merged pat's trim seqs edits with sarah's major overhaul of global data; also added...

[mothur.git] / readdistcommand.cpp

diff --git a/readdistcommand.cpp b/readdistcommand.cpp
index 31d8308414755601166268f6088dd7142f7dfaad..b03f12e7f711c471043f879cb172cf7e99a60929 100644 (file)
--- a/readdistcommand.cpp
+++ b/readdistcommand.cpp
@@ -22,33 +22,33 @@ ReadDistCommand::ReadDistCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"phylip","column", "name","cutoff","precision", "group"};
+                       string Array[] =  {"phylip", "column", "name", "cutoff", "precision", "group"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
-                       parser = new OptionParser();
-                       parser->parse(option, parameters);  delete parser;
+                       OptionParser parser(option);
+                       map<string, string> parameters = parser.getParameters();
                        
-                       ValidParameters* validParameter = new ValidParameters();
+                       ValidParameters validParameter;
                
                        //check to make sure all parameters are valid for command
-                       for (it = parameters.begin(); it != parameters.end(); it++) { 
-                               if (validParameter->isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+                       for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+                               if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
                        globaldata->newRead();
                        
                        //check for required parameters
-                       phylipfile = validParameter->validFile(parameters, "phylip", true);
+                       phylipfile = validParameter.validFile(parameters, "phylip", true);
                        if (phylipfile == "not open") { abort = true; }
                        else if (phylipfile == "not found") { phylipfile = ""; }        
                        else {  globaldata->setPhylipFile(phylipfile);  globaldata->setFormat("phylip");        }
                        
-                       columnfile = validParameter->validFile(parameters, "column", true);
+                       columnfile = validParameter.validFile(parameters, "column", true);
                        if (columnfile == "not open") { abort = true; } 
                        else if (columnfile == "not found") { columnfile = ""; }
                        else {  globaldata->setColumnFile(columnfile); globaldata->setFormat("column"); }
                        
-                       groupfile = validParameter->validFile(parameters, "group", true);
+                       groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }  
                        else if (groupfile == "not found") { groupfile = ""; }
                        else {  
@@ -56,15 +56,16 @@ ReadDistCommand::ReadDistCommand(string option){
                                groupMap = new GroupMap(groupfile);
                                groupMap->readMap();
                        }
-                       
-                       namefile = validParameter->validFile(parameters, "name", true);
+
+                       namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }   
                        else if (namefile == "not found") { namefile = ""; }
                        else {  globaldata->setNameFile(namefile);      }
 
                        
                        //you are doing a list and group shared
-                       if ((phylipfile != "") && (groupfile != "")) { globaldata->setFormat("matrix"); }
+                       if ((phylipfile != "") && (groupfile != "")) { 
+                       globaldata->setFormat("matrix"); }
                        
                        if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist command you must enter a phylip or a column." << endl; abort = true; }
                        else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist command you must enter ONLY ONE of the following: phylip or column." << endl; abort = true; }
@@ -77,21 +78,19 @@ ReadDistCommand::ReadDistCommand(string option){
                        // ...at some point should added some additional type checking...
                        //get user cutoff and precision or use defaults
                        string temp;
-                       temp = validParameter->validFile(parameters, "precision", false);                       if (temp == "not found") { temp = "100"; }
+                       temp = validParameter.validFile(parameters, "precision", false);                        if (temp == "not found") { temp = "100"; }
                        convert(temp, precision); 
                        
-                       temp = validParameter->validFile(parameters, "cutoff", false);                  if (temp == "not found") { temp = "10"; }
+                       temp = validParameter.validFile(parameters, "cutoff", false);                   if (temp == "not found") { temp = "10"; }
                        convert(temp, cutoff); 
                        cutoff += (5 / (precision * 10.0));
-
-                       delete validParameter;
                        
                        if (abort == false) {
-                               filename = globaldata->inputFileName;
+                               distFileName = globaldata->inputFileName;
                                format = globaldata->getFormat();       
                
-                               if (format == "column") { read = new ReadColumnMatrix(filename); }      
-                               else if (format == "phylip") { read = new ReadPhylipMatrix(filename); }
+                               if (format == "column") { read = new ReadColumnMatrix(distFileName); }  
+                               else if (format == "phylip") { read = new ReadPhylipMatrix(distFileName); }
                                else if (format == "matrix") { 
                                        groupMap = new GroupMap(groupfile);
                                        groupMap->readMap();
@@ -149,6 +148,7 @@ void ReadDistCommand::help(){
 }
 
 //**********************************************************************************************************************
+
 ReadDistCommand::~ReadDistCommand(){
        delete read;
        delete nameMap;
@@ -162,7 +162,7 @@ int ReadDistCommand::execute(){
                
                if (format == "matrix") {
                        ifstream in;
-                       openInputFile(filename, in);
+                       openInputFile(distFileName, in);
                        matrix = new FullMatrix(in); //reads the matrix file
                        //memory leak prevention
                        //if (globaldata->gMatrix != NULL) { delete globaldata->gMatrix;  }