fixed some bugs

[mothur.git] / deconvolutecommand.cpp

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index 51362e55a0780ced0cfc9833a51ed8d71870edf2..2fe7a251ca41a5d833ad7f643970a1d9847a8361 100644 (file)
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -9,20 +9,81 @@
 
 #include "deconvolutecommand.h"
 
+/**************************************************************************************/
+DeconvoluteCommand::DeconvoluteCommand(string option) {        
+       try {
+               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)));
+                       
+                       OptionParser parser(option);
+                       map<string,string> parameters = parser.getParameters();
+                       
+                       ValidParameters validParameter;
+               
+                       //check to make sure all parameters are valid for command
+                       for (map<string, string>::iterator 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;  }       
+                       
+               }
+
+       }
+       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 {
-               globaldata = GlobalData::getInstance();
+               
+               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();
        
@@ -35,6 +96,7 @@ int DeconvoluteCommand::execute() {
                fastamap->printNamesFile(out);
                fastamap->printCondensedFasta(outFasta);
                
+               in.close();
                out.close();
                outFasta.close();