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

[mothur.git] / heatmapcommand.cpp

diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp
index b0950419d492eca91c03f263bec08b9217e67d00..766f7da570168ca456b0ca0a9356911fa5c93f80 100644 (file)
--- a/heatmapcommand.cpp
+++ b/heatmapcommand.cpp
@@ -28,14 +28,14 @@ HeatMapCommand::HeatMapCommand(string option){
                        string AlignArray[] =  {"groups","line","label","sorted","scale"};
                        vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
                        
-                       parser = new OptionParser();
-                       parser->parse(option, parameters);  delete parser;
+                       OptionParser parser(option);
+                       map<string,string> parameters = parser.getParameters();
+                       
+                       ValidParameters validParameter;
                        
-                       ValidParameters* validParameter = new ValidParameters();
-               
                        //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;  }
                        }
                        
                        //make sure the user has already run the read.otu command
@@ -45,14 +45,14 @@ HeatMapCommand::HeatMapCommand(string option){
 
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
-                       line = validParameter->validFile(parameters, "line", false);                            
+                       line = validParameter.validFile(parameters, "line", false);                             
                        if (line == "not found") { line = "";  }
                        else { 
                                if(line != "all") {  splitAtDash(line, lines);  allLines = 0;  }
                                else { allLines = 1;  }
                        }
                        
-                       label = validParameter->validFile(parameters, "label", false);                  
+                       label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; }
                        else { 
                                if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
@@ -68,19 +68,16 @@ HeatMapCommand::HeatMapCommand(string option){
                                lines = globaldata->lines;
                        }
                        
-                       groups = validParameter->validFile(parameters, "groups", false);                        
+                       groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; }
                        else { 
                                splitAtDash(groups, Groups);
                                globaldata->Groups = Groups;
                        }
                        
-                       sorted = validParameter->validFile(parameters, "sorted", false);                        if (sorted == "not found") { sorted = "T"; }
+                       sorted = validParameter.validFile(parameters, "sorted", false);                 if (sorted == "not found") { sorted = "T"; }
                 
-                       scale = validParameter->validFile(parameters, "scale", false);                          if (scale == "not found") { scale = "log10"; }
-                 
-
-                       delete validParameter;
+                       scale = validParameter.validFile(parameters, "scale", false);                           if (scale == "not found") { scale = "log10"; }
                        
                        if (abort == false) {
                                heatmap = new HeatMap(sorted, scale);