broke up globaldata and moved error checking and help into commands

[mothur.git] / deconvolutecommand.cpp

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index 51362e55a0780ced0cfc9833a51ed8d71870edf2..96682af26b8bcb1b62c17987c82355856cfaf919 100644 (file)
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -10,19 +10,83 @@
 #include "deconvolutecommand.h"
 
 /**************************************************************************************/
-int DeconvoluteCommand::execute() {    
+DeconvoluteCommand::DeconvoluteCommand(string option) {        
        try {
                globaldata = GlobalData::getInstance();
+               abort = false;
+               
+               //allow user to run help
+               if(option == "help") { help(); abort = true; }
+               
+               else {
+                       //valid paramters for this command
+                       string Array[] =  {"fasta"};
+                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       
+                       parser = new OptionParser();
+                       parser->parse(option, parameters);  delete parser;
+                       
+                       ValidParameters* validParameter = new ValidParameters();
+               
+                       //check to make sure all parameters are valid for command
+                       for (it = parameters.begin(); it != parameters.end(); it++) { 
+                               if (validParameter->isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+                       }
+                       
+                       //check for required parameters
+                       filename = validParameter->validFile(parameters, "fasta", true);
+                       if (filename == "not open") { abort = true; }
+                       else if (filename == "not found") { filename = ""; cout << "fasta is a required parameter for the unique.seqs command." << endl; abort = true;  }       
+                       else {  globaldata->setFastaFile(filename);  globaldata->setFormat("fasta");    }
+                       
+                       delete validParameter;
+               }
+
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the DeconvoluteCommand class Function DeconvoluteCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the DeconvoluteCommand class function DeconvoluteCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+
+void DeconvoluteCommand::help(){
+       try {
+               cout << "The unique.seqs command reads a fastafile and creates a namesfile." << "\n";
+               cout << "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";
+               cout << "If the sequence is unique the second column will just contain its name. " << "\n";
+               cout << "The unique.seqs command parameter is fasta and it is required." << "\n";
+               cout << "The unique.seqs command should be in the following format: " << "\n";
+               cout << "unique.seqs(fasta=yourFastaFile) " << "\n";    
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the DeconvoluteCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the DeconvoluteCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }       
+}
+
+/**************************************************************************************/
+int DeconvoluteCommand::execute() {    
+       try {
+               
+               if (abort == true) { return 0; }
        
                //prepare filenames and open files
-               filename = globaldata->getFastaFile();
                outputFileName = (getRootName(filename) + "names");
                outFastafile = (getRootName(filename) + "unique.fasta");
                
                openInputFile(filename, in);
                openOutputFile(outputFileName, out);
                openOutputFile(outFastafile, outFasta);
-       
+
                //constructor reads in file and store internally
                fastamap = new FastaMap();