Changes to seq.error so that an alignment is not necessary

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 9d4a609963316d31bcf0740649b88f4b798747ba..a871244f4538881c8d285c2a1202597be319498d 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -27,8 +27,8 @@ vector<string> AlignCommand::setParameters(){
                CommandParameter pmatch("match", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pmatch);
                CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "","",false,false,true); parameters.push_back(palign);
                CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pmismatch);
-               CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "","",false,false); parameters.push_back(pgapopen);
-               CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pgapextend);
+               CommandParameter pgapopen("gapopen", "Number", "", "-5.0", "", "", "","",false,false); parameters.push_back(pgapopen);
+               CommandParameter pgapextend("gapextend", "Number", "", "-2.0", "", "", "","",false,false); parameters.push_back(pgapextend);
                CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
                CommandParameter pflip("flip", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pflip);
                CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
@@ -57,8 +57,8 @@ string AlignCommand::getHelpString(){
                helpString += "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate.  The default is 8.";
                helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.";
                helpString += "The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.";
-               helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.";
-               helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.";
+               helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -5.0.";
+               helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -2.0.";
                helpString += "The flip parameter is used to specify whether or not you want mothur to try the reverse complement if a sequence falls below the threshold.  The default is false.";
                helpString += "The threshold is used to specify a cutoff at which an alignment is deemed 'bad' and the reverse complement may be tried. The default threshold is 0.50, meaning 50% of the bases are removed in the alignment.";
                helpString += "If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.";
@@ -249,10 +249,10 @@ AlignCommand::AlignCommand(string option)  {
                        temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
                        m->mothurConvert(temp, misMatch);  
                        
-                       temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
+                       temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-5.0";                  }
                        m->mothurConvert(temp, gapOpen);  
                        
-                       temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
+                       temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-2.0";                  }
                        m->mothurConvert(temp, gapExtend); 
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }