created mothurOut class to handle logfiles

[mothur.git] / distancedb.cpp

diff --git a/distancedb.cpp b/distancedb.cpp
index 25641eb0dacdf63d812cd1bf2a828a7cdfd5f8d2..0c1aeebe43af3ca586bfd6416f95db924a047054 100644 (file)
--- a/distancedb.cpp
+++ b/distancedb.cpp
@@ -21,7 +21,7 @@ DistanceDB::DistanceDB() {
                distCalculator = new eachGapDist();
        }
        catch(exception& e) {
-               errorOut(e, "DistanceDB", "DistanceDB");
+               m->errorOut(e, "DistanceDB", "DistanceDB");
                exit(1);
        }       
 }
@@ -29,14 +29,14 @@ DistanceDB::DistanceDB() {
 void DistanceDB::addSequence(Sequence seq) {
        try {
                //are the template sequences aligned
-               if (!isAligned(seq.getAligned())) { templateAligned = false; mothurOut(seq.getName() + " is not aligned. Sequences must be aligned to use the distance method."); mothurOutEndLine(); }
+               if (!isAligned(seq.getAligned())) { templateAligned = false; m->mothurOut(seq.getName() + " is not aligned. Sequences must be aligned to use the distance method."); m->mothurOutEndLine(); }
                
                if (templateSeqsLength == 0) { templateSeqsLength = seq.getAligned().length(); }
                                
                data.push_back(seq);
        }
        catch(exception& e) {
-               errorOut(e, "DistanceDB", "addSequence");
+               m->errorOut(e, "DistanceDB", "addSequence");
                exit(1);
        }       
 }
@@ -49,7 +49,7 @@ vector<int> DistanceDB::findClosestSequences(Sequence* query, int numWanted){
                string sequence = query->getAligned();
                vector<seqDist> dists;
                
-               if (numWanted > data.size()) { mothurOut("numwanted is larger than the number of template sequences, using 10."); mothurOutEndLine(); numWanted = 10; }
+               if (numWanted > data.size()) { m->mothurOut("numwanted is larger than the number of template sequences, using 10."); m->mothurOutEndLine(); numWanted = 10; }
                
                if (sequence.length() != templateSeqsLength) { templateSameLength = false; }
                
@@ -72,14 +72,14 @@ vector<int> DistanceDB::findClosestSequences(Sequence* query, int numWanted){
                        }
                
                }else{
-                       mothurOut("cannot find closest matches using distance method for " + query->getName() + " without aligned template sequences of the same length."); mothurOutEndLine();
+                       m->mothurOut("cannot find closest matches using distance method for " + query->getName() + " without aligned template sequences of the same length."); m->mothurOutEndLine();
                        exit(1);
                }
                
                return topMatches;
        }
        catch(exception& e) {
-               errorOut(e, "DistanceDB", "findClosestSequence");
+               m->errorOut(e, "DistanceDB", "findClosestSequence");
                exit(1);
        }       
 }
@@ -98,7 +98,7 @@ bool DistanceDB::isAligned(string seq){
                return aligned;
        }
        catch(exception& e) {
-               errorOut(e, "DistanceDB", "isAligned");
+               m->errorOut(e, "DistanceDB", "isAligned");
                exit(1);
        }       
 }