added count.seqs command and made some modifcations to the uchime code to allow it...

[mothur.git] / parsefastaqcommand.cpp

diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp
index f0a7abcc3692b8e290863a71c93bcc1831e87fca..1033ba5d5dd3a64b001e2e8bc120b792df02e824 100644 (file)
--- a/parsefastaqcommand.cpp
+++ b/parsefastaqcommand.cpp
@@ -11,65 +11,61 @@
 #include "sequence.hpp"
 
 //**********************************************************************************************************************
-vector<string> ParseFastaQCommand::getValidParameters(){       
+vector<string> ParseFastaQCommand::setParameters(){    
        try {
-               string Array[] =  {"fastq", "outputdir","inputdir"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               CommandParameter pfastq("fastq", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfastq);
+               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, "ParseFastaQCommand", "getValidParameters");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-ParseFastaQCommand::ParseFastaQCommand(){      
-       try {
-               abort = true;
-               //initialize outputTypes
-               vector<string> tempOutNames;
-               outputTypes["fasta"] = tempOutNames;
-               outputTypes["qual"] = tempOutNames;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ParseFastaQCommand", "ParseFastaQCommand");
+               m->errorOut(e, "ParseFastaQCommand", "setParameters");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-vector<string> ParseFastaQCommand::getRequiredParameters(){    
+string ParseFastaQCommand::getHelpString(){    
        try {
-               string Array[] =  {"fastq"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-               return myArray;
+               string helpString = "";
+               helpString += "The fastq.info command reads a fastq file and creates a fasta and quality file.\n";
+               helpString += "The fastq.info command parameter is fastq, and it is required.\n";
+               helpString += "The fastq.info command should be in the following format: fastq.info(fastaq=yourFastaQFile).\n";
+               helpString += "Example fastq.info(fastaq=test.fastaq).\n";
+               helpString += "Note: No spaces between parameter labels (i.e. fastq), '=' and yourFastQFile.\n";
+               return helpString;
        }
        catch(exception& e) {
-               m->errorOut(e, "ParseFastaQCommand", "getRequiredParameters");
+               m->errorOut(e, "ParseFastaQCommand", "getHelpString");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-vector<string> ParseFastaQCommand::getRequiredFiles(){ 
+ParseFastaQCommand::ParseFastaQCommand(){      
        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, "ParseFastaQCommand", "getRequiredFiles");
+               m->errorOut(e, "ParseFastaQCommand", "ParseFastaQCommand");
                exit(1);
        }
 }
 //**********************************************************************************************************************
 ParseFastaQCommand::ParseFastaQCommand(string option){
        try {
-               abort = false;
+               abort = false; calledHelp = false;   
                
-               if(option == "help") {  help(); abort = true; }
+               if(option == "help") {  help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
-                       //valid paramters for this command
-                       string Array[] =  {"fastq", "outputdir", "inputdir"};
-                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       vector<string> myArray = setParameters();
                        
                        OptionParser parser(option);
                        map<string,string> parameters = parser.getParameters();
@@ -85,7 +81,7 @@ ParseFastaQCommand::ParseFastaQCommand(string option){
                        //initialize outputTypes
                        vector<string> tempOutNames;
                        outputTypes["fasta"] = tempOutNames;
-                       outputTypes["qual"] = tempOutNames;
+                       outputTypes["qfile"] = tempOutNames;
                        
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
@@ -118,36 +114,16 @@ ParseFastaQCommand::ParseFastaQCommand(string option){
 }
 //**********************************************************************************************************************
 
-void ParseFastaQCommand::help(){
-       try {
-               m->mothurOut("The fastq.info command reads a fastq file and creates a fasta and quality file.\n");
-               m->mothurOut("The fastq.info command parameter is fastq, and it is required.\n");
-               m->mothurOut("The fastq.info command should be in the following format: fastq.info(fastaq=yourFastaQFile).\n");
-               m->mothurOut("Example fastq.info(fastaq=test.fastaq).\n");
-               m->mothurOut("Note: No spaces between parameter labels (i.e. fastq), '=' and yourFastQFile.\n");
-               m->mothurOutEndLine();
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ParseFastaQCommand", "help");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-
-ParseFastaQCommand::~ParseFastaQCommand()      {       /*      do nothing      */      }
-
-//**********************************************************************************************************************
-
 int ParseFastaQCommand::execute(){
        try {
-               if (abort == true) {    return 0;       }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                //open Output Files
                string fastaFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "fasta";
                string qualFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "qual";
                ofstream outFasta, outQual;
                m->openOutputFile(fastaFile, outFasta);  outputNames.push_back(fastaFile); outputTypes["fasta"].push_back(fastaFile);
-               m->openOutputFile(qualFile, outQual);   outputNames.push_back(qualFile);  outputTypes["qual"].push_back(qualFile);
+               m->openOutputFile(qualFile, outQual);   outputNames.push_back(qualFile);  outputTypes["qfile"].push_back(qualFile);
                
                ifstream in;
                m->openInputFile(fastaQFile, in);
@@ -195,6 +171,18 @@ int ParseFastaQCommand::execute(){
                
                if (m->control_pressed) { outputTypes.clear(); remove(fastaFile.c_str()); remove(qualFile.c_str()); return 0; }
                
+               //set fasta file as new current fastafile
+               string current = "";
+               itTypes = outputTypes.find("fasta");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+               }
+               
+               itTypes = outputTypes.find("qfile");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
+               }               
+               
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }