created mothurOut class to handle logfiles

[mothur.git] / readblast.cpp

diff --git a/readblast.cpp b/readblast.cpp
index a6d23e95bfddf71afb20a2d4c2b2d8d1377db71d..616d4f7824c0bc3458d55a3e7eb18aa82751d75d 100644 (file)
--- a/readblast.cpp
+++ b/readblast.cpp
@@ -16,12 +16,13 @@ inline bool compareOverlap(seqDist left, seqDist right){
        return (left.dist < right.dist);        
 } 
 /*********************************************************************************************/
-ReadBlast::ReadBlast(string file, float c, float p, int l, bool m, bool h) : blastfile(file), cutoff(c), penalty(p), length(l), minWanted(m), hclusterWanted(h) {
+ReadBlast::ReadBlast(string file, float c, float p, int l, bool ms, bool h) : blastfile(file), cutoff(c), penalty(p), length(l), minWanted(ms), hclusterWanted(h) {
        try {
+               m = MothurOut::getInstance();
                matrix = NULL;
        }
        catch(exception& e) {
-               errorOut(e, "ReadBlast", "ReadBlast");
+               m->errorOut(e, "ReadBlast", "ReadBlast");
                exit(1);
        }
 } 
@@ -98,7 +99,7 @@ void ReadBlast::read(NameAssignment* nameMap) {
                                        }
                                }
                        }
-               }else { mothurOut("Error in your blast file, cannot read."); mothurOutEndLine(); exit(1); }
+               }else { m->mothurOut("Error in your blast file, cannot read."); m->mothurOutEndLine(); exit(1); }
 
                                
                //read file
@@ -260,14 +261,14 @@ void ReadBlast::read(NameAssignment* nameMap) {
                fileHandle.close();
        }
        catch(exception& e) {
-               errorOut(e, "ReadBlast", "read");
+               m->errorOut(e, "ReadBlast", "read");
                exit(1);
        }
 } 
 /*********************************************************************************************/
 void ReadBlast::readNames(NameAssignment* nameMap) {
        try {
-               mothurOut("Reading names... "); cout.flush();
+               m->mothurOut("Reading names... "); cout.flush();
                
                string name, hold, prevName;
                int num = 1;
@@ -307,11 +308,11 @@ void ReadBlast::readNames(NameAssignment* nameMap) {
                //nameMap->print(out);
                //out.close();
                
-               mothurOut(toString(num) + " names read."); mothurOutEndLine();
+               m->mothurOut(toString(num) + " names read."); m->mothurOutEndLine();
                
        }
        catch(exception& e) {
-               errorOut(e, "ReadBlast", "readNames");
+               m->errorOut(e, "ReadBlast", "readNames");
                exit(1);
        }
 }