merged pat's trim seqs edits with sarah's major overhaul of global data; also added...

[mothur.git] / deconvolutecommand.cpp

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index f2dfdd5bae38d5994ff03150013aab9db0ecfb7c..3ec5f734eebb393c6ff630a1adc8d7e94ab6729f 100644 (file)
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -9,17 +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();
        
@@ -29,7 +93,11 @@ int DeconvoluteCommand::execute() {
                //print out new names file 
                //file contains 2 columns separated by tabs.  the first column is the groupname(name of first sequence found.
                //the second column is the list of names of identical sequences separated by ','.
-               fastamap->print(out);
+               fastamap->printNamesFile(out);
+               fastamap->printCondensedFasta(outFasta);
+               
+               out.close();
+               outFasta.close();
        
                return 0;
        }