removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 024fbab7221c328a02958d34084e4704da55b150..74669ed0d9dba0425c81e74852482a62e4f29b46 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -26,64 +26,56 @@
 #define MIN_WEIGHT 0.1
 #define MIN_TAU 0.0001
 #define MIN_ITER 10
-
 //**********************************************************************************************************************
-
-vector<string> ShhherCommand::getValidParameters(){    
+vector<string> ShhherCommand::setParameters(){ 
        try {
-               string Array[] =  {     
-                       "file", "flow", "lookup", "cutoff", "sigma", "outputdir","inputdir", "processors", "maxiter", "mindelta", "order"       
-               };
+               CommandParameter pflow("flow", "InputTypes", "", "", "none", "fileflow", "none",false,false); parameters.push_back(pflow);
+               CommandParameter pfile("file", "InputTypes", "", "", "none", "fileflow", "none",false,false); parameters.push_back(pfile);
+               CommandParameter plookup("lookup", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(plookup);
+               CommandParameter pcutoff("cutoff", "Number", "", "0.01", "", "", "",false,false); parameters.push_back(pcutoff);
+               CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+               CommandParameter pmaxiter("maxiter", "Number", "", "1000", "", "", "",false,false); parameters.push_back(pmaxiter);
+               CommandParameter psigma("sigma", "Number", "", "60", "", "", "",false,false); parameters.push_back(psigma);
+               CommandParameter pmindelta("mindelta", "Number", "", "0.000001", "", "", "",false,false); parameters.push_back(pmindelta);
+               CommandParameter porder("order", "String", "", "", "", "", "",false,false); parameters.push_back(porder);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
                
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               vector<string> myArray;
+               for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
                return myArray;
        }
        catch(exception& e) {
-               m->errorOut(e, "ShhherCommand", "getValidParameters");
+               m->errorOut(e, "ShhherCommand", "setParameters");
                exit(1);
        }
 }
-
 //**********************************************************************************************************************
-
-ShhherCommand::ShhherCommand(){        
+string ShhherCommand::getHelpString(){ 
        try {
-               abort = true; calledHelp = true;
-               
-               //initialize outputTypes
-               vector<string> tempOutNames;
-               outputTypes["pn.dist"] = tempOutNames;
-
+               string helpString = "";
+               helpString += "The shhh.seqs command reads a file containing flowgrams and creates a file of corrected sequences.\n";
+               return helpString;
        }
        catch(exception& e) {
-               m->errorOut(e, "ShhherCommand", "ShhherCommand");
+               m->errorOut(e, "ShhherCommand", "getHelpString");
                exit(1);
        }
 }
-
 //**********************************************************************************************************************
 
-vector<string> ShhherCommand::getRequiredParameters(){ 
+ShhherCommand::ShhherCommand(){        
        try {
-               string Array[] =  {"flow"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-               return myArray;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ShhherCommand", "getRequiredParameters");
-               exit(1);
-       }
-}
-
-//**********************************************************************************************************************
+               abort = true; calledHelp = true;
+               setParameters();
+               
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["pn.dist"] = tempOutNames;
 
-vector<string> ShhherCommand::getRequiredFiles(){      
-       try {
-               vector<string> myArray;
-               return myArray;
        }
        catch(exception& e) {
-               m->errorOut(e, "ShhherCommand", "getRequiredFiles");
+               m->errorOut(e, "ShhherCommand", "ShhherCommand");
                exit(1);
        }
 }
@@ -108,13 +100,7 @@ ShhherCommand::ShhherCommand(string option) {
                if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
-                       
-                       //valid paramters for this command
-                       string AlignArray[] =  {
-                               "file", "flow", "lookup", "cutoff", "sigma", "outputdir","inputdir", "processors", "maxiter", "mindelta", "order"       
-                       };
-                       
-                       vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+                       vector<string> myArray = setParameters();
                        
                        OptionParser parser(option);
                        map<string,string> parameters = parser.getParameters();
@@ -196,8 +182,9 @@ ShhherCommand::ShhherCommand(string option) {
                        else if(temp == "not open")     {       abort = true;                   } 
                        else                                            {       lookupFileName = temp;  }
                        
-                       temp = validParameter.validFile(parameters, "processors", false);if (temp == "not found"){      temp = "1";                     }
-                       convert(temp, processors); 
+                       temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
+                       m->setProcessors(temp);
+                       convert(temp, processors);
 
                        temp = validParameter.validFile(parameters, "cutoff", false);   if (temp == "not found"){       temp = "0.01";          }
                        convert(temp, cutoff); 
@@ -217,7 +204,6 @@ ShhherCommand::ShhherCommand(string option) {
                                m->mothurOut("The value of the order option must be four bases long\n");
                        }
                        
-                       globaldata = GlobalData::getInstance();
                }
                        
 #ifdef USE_MPI
@@ -230,23 +216,6 @@ ShhherCommand::ShhherCommand(string option) {
                exit(1);
        }
 }
-
-//**********************************************************************************************************************
-
-ShhherCommand::~ShhherCommand(){}
-
-//**********************************************************************************************************************
-
-void ShhherCommand::help(){
-       try {
-               m->mothurOut("The shhher command reads a file containing flowgrams and creates a file of corrected sequences.\n");
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ShhherCommand", "help");
-               exit(1);
-       }
-}
-
 //**********************************************************************************************************************
 #ifdef USE_MPI
 int ShhherCommand::execute(){
@@ -1154,11 +1123,6 @@ string ShhherCommand::createNamesFile(){
 string ShhherCommand::cluster(string distFileName, string namesFileName){
        try {
                
-               
-               globaldata->setNameFile(namesFileName);
-               globaldata->setColumnFile(distFileName);
-               globaldata->setFormat("column");
-               
                ReadMatrix* read = new ReadColumnMatrix(distFileName);  
                read->setCutoff(cutoff);