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

[mothur.git] / hclustercommand.cpp

diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index fd95323e745bd0ce499368c5ea4cb7bd0ce21bf8..e236d86cf2934a349500bbd2aacf2737d3f351b7 100644 (file)
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -9,6 +9,55 @@
 
 #include "hclustercommand.h"
 
+//**********************************************************************************************************************
+vector<string> HClusterCommand::getValidParameters(){  
+       try {
+               string Array[] =  {"cutoff","hard","precision","method","phylip","column","name","sorted","showabund","timing","outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "HClusterCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+HClusterCommand::HClusterCommand(){    
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["list"] = tempOutNames;
+               outputTypes["rabund"] = tempOutNames;
+               outputTypes["sabund"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "HClusterCommand", "HClusterCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> HClusterCommand::getRequiredParameters(){       
+       try {
+               string Array[] =  {"phylip","column","or"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "HClusterCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> HClusterCommand::getRequiredFiles(){    
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "HClusterCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 //This function checks to make sure the cluster command has no errors and then clusters based on the method chosen.
 HClusterCommand::HClusterCommand(string option)  {
@@ -37,6 +86,12 @@ HClusterCommand::HClusterCommand(string option)  {
                                }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["list"] = tempOutNames;
+                       outputTypes["rabund"] = tempOutNames;
+                       outputTypes["sabund"] = tempOutNames;
+               
                        globaldata->newRead();
                        
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
@@ -142,9 +197,9 @@ HClusterCommand::HClusterCommand(string option)  {
                                m->openOutputFile(fileroot+ tag + ".rabund",    rabundFile);
                                m->openOutputFile(fileroot+ tag + ".list",              listFile);
                                
-                               outputNames.push_back(fileroot+ tag + ".sabund");
-                               outputNames.push_back(fileroot+ tag + ".rabund");
-                               outputNames.push_back(fileroot+ tag + ".list");
+                               outputNames.push_back(fileroot+ tag + ".sabund"); outputTypes["sabund"].push_back(fileroot+ tag + ".sabund");
+                               outputNames.push_back(fileroot+ tag + ".rabund"); outputTypes["rabund"].push_back(fileroot+ tag + ".rabund");
+                               outputNames.push_back(fileroot+ tag + ".list"); outputTypes["list"].push_back(fileroot+ tag + ".list");
                        }
                }
        }
@@ -201,7 +256,7 @@ int HClusterCommand::execute(){
                                sabundFile.close();
                                rabundFile.close();
                                listFile.close();
-                               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;  
                        }
                        
@@ -217,7 +272,7 @@ int HClusterCommand::execute(){
                        sabundFile.close();
                        rabundFile.close();
                        listFile.close();
-                       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;  
                }
 
@@ -247,7 +302,7 @@ int HClusterCommand::execute(){
                                sabundFile.close();
                                rabundFile.close();
                                listFile.close();
-                               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;  
                }
 
@@ -261,7 +316,7 @@ int HClusterCommand::execute(){
                                sabundFile.close();
                                rabundFile.close();
                                listFile.close();
-                               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;  
                        }
 
@@ -275,7 +330,7 @@ int HClusterCommand::execute(){
                                                sabundFile.close();
                                                rabundFile.close();
                                                listFile.close();
-                                               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;  
                                        }
 
@@ -308,7 +363,7 @@ int HClusterCommand::execute(){
                        sabundFile.close();
                        rabundFile.close();
                        listFile.close();
-                       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;  
                }
                                        
@@ -336,7 +391,7 @@ int HClusterCommand::execute(){
                delete cluster;
                
                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;  
                }