fixes while testing 1.33.0

[mothur.git] / suffixnodes.cpp

diff --git a/suffixnodes.cpp b/suffixnodes.cpp
index 1e5d7056edb318813f8e699288810a31c096006b..130b2be9166ea28f3e4a54066dc31e6d01afdafb 100644 (file)
--- a/suffixnodes.cpp
+++ b/suffixnodes.cpp
@@ -35,7 +35,7 @@ SuffixNode::SuffixNode(int parent, int start, int end) :
                parentNode(parent),                     //      we store the parent node as an int
                startCharPosition(start),       //      the suffix tree class will hold the sequence that the startCharPosition and 
                endCharPosition(end)            //      endCharPosition indices correspond to
-               {       /*      do nothing      */                      }
+               {       /*      do nothing      */              m = MothurOut::getInstance();   }
 
 
 void SuffixNode::setChildren(char, int)                        {       /*      do nothing      */                      }       //      there's no children in a leaf
@@ -57,14 +57,14 @@ SuffixLeaf::SuffixLeaf(int parent, int start, int end) : SuffixNode(parent, star
 
 void SuffixLeaf::print(string sequence, int nodeNumber){
        
-       mothurOut(toString(this) + "\t" + toString(parentNode) + "\t" + toString(nodeNumber) + "\t" +
+       m->mothurOut(toString(this) + "\t" + toString(parentNode) + "\t" + toString(nodeNumber) + "\t" +
        toString(-1) + "\t" + toString(startCharPosition) + "\t" + toString(endCharPosition) + "\t");
        
-       mothurOut("/");
+       m->mothurOut("/");
        for(int i=startCharPosition;i<=endCharPosition;i++){
-               mothurOut(toString(deCodeSequence(sequence[i])));
+               m->mothurOut(toString(deCodeSequence(sequence[i])));
        }
-       mothurOut("/");  mothurOutEndLine();
+       m->mothurOut("/");  m->mothurOutEndLine();
 }
 
 //********************************************************************************************************************
@@ -74,14 +74,14 @@ SuffixBranch::SuffixBranch(int parent, int start, int end) : SuffixNode(parent,
 }
        
 void SuffixBranch::print(string sequence, int nodeNumber){                                             //      this method is different that than
-       mothurOut(toString(this) + "\t" + toString(parentNode) + "\t" + toString(nodeNumber) + "\t" +           //      of a leaf because it prints out a
+       m->mothurOut(toString(this) + "\t" + toString(parentNode) + "\t" + toString(nodeNumber) + "\t" +                //      of a leaf because it prints out a
        toString(suffixNode) + "\t" + toString(startCharPosition) + "\t" + toString(endCharPosition) + "\t");  //       value for the suffix node
        
-       mothurOut("/");
+       m->mothurOut("/");
        for(int i=startCharPosition;i<=endCharPosition;i++){
-               mothurOut(toString(deCodeSequence(sequence[i])));
+               m->mothurOut(toString(deCodeSequence(sequence[i])));
        }
-       mothurOut("/");  mothurOutEndLine();
+       m->mothurOut("/");  m->mothurOutEndLine();
 }
 
 //     we can access the children by subtracting '0' from the the char value from the string, the difference is an int