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

[mothur.git] / degapseqscommand.cpp

diff --git a/degapseqscommand.cpp b/degapseqscommand.cpp
index 7fd2803a4ec6c5e578d7b180a9e08fda1af33385..81002c8385e78610794e2faa5f0241d67befbab7 100644 (file)
--- a/degapseqscommand.cpp
+++ b/degapseqscommand.cpp
@@ -11,49 +11,50 @@
 #include "sequence.hpp"
 
 //**********************************************************************************************************************
-vector<string> DegapSeqsCommand::getValidParameters(){ 
+vector<string> DegapSeqsCommand::setParameters(){      
        try {
-               string Array[] =  {"fasta", "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 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, "DegapSeqsCommand", "getValidParameters");
+               m->errorOut(e, "DegapSeqsCommand", "setParameters");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-DegapSeqsCommand::DegapSeqsCommand(){  
+string DegapSeqsCommand::getHelpString(){      
        try {
-               abort = true; calledHelp = true; 
-               vector<string> tempOutNames;
-               outputTypes["fasta"] = tempOutNames;
+               string helpString = "";
+               helpString += "The degap.seqs command reads a fastafile and removes all gap characters.\n";
+               helpString += "The degap.seqs command parameter is fasta.\n";
+               helpString += "The fasta parameter allows you to enter the fasta file containing your sequences, and is required unless you have a valid current fasta file. \n";
+               helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n";
+               helpString += "The degap.seqs command should be in the following format: \n";
+               helpString += "degap.seqs(fasta=yourFastaFile) \n";     
+               helpString += "Example: degap.seqs(fasta=abrecovery.align) \n";
+               helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n";     
+               return helpString;
        }
        catch(exception& e) {
-               m->errorOut(e, "DegapSeqsCommand", "DegapSeqsCommand");
+               m->errorOut(e, "DegapSeqsCommand", "getHelpString");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-vector<string> DegapSeqsCommand::getRequiredParameters(){      
-       try {
-               string Array[] =  {"fasta"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-               return myArray;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "DegapSeqsCommand", "getRequiredParameters");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-vector<string> DegapSeqsCommand::getRequiredFiles(){   
+DegapSeqsCommand::DegapSeqsCommand(){  
        try {
-               vector<string> myArray;
-               return myArray;
+               abort = true; calledHelp = true; 
+               setParameters();
+               vector<string> tempOutNames;
+               outputTypes["fasta"] = tempOutNames;
        }
        catch(exception& e) {
-               m->errorOut(e, "DegapSeqsCommand", "getRequiredFiles");
+               m->errorOut(e, "DegapSeqsCommand", "DegapSeqsCommand");
                exit(1);
        }
 }
@@ -66,9 +67,7 @@ DegapSeqsCommand::DegapSeqsCommand(string option)  {
                if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
-                       //valid paramters for this command
-                       string Array[] =  {"fasta", "outputdir","inputdir"};
-                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       vector<string> myArray = setParameters();
                        
                        OptionParser parser(option);
                        map<string,string> parameters = parser.getParameters();
@@ -92,7 +91,11 @@ DegapSeqsCommand::DegapSeqsCommand(string option)  {
                        
                        //check for required parameters
                        fastafile = validParameter.validFile(parameters, "fasta", false);
-                       if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the degap.seqs command."); m->mothurOutEndLine(); abort = true;  }
+                       if (fastafile == "not found") {                                 
+                               fastafile = m->getFastaFile(); 
+                               if (fastafile != "") { fastaFileNames.push_back(fastafile); m->mothurOut("Using " + fastafile + " 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; }
+                       }
                        else { 
                                m->splitAtDash(fastafile, fastaFileNames);
                                
@@ -159,32 +162,7 @@ DegapSeqsCommand::DegapSeqsCommand(string option)  {
                exit(1);
        }
 }
-//**********************************************************************************************************************
-
-void DegapSeqsCommand::help(){
-       try {
-               m->mothurOut("The degap.seqs command reads a fastafile and removes all gap characters.\n");
-               m->mothurOut("The degap.seqs command parameter is fasta.\n");
-               m->mothurOut("The fasta parameter allows you to enter the fasta file containing your sequences, and is required. \n");
-               m->mothurOut("You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
-               m->mothurOut("The degap.seqs command should be in the following format: \n");
-               m->mothurOut("degap.seqs(fasta=yourFastaFile) \n");     
-               m->mothurOut("Example: degap.seqs(fasta=abrecovery.align) \n");
-               m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");     
-       }
-       catch(exception& e) {
-               m->errorOut(e, "DegapSeqsCommand", "help");
-               exit(1);
-       }
-}
-
 //***************************************************************************************************************
-
-DegapSeqsCommand::~DegapSeqsCommand(){ /*      do nothing      */      }
-
-//***************************************************************************************************************
-
-
 int DegapSeqsCommand::execute(){
        try{