fixed bugg in shhh.seqs command

[mothur.git] / hclustercommand.cpp

diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index fd95323e745bd0ce499368c5ea4cb7bd0ce21bf8..94082dfc74dfe0969e769572fc6df219ecaa69d2 100644 (file)
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -9,15 +9,64 @@
 
 #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 {
+               abort = true; calledHelp = true; 
+               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)  {
        try{
                globaldata = GlobalData::getInstance();
-               abort = false;
+               abort = false; calledHelp = false;   
                
                //allow user to run help
-               if(option == "help") { help(); abort = true; }
+               if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
                        //valid paramters for this command
@@ -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 
@@ -115,8 +170,8 @@ HClusterCommand::HClusterCommand(string option)  {
                        method = validParameter.validFile(parameters, "method", false);
                        if (method == "not found") { method = "furthest"; }
                        
-                       if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
-                       else { m->mothurOut("Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average."); m->mothurOutEndLine(); abort = true; }
+                       if ((method == "furthest") || (method == "nearest") || (method == "average") || (method == "weighted")) { }
+                       else { m->mothurOut("Not a valid clustering method.  Valid clustering algorithms are furthest, nearest, average or weighted."); m->mothurOutEndLine(); abort = true; }
 
                        showabund = validParameter.validFile(parameters, "showabund", false);
                        if (showabund == "not found") { showabund = "T"; }
@@ -136,15 +191,16 @@ HClusterCommand::HClusterCommand(string option)  {
                                
                                if (method == "furthest")               { tag = "fn";  }
                                else if (method == "nearest")   { tag = "nn";  }
+                               else if (method == "weighted")  { tag = "wn";  }
                                else                                                    { tag = "an";  }
                        
                                m->openOutputFile(fileroot+ tag + ".sabund",    sabundFile);
                                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");
                        }
                }
        }
@@ -163,7 +219,7 @@ void HClusterCommand::help(){
                m->mothurOut("The name parameter allows you to enter your name file and is required if your distance file is in column format. \n");
                m->mothurOut("The hcluster command should be in the following format: \n");
                m->mothurOut("hcluster(column=youDistanceFile, name=yourNameFile, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
-               m->mothurOut("The acceptable hcluster methods are furthest, nearest and average.\n\n"); 
+               m->mothurOut("The acceptable hcluster methods are furthest, nearest, weighted and average.\n\n");       
        }
        catch(exception& e) {
                m->errorOut(e, "HClusterCommand", "help");
@@ -180,7 +236,7 @@ HClusterCommand::~HClusterCommand(){}
 int HClusterCommand::execute(){
        try {
        
-               if (abort == true) {    return 0;       }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                if(namefile != ""){     
                        globaldata->nameMap = new NameAssignment(namefile);
@@ -201,7 +257,7 @@ 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 +273,7 @@ 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 +303,7 @@ 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 +317,7 @@ 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 +331,7 @@ 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 +364,7 @@ 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 +392,7 @@ 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;  
                }