added get.repseqs command, started matrix output command

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 81f8e6ab78c7dbc90d351894bd420a7d7e2cca9e..f5eb48cacfc300f6bd46673088319aa8111af8cb 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"
@@ -50,7 +49,6 @@ AlignCommand::AlignCommand(){
                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);            }