added logfile feature

[mothur.git] / suffixnodes.cpp

diff --git a/suffixnodes.cpp b/suffixnodes.cpp
index 81346953d6de431b00b57dad5b8c3681a15e153e..1e5d7056edb318813f8e699288810a31c096006b 100644 (file)
--- a/suffixnodes.cpp
+++ b/suffixnodes.cpp
@@ -57,14 +57,14 @@ SuffixLeaf::SuffixLeaf(int parent, int start, int end) : SuffixNode(parent, star
 
 void SuffixLeaf::print(string sequence, int nodeNumber){
        
-       cout << this << '\t' << parentNode << '\t' << nodeNumber << '\t' <<
-       -1 << '\t' << startCharPosition << '\t' << endCharPosition << '\t';
+       mothurOut(toString(this) + "\t" + toString(parentNode) + "\t" + toString(nodeNumber) + "\t" +
+       toString(-1) + "\t" + toString(startCharPosition) + "\t" + toString(endCharPosition) + "\t");
        
-       cout << '\'';
+       mothurOut("/");
        for(int i=startCharPosition;i<=endCharPosition;i++){
-               cout << deCodeSequence(sequence[i]);
+               mothurOut(toString(deCodeSequence(sequence[i])));
        }
-       cout << '\'' << endl;
+       mothurOut("/");  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
-       cout << this << '\t' << parentNode << '\t' << nodeNumber << '\t' <<                     //      of a leaf because it prints out a
-       suffixNode << '\t' << startCharPosition << '\t' << endCharPosition << '\t';     //      value for the suffix node       
+       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
        
-       cout << '\'';
+       mothurOut("/");
        for(int i=startCharPosition;i<=endCharPosition;i++){
-               cout << deCodeSequence(sequence[i]);
+               mothurOut(toString(deCodeSequence(sequence[i])));
        }
-       cout << '\'' << endl;
+       mothurOut("/");  mothurOutEndLine();
 }
 
 //     we can access the children by subtracting '0' from the the char value from the string, the difference is an int