trim.seqs linker and spacer mods

[mothur.git] / distancecommand.cpp

diff --git a/distancecommand.cpp b/distancecommand.cpp
index 0f067aeab3b6ce1a50ba5e60870b410bbf72ba67..0ac17877b2bed9bfc441a70dcece14cd99081727 100644 (file)
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -179,11 +179,11 @@ DistanceCommand::DistanceCommand(string option) {
                        convert(temp, countends); 
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);           if(temp == "not found"){        temp = "1.0"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        temp = validParameter.validFile(parameters, "compress", false);         if(temp == "not found"){  temp = "F"; }
                        convert(temp, compress);
@@ -1094,7 +1094,7 @@ int DistanceCommand::convertMatrix(string outputFile) {
                exit(1);
        }
 }
-/**************************************************************************************************
+**************************************************************************************************
 int DistanceCommand::convertToLowerTriangle(string outputFile) {
        try{
 
@@ -1188,7 +1188,7 @@ int DistanceCommand::convertToLowerTriangle(string outputFile) {
                exit(1);
        }
 }
-/**************************************************************************************************/
+**************************************************************************************************/
 //its okay if the column file does not contain all the names in the fasta file, since some distance may have been above a cutoff,
 //but no sequences can be in the column file that are not in oldfasta. also, if a distance is above the cutoff given then remove it.
 //also check to make sure the 2 files have the same alignment length.