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

[mothur.git] / deconvolutecommand.cpp

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index 62daa612d52a04fa72b85c1c621b89b539d14ab0..33e51ffdff96a570d2a91d85590b3a2111ddcf63 100644 (file)
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -10,50 +10,50 @@
 #include "deconvolutecommand.h"
 
 //**********************************************************************************************************************
-vector<string> DeconvoluteCommand::getValidParameters(){       
+vector<string> DeconvoluteCommand::setParameters(){    
        try {
-               string Array[] =  {"fasta", "name","outputdir","inputdir"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+               CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+               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, "DeconvoluteCommand", "getValidParameters");
+               m->errorOut(e, "DeconvoluteCommand", "setParameters");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-DeconvoluteCommand::DeconvoluteCommand(){      
+string DeconvoluteCommand::getHelpString(){    
        try {
-               abort = true; calledHelp = true; 
-               vector<string> tempOutNames;
-               outputTypes["fasta"] = tempOutNames;
-               outputTypes["name"] = tempOutNames;
+               string helpString = "";
+               helpString += "The unique.seqs command reads a fastafile and creates a namesfile.\n";
+               helpString += "It creates a file where the first column is the groupname and the second column is a list of sequence names who have the same sequence. \n";
+               helpString += "If the sequence is unique the second column will just contain its name. \n";
+               helpString += "The unique.seqs command parameters are fasta and name.  fasta is required, unless there is a valid current fasta file.\n";
+               helpString += "The unique.seqs command should be in the following format: \n";
+               helpString += "unique.seqs(fasta=yourFastaFile) \n";    
+               return helpString;
        }
        catch(exception& e) {
-               m->errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
+               m->errorOut(e, "DeconvoluteCommand", "getHelpString");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-vector<string> DeconvoluteCommand::getRequiredParameters(){    
-       try {
-               string Array[] =  {"fasta"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-               return myArray;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "DeconvoluteCommand", "getRequiredParameters");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-vector<string> DeconvoluteCommand::getRequiredFiles(){ 
+DeconvoluteCommand::DeconvoluteCommand(){      
        try {
-               vector<string> myArray;
-               return myArray;
+               abort = true; calledHelp = true; 
+               setParameters();
+               vector<string> tempOutNames;
+               outputTypes["fasta"] = tempOutNames;
+               outputTypes["name"] = tempOutNames;
        }
        catch(exception& e) {
-               m->errorOut(e, "DeconvoluteCommand", "getRequiredFiles");
+               m->errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
                exit(1);
        }
 }
@@ -66,9 +66,7 @@ DeconvoluteCommand::DeconvoluteCommand(string option)  {
                if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
-                       //valid paramters for this command
-                       string Array[] =  {"fasta", "name","outputdir","inputdir"};
-                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       vector<string> myArray = setParameters();
                        
                        OptionParser parser(option);
                        map<string,string> parameters = parser.getParameters();
@@ -112,7 +110,11 @@ DeconvoluteCommand::DeconvoluteCommand(string option)  {
                        //check for required parameters
                        inFastaName = validParameter.validFile(parameters, "fasta", true);
                        if (inFastaName == "not open") { abort = true; }
-                       else if (inFastaName == "not found") { inFastaName = ""; m->mothurOut("fasta is a required parameter for the unique.seqs command."); m->mothurOutEndLine(); abort = true;  }    
+                       else if (inFastaName == "not found") {                          
+                               inFastaName = m->getFastaFile(); 
+                               if (inFastaName != "") { m->mothurOut("Using " + inFastaName + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+                               else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+                       }       
                        
                        //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"){  
@@ -131,23 +133,6 @@ DeconvoluteCommand::DeconvoluteCommand(string option)  {
                exit(1);
        }
 }
-//**********************************************************************************************************************
-
-void DeconvoluteCommand::help(){
-       try {
-               m->mothurOut("The unique.seqs command reads a fastafile and creates a namesfile.\n");
-               m->mothurOut("It creates a file where the first column is the groupname and the second column is a list of sequence names who have the same sequence. \n");
-               m->mothurOut("If the sequence is unique the second column will just contain its name. \n");
-               m->mothurOut("The unique.seqs command parameter is fasta and it is required.\n");
-               m->mothurOut("The unique.seqs command should be in the following format: \n");
-               m->mothurOut("unique.seqs(fasta=yourFastaFile) \n");    
-       }
-       catch(exception& e) {
-               m->errorOut(e, "DeconvoluteCommand", "help");
-               exit(1);
-       }
-}
-
 /**************************************************************************************/
 int DeconvoluteCommand::execute() {    
        try {