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

[mothur.git] / mgclustercommand.cpp

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index eef54ef23b290a930d5560e8dbf444a20da46073..e5dd1a30141af8a7573f7117f5883399a3a409e4 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -9,6 +9,56 @@
 
 #include "mgclustercommand.h"
 
+
+//**********************************************************************************************************************
+vector<string> MGClusterCommand::getValidParameters(){ 
+       try {
+               string Array[] =  {"blast", "method", "name", "hard", "cutoff", "precision", "length", "min", "penalty", "hcluster","merge","outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "MGClusterCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+MGClusterCommand::MGClusterCommand(){  
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["list"] = tempOutNames;
+               outputTypes["rabund"] = tempOutNames;
+               outputTypes["sabund"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "MGClusterCommand", "MGClusterCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> MGClusterCommand::getRequiredParameters(){      
+       try {
+               string Array[] =  {"blast"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "MGClusterCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> MGClusterCommand::getRequiredFiles(){   
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "MGClusterCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 MGClusterCommand::MGClusterCommand(string option) {
        try {
@@ -34,6 +84,12 @@ MGClusterCommand::MGClusterCommand(string option) {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["list"] = tempOutNames;
+                       outputTypes["rabund"] = tempOutNames;
+                       outputTypes["sabund"] = 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 = "";          }
@@ -167,7 +223,7 @@ int MGClusterCommand::execute(){
                list = new ListVector(nameMap->getListVector());
                RAbundVector* rabund = new RAbundVector(list->getRAbundVector());
                
-               if (m->control_pressed) { delete nameMap; delete read; delete list; delete rabund; return 0; }
+               if (m->control_pressed) { outputTypes.clear(); delete nameMap; delete read; delete list; delete rabund; return 0; }
                
                start = time(NULL);
                oldList = *list;
@@ -186,6 +242,7 @@ int MGClusterCommand::execute(){
                if (m->control_pressed) { 
                        delete nameMap; delete read; delete list; delete rabund; 
                        listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+                       outputTypes.clear();
                        return 0; 
                }
                
@@ -206,6 +263,7 @@ int MGClusterCommand::execute(){
                        if (m->control_pressed) { 
                                delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster;
                                listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+                               outputTypes.clear();
                                return 0; 
                        }
                
@@ -217,6 +275,7 @@ int MGClusterCommand::execute(){
                                if (m->control_pressed) { 
                                        delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster;
                                        listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+                                       outputTypes.clear();
                                        return 0; 
                                }
                                
@@ -239,6 +298,7 @@ int MGClusterCommand::execute(){
                                                if (m->control_pressed) { 
                                                        delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster; delete temp;
                                                        listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+                                                       outputTypes.clear();
                                                        return 0; 
                                                }
                                                
@@ -269,6 +329,7 @@ int MGClusterCommand::execute(){
                                        if (m->control_pressed) { 
                                                        delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster; delete temp;
                                                        listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+                                                       outputTypes.clear();
                                                        return 0; 
                                        }
                                        
@@ -298,6 +359,7 @@ int MGClusterCommand::execute(){
                        if (m->control_pressed) { 
                                delete nameMap;  delete list; delete rabund; 
                                listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+                               outputTypes.clear();
                                return 0; 
                        }
                
@@ -314,6 +376,7 @@ int MGClusterCommand::execute(){
                        if (m->control_pressed) { 
                                delete nameMap;  delete list; delete rabund; delete hcluster;
                                listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+                               outputTypes.clear();
                                return 0; 
                        }
 
@@ -326,6 +389,7 @@ int MGClusterCommand::execute(){
                                        listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
                                        remove(distFile.c_str());
                                        remove(overlapFile.c_str());
+                                       outputTypes.clear();
                                        return 0; 
                                }
                                
@@ -340,6 +404,7 @@ int MGClusterCommand::execute(){
                                                        listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
                                                        remove(distFile.c_str());
                                                        remove(overlapFile.c_str());
+                                                       outputTypes.clear();
                                                        return 0; 
                                                }
        
@@ -363,6 +428,7 @@ int MGClusterCommand::execute(){
                                                                        listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
                                                                        remove(distFile.c_str());
                                                                        remove(overlapFile.c_str());
+                                                                       outputTypes.clear();
                                                                        return 0; 
                                                                }
 
@@ -398,6 +464,7 @@ int MGClusterCommand::execute(){
                                                        listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
                                                        remove(distFile.c_str());
                                                        remove(overlapFile.c_str());
+                                                       outputTypes.clear();
                                                        return 0; 
                                        }
                                        
@@ -429,14 +496,15 @@ int MGClusterCommand::execute(){
                        listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
                        globaldata->setListFile("");
                        globaldata->setFormat("");
+                       outputTypes.clear();
                        return 0; 
                }
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
-               m->mothurOut(fileroot+ tag + ".list"); m->mothurOutEndLine();   
-               m->mothurOut(fileroot+ tag + ".rabund"); m->mothurOutEndLine(); 
-               m->mothurOut(fileroot+ tag + ".sabund"); m->mothurOutEndLine(); 
+               m->mothurOut(fileroot+ tag + ".list"); m->mothurOutEndLine();   outputNames.push_back(fileroot+ tag + ".list"); outputTypes["list"].push_back(fileroot+ tag + ".list");
+               m->mothurOut(fileroot+ tag + ".rabund"); m->mothurOutEndLine(); outputNames.push_back(fileroot+ tag + ".rabund"); outputTypes["rabund"].push_back(fileroot+ tag + ".rabund");
+               m->mothurOut(fileroot+ tag + ".sabund"); m->mothurOutEndLine(); outputNames.push_back(fileroot+ tag + ".sabund"); outputTypes["sabund"].push_back(fileroot+ tag + ".sabund");
                m->mothurOutEndLine();
                
                m->mothurOut("It took " + toString(time(NULL) - start) + " seconds to cluster."); m->mothurOutEndLine();