                       
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["list"] = tempOutNames;                     
+                                                                                               
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
                        if (inputDir == "not found"){   inputDir = "";          }
@@ -121,7 +173,6 @@ int ParseListCommand::execute(){
                
                //set fileroot
                string fileroot = outputDir + m->getRootName(m->getSimpleName(listfile));
-               vector<string> outputNames;
                
                //fill filehandles with neccessary ofstreams
                int i;
@@ -131,7 +182,7 @@ int ParseListCommand::execute(){
                        filehandles[groupMap->namesOfGroups[i]] = temp;
                        
                        string filename = fileroot +  groupMap->namesOfGroups[i] + ".list";
-                       outputNames.push_back(filename);
+                       outputNames.push_back(filename); outputTypes["list"].push_back(filename);
                        m->openOutputFile(filename, *temp);
                }
                
@@ -146,7 +197,7 @@ 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 (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
+                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
                        return 0;
                }
                
@@ -155,7 +206,7 @@ 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 (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
+                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
                                return 0;
                        }
                        
@@ -194,7 +245,7 @@ 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()); }
+                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
                                return 0;
                }
                
@@ -215,7 +266,7 @@ 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()); }
+                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
                                return 0;
                }
                
@@ -240,7 +291,7 @@ int ParseListCommand::execute(){
                delete input;
                
                if (m->control_pressed) { 
-                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
+                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
                        return 0;
                }