X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pairwiseseqscommand.cpp;h=a4ccbf8f33b34b5dd8eccebf91242249cc465f28;hb=9d241ddf4c0e2467298a523e21a3b0de46902448;hp=98b0fde32dbb4cf9bf86aad283fa1d6ad3a7ea44;hpb=7dab6ac3ae5a5f1ce37dca8cfacaa719881fd5b2;p=mothur.git

diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index 98b0fde..a4ccbf8 100644
--- a/pairwiseseqscommand.cpp
+++ b/pairwiseseqscommand.cpp
@@ -203,12 +203,15 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option)  {
 			
 			temp = validParameter.validFile(parameters, "mismatch", false);		if (temp == "not found"){	temp = "-1.0";			}
 			m->mothurConvert(temp, misMatch);  
+            if (misMatch > 0) { m->mothurOut("[ERROR]: mismatch must be negative.\n"); abort=true; }
 			
 			temp = validParameter.validFile(parameters, "gapopen", false);		if (temp == "not found"){	temp = "-2.0";			}
 			m->mothurConvert(temp, gapOpen);  
+            if (gapOpen > 0) { m->mothurOut("[ERROR]: gapopen must be negative.\n"); abort=true; }
 			
 			temp = validParameter.validFile(parameters, "gapextend", false);	if (temp == "not found"){	temp = "-1.0";			}
 			m->mothurConvert(temp, gapExtend); 
+            if (gapExtend > 0) { m->mothurOut("[ERROR]: gapextend must be negative.\n"); abort=true; }
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);