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

[mothur.git] / pcoacommand.cpp

diff --git a/pcoacommand.cpp b/pcoacommand.cpp
index 3cd844a36d5a5c253786b4eb29745388b042d2d4..6ebf6536e70042941fe4d4ec401f7035949da66c 100644 (file)
--- a/pcoacommand.cpp
+++ b/pcoacommand.cpp
@@ -11,51 +11,53 @@
 #include "pcoacommand.h"
 #include "readphylipvector.h"
 
+
 //**********************************************************************************************************************
-vector<string> PCOACommand::getValidParameters(){      
+vector<string> PCOACommand::setParameters(){   
        try {
-               string Array[] =  {"phylip", "metric","outputdir","inputdir"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
+               CommandParameter pmetric("metric", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmetric);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               
+               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, "PCOACommand", "getValidParameters");
+               m->errorOut(e, "PCOACommand", "setParameters");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-PCOACommand::PCOACommand(){    
+string PCOACommand::getHelpString(){   
        try {
-               abort = true; calledHelp = true; 
-               vector<string> tempOutNames;
-               outputTypes["pcoa"] = tempOutNames;
-               outputTypes["loadings"] = tempOutNames;
+               string helpString = "";
+               helpString += "The pcoa command parameters are phylip and metric"; 
+               helpString += "The phylip parameter allows you to enter your distance file.";
+               helpString += "The metric parameter allows indicate you if would like the pearson correlation coefficient calculated. Default=True"; 
+               helpString += "Example pcoa(phylip=yourDistanceFile).\n";
+               helpString += "Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\n\n";
+               return helpString;
        }
        catch(exception& e) {
-               m->errorOut(e, "PCOACommand", "PCOACommand");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-vector<string> PCOACommand::getRequiredParameters(){   
-       try {
-               string Array[] =  {"phylip"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-               return myArray;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "PCOACommand", "getRequiredParameters");
+               m->errorOut(e, "PCOACommand", "getHelpString");
                exit(1);
        }
 }
+
+
 //**********************************************************************************************************************
-vector<string> PCOACommand::getRequiredFiles(){        
+PCOACommand::PCOACommand(){    
        try {
-               vector<string> myArray;
-               return myArray;
+               abort = true; calledHelp = true; 
+               setParameters();
+               vector<string> tempOutNames;
+               outputTypes["pcoa"] = tempOutNames;
+               outputTypes["loadings"] = tempOutNames;
        }
        catch(exception& e) {
-               m->errorOut(e, "PCOACommand", "getRequiredFiles");
+               m->errorOut(e, "PCOACommand", "PCOACommand");
                exit(1);
        }
 }
@@ -69,9 +71,7 @@ PCOACommand::PCOACommand(string option)  {
                if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
-                       //valid paramters for this command
-                       string Array[] =  {"phylip","metric","outputdir", "inputdir"};
-                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       vector<string> myArray = setParameters();
                        
                        OptionParser parser(option);
                        map<string, string> parameters = parser. getParameters();
@@ -105,8 +105,14 @@ PCOACommand::PCOACommand(string option)  {
                        //required parameters
                        phylipfile = validParameter.validFile(parameters, "phylip", true);
                        if (phylipfile == "not open") { abort = true; }
-                       else if (phylipfile == "not found") { phylipfile = ""; abort = true; }  
-                       else {  filename = phylipfile;  }
+                       else if (phylipfile == "not found") {                   
+                               //if there is a current phylip file, use it
+                               phylipfile = m->getPhylipFile(); 
+                               if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
+                               else {  m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; }
+                       }       
+                       
+                       filename = phylipfile;  
                        
                        //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"){  
@@ -114,9 +120,6 @@ PCOACommand::PCOACommand(string option)  {
                                outputDir += m->hasPath(phylipfile); //if user entered a file with a path then preserve it      
                        }
                        
-                       //error checking on files       
-                       if (phylipfile == "")   { m->mothurOut("You must provide a distance file before running the pcoa command."); m->mothurOutEndLine(); abort = true; }             
-               
                        string temp = validParameter.validFile(parameters, "metric", false);    if (temp == "not found"){       temp = "T";                             }
                        metric = m->isTrue(temp); 
                }
@@ -128,23 +131,6 @@ PCOACommand::PCOACommand(string option)  {
        }
 }
 //**********************************************************************************************************************
-void PCOACommand::help(){
-       try {
-       
-               m->mothurOut("The pcoa command parameters are phylip and metric"); m->mothurOutEndLine();
-               m->mothurOut("The phylip parameter allows you to enter your distance file."); m->mothurOutEndLine();
-               m->mothurOut("The metric parameter allows indicate you if would like the pearson correlation coefficient calculated. Default=True"); m->mothurOutEndLine();
-               m->mothurOut("Example pcoa(phylip=yourDistanceFile).\n");
-               m->mothurOut("Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\n\n");
-       }
-       catch(exception& e) {
-               m->errorOut(e, "PCOACommand", "help");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-PCOACommand::~PCOACommand(){}
-//**********************************************************************************************************************
 int PCOACommand::execute(){
        try {