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

[mothur.git] / reversecommand.cpp

diff --git a/reversecommand.cpp b/reversecommand.cpp
index fffe8a2b9de510bead87e0c9762cf75f71af8ef3..0a2e9380ebd71a5deae50725d3b36c2d10b52c4e 100644 (file)
--- a/reversecommand.cpp
+++ b/reversecommand.cpp
@@ -12,56 +12,53 @@
 #include "qualityscores.h"
 
 //**********************************************************************************************************************
-vector<string> ReverseSeqsCommand::getValidParameters(){       
+vector<string> ReverseSeqsCommand::setParameters(){    
        try {
-               string Array[] =  {"fasta", "qfile", "outputdir", "inputdir"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "fastaQual", "none",false,false); parameters.push_back(pfasta);
+               CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "fastaQual", "none",false,false); parameters.push_back(pqfile);
+               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, "ReverseSeqsCommand", "getValidParameters");
+               m->errorOut(e, "ReverseSeqsCommand", "setParameters");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-ReverseSeqsCommand::ReverseSeqsCommand(){      
+string ReverseSeqsCommand::getHelpString(){    
        try {
-               abort = true; calledHelp = true; 
-               vector<string> tempOutNames;
-               outputTypes["fasta"] = tempOutNames;
-               outputTypes["qfile"] = tempOutNames;
+               string helpString = "";
+               helpString += "The reverse.seqs command reads a fastafile and outputs a fasta file containing the reverse compliment.\n";
+               helpString += "The reverse.seqs command parameters fasta or qfile are required.\n";
+               helpString += "The reverse.seqs command should be in the following format: \n";
+               helpString += "reverse.seqs(fasta=yourFastaFile) \n";   
+               return helpString;
        }
        catch(exception& e) {
-               m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-
-vector<string> ReverseSeqsCommand::getRequiredParameters(){    
-       try {
-               string Array[] =  {"fasta", "qfile"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-               return myArray;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ReverseSeqsCommand", "getRequiredParameters");
+               m->errorOut(e, "ReverseSeqsCommand", "getHelpString");
                exit(1);
        }
 }
 
 //**********************************************************************************************************************
-
-vector<string> ReverseSeqsCommand::getRequiredFiles(){ 
+ReverseSeqsCommand::ReverseSeqsCommand(){      
        try {
-               vector<string> myArray;
-               return myArray;
+               abort = true; calledHelp = true; 
+               setParameters();
+               vector<string> tempOutNames;
+               outputTypes["fasta"] = tempOutNames;
+               outputTypes["qfile"] = tempOutNames;
        }
        catch(exception& e) {
-               m->errorOut(e, "ReverseSeqsCommand", "getRequiredFiles");
+               m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
                exit(1);
        }
-}//***************************************************************************************************************
+}
+//***************************************************************************************************************
 
 ReverseSeqsCommand::ReverseSeqsCommand(string option)  {
        try {
@@ -71,9 +68,7 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option)  {
                if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
-                       //valid paramters for this command
-                       string Array[] =  {"fasta", "qfile", "outputdir","inputdir"};
-                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       vector<string> myArray = setParameters();
                        
                        OptionParser parser(option);
                        map<string,string> parameters = parser.getParameters();
@@ -103,6 +98,14 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option)  {
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
                                }
+                               
+                               it = parameters.find("qfile");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = m->hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
+                               }
                        }
 
                        //check for required parameters
@@ -114,16 +117,22 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option)  {
                        if (qualFileName == "not open") { abort = true; }
                        else if (qualFileName == "not found") { qualFileName = ""; }//m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true;  }      
 
-                       if(fastaFileName == "not open" && qualFileName == "not open"){
-                               m->mothurOut("fasta or qfile is a required parameter for the reverse.seqs command.");
-                               m->mothurOutEndLine();
-                               abort = true;
+                       if((fastaFileName == "") && (qualFileName == "")){
+                               fastaFileName = m->getFastaFile(); 
+                               if (fastaFileName != "") {  m->mothurOut("Using " + fastaFileName + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+                               else { 
+                                       qualFileName = m->getQualFile(); 
+                                       if (qualFileName != "") {  m->mothurOut("Using " + qualFileName + " as input file for the qfile parameter."); m->mothurOutEndLine(); }
+                                       else { 
+                                               m->mothurOut("You have no current files for fasta or qfile, and fasta or qfile is a required parameter for the reverse.seqs command."); 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"){  
                                outputDir = ""; 
-                               outputDir += m->hasPath(fastaFileName); //if user entered a file with a path then preserve it   
                        }
 
                }
@@ -133,25 +142,6 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option)  {
                exit(1);
        }
 }
-//**********************************************************************************************************************
-
-void ReverseSeqsCommand::help(){
-       try {
-               m->mothurOut("The reverse.seqs command reads a fastafile and outputs a fasta file containing the reverse compliment.\n");
-               m->mothurOut("The reverse.seqs command parameters fasta or qfile are required.\n");
-               m->mothurOut("The reverse.seqs command should be in the following format: \n");
-               m->mothurOut("reverse.seqs(fasta=yourFastaFile) \n");   
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ReverseSeqsCommand", "help");
-               exit(1);
-       }
-}
-
-//***************************************************************************************************************
-
-ReverseSeqsCommand::~ReverseSeqsCommand(){     /*      do nothing      */      }
-
 //***************************************************************************************************************
 
 
@@ -167,7 +157,9 @@ int ReverseSeqsCommand::execute(){
                        m->openInputFile(fastaFileName, inFASTA);
                        
                        ofstream outFASTA;
-                       fastaReverseFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileName)) + "rc" + m->getExtension(fastaFileName);
+                       string tempOutputDir = outputDir;
+                       if (outputDir == "") { tempOutputDir += m->hasPath(fastaFileName); } //if user entered a file with a path then preserve it
+                       fastaReverseFileName = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileName)) + "rc" + m->getExtension(fastaFileName);
                        m->openOutputFile(fastaReverseFileName, outFASTA);
                        
                        while(!inFASTA.eof()){
@@ -193,7 +185,9 @@ int ReverseSeqsCommand::execute(){
                        m->openInputFile(qualFileName, inQual);
                        
                        ofstream outQual;
-                       string qualReverseFileName = outputDir + m->getRootName(m->getSimpleName(qualFileName)) + "rc" + m->getExtension(qualFileName);
+                       string tempOutputDir = outputDir;
+                       if (outputDir == "") { tempOutputDir += m->hasPath(qualFileName); } //if user entered a file with a path then preserve it
+                       string qualReverseFileName = tempOutputDir + m->getRootName(m->getSimpleName(qualFileName)) + "rc" + m->getExtension(qualFileName);
                        m->openOutputFile(qualReverseFileName, outQual);
 
                        while(!inQual.eof()){