chimera.seqs pintail is working.

[mothur.git] / deconvolutecommand.cpp

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index 51362e55a0780ced0cfc9833a51ed8d71870edf2..a936c820b56f88609e621894565359892384224a 100644 (file)
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -9,43 +9,84 @@
 
 #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", "name"};
+                       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
+                       inFastaName = validParameter.validFile(parameters, "fasta", true);
+                       if (inFastaName == "not open") { abort = true; }
+                       else if (inFastaName == "not found") { inFastaName = ""; mothurOut("fasta is a required parameter for the unique.seqs command."); mothurOutEndLine(); abort = true;  }  
+                       
+                       oldNameMapFName = validParameter.validFile(parameters, "name", true);
+                       if (oldNameMapFName == "not open") { abort = true; }
+                       else if (oldNameMapFName == "not found"){       oldNameMapFName = "";   }
+               }
+
+       }
+       catch(exception& e) {
+               errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+
+void DeconvoluteCommand::help(){
+       try {
+               mothurOut("The unique.seqs command reads a fastafile and creates a namesfile.\n");
+               mothurOut("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");
+               mothurOut("If the sequence is unique the second column will just contain its name. \n");
+               mothurOut("The unique.seqs command parameter is fasta and it is required.\n");
+               mothurOut("The unique.seqs command should be in the following format: \n");
+               mothurOut("unique.seqs(fasta=yourFastaFile) \n");       
+       }
+       catch(exception& e) {
+               errorOut(e, "DeconvoluteCommand", "help");
+               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");
+               string outNameFile = (getRootName(inFastaName) + "names");
+               string outFastaFile = (getRootName(inFastaName) + "unique" + getExtension(inFastaName));
                
-               openInputFile(filename, in);
-               openOutputFile(outputFileName, out);
-               openOutputFile(outFastafile, outFasta);
-       
-               //constructor reads in file and store internally
-               fastamap = new FastaMap();
+               FastaMap fastamap;
        
-               //two columns separated by tabs sequence name and then sequence
-               fastamap->readFastaFile(in);
+               if(oldNameMapFName == "")       {       fastamap.readFastaFile(inFastaName);                                    }
+               else                                            {       fastamap.readFastaFile(inFastaName, oldNameMapFName);   }
                
-               //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->printNamesFile(out);
-               fastamap->printCondensedFasta(outFasta);
+               fastamap.printCondensedFasta(outFastaFile);
+               fastamap.printNamesFile(outNameFile);
                
-               out.close();
-               outFasta.close();
-       
                return 0;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the DeconvoluteCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the DeconvoluteCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "DeconvoluteCommand", "execute");
                exit(1);
        }
 }