modified seqerror and qualscores

[mothur.git] / clustercommand.cpp

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 6df5faad98cd9a0cd1a78644794cecc3eef0df7d..5d9225b0f9ca4c6f39de259454dfc1fb92e6c919 100644 (file)
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -9,16 +9,65 @@
 
 #include "clustercommand.h"
 
+//**********************************************************************************************************************
+vector<string> ClusterCommand::getValidParameters(){   
+       try {
+               string AlignArray[] =  {"cutoff","precision","method","showabund","timing","hard","outputdir","inputdir"};
+               vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ClusterCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+ClusterCommand::ClusterCommand(){      
+       try {
+               abort = true; calledHelp = true; 
+               vector<string> tempOutNames;
+               outputTypes["list"] = tempOutNames;
+               outputTypes["rabund"] = tempOutNames;
+               outputTypes["sabund"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ClusterCommand", "ClusterCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ClusterCommand::getRequiredParameters(){        
+       try {
+               vector<string> myArray; 
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ClusterCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ClusterCommand::getRequiredFiles(){     
+       try {
+               string Array[] =  {"phylip","column","or"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ClusterCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 //This function checks to make sure the cluster command has no errors and then clusters based on the method chosen.
 ClusterCommand::ClusterCommand(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 @@ ClusterCommand::ClusterCommand(string option)  {
                                }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["list"] = tempOutNames;
+                       outputTypes["rabund"] = tempOutNames;
+                       outputTypes["sabund"] = tempOutNames;
+               
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
                        
@@ -101,9 +156,9 @@ ClusterCommand::ClusterCommand(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");
                        }
                }
        }
@@ -143,7 +198,7 @@ ClusterCommand::~ClusterCommand(){
 int ClusterCommand::execute(){
        try {
        
-               if (abort == true) {    return 0;       }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                time_t estart = time(NULL);
                //int ndist = matrix->getNNodes();
@@ -165,7 +220,7 @@ int ClusterCommand::execute(){
                                if (globaldata->getFormat() == "phylip") { globaldata->setPhylipFile(""); }
                                else if (globaldata->getFormat() == "column") { globaldata->setColumnFile(""); }
                                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;
                        }