added screen.seqs command - pds

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 81f8e6ab78c7dbc90d351894bd420a7d7e2cca9e..242e9a8fe0e3ba7a7f199846ae0e80cba10f0edb 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -32,7 +32,6 @@
 #include "kmerdb.hpp"
 #include "suffixdb.hpp"
 #include "blastdb.hpp"
-#include "distancedb.hpp"
 
 #include "nast.hpp"
 #include "nastreport.hpp"
@@ -42,15 +41,14 @@
 AlignCommand::AlignCommand(){
        try {
                globaldata = GlobalData::getInstance();
-               candidateFileName = globaldata->inputFileName;
-               templateFileName = globaldata->getTemplateFile();
+               candidateFileName = globaldata->getCandidateFile();
+               templateFileName = globaldata->getFastaFile();
                openInputFile(candidateFileName, in);
                convert(globaldata->getKSize(), kmerSize);
                convert(globaldata->getMatch(), match);
                convert(globaldata->getMismatch(), misMatch);
                convert(globaldata->getGapopen(), gapOpen);
                convert(globaldata->getGapextend(), gapExtend);
-               distanceFileName = "????";
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the AlignCommand class Function AlignCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -78,7 +76,6 @@ int AlignCommand::execute(){
                if(globaldata->getSearch() == "kmer")                   {       templateDB = new KmerDB(templateFileName, kmerSize);                                                            }
                else if(globaldata->getSearch() == "suffix")    {       templateDB = new SuffixDB(templateFileName);                                                                            }
                else if(globaldata->getSearch() == "blast")             {       templateDB = new BlastDB(templateFileName, gapOpen, gapExtend, match, misMatch);        }
-               else if(globaldata->getSearch() == "distance")  {       templateDB = new DistanceDB(templateFileName, distanceFileName);                                        }
                else {  cout << globaldata->getSearch() << " is not a valid search option. I will run the command using suffix." << endl;
                                templateDB = new SuffixDB(templateFileName);            }