X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=suffixnodes.cpp;h=130b2be9166ea28f3e4a54066dc31e6d01afdafb;hp=79826ff47d045c5fba48f77b70efbef37bc9c17d;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=526a868606faa50caf86e7399f7554c0335b39e5

diff --git a/suffixnodes.cpp b/suffixnodes.cpp
index 79826ff..130b2be 100644
--- a/suffixnodes.cpp
+++ b/suffixnodes.cpp
@@ -15,7 +15,6 @@
 
 #include "suffixnodes.hpp"
 
-using namespace std;
 
 //********************************************************************************************************************
 
@@ -36,7 +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
@@ -58,14 +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';
+	m->mothurOut(toString(this) + "\t" + toString(parentNode) + "\t" + toString(nodeNumber) + "\t" +
+	toString(-1) + "\t" + toString(startCharPosition) + "\t" + toString(endCharPosition) + "\t");
 	
-	cout << '\'';
+	m->mothurOut("/");
 	for(int i=startCharPosition;i<=endCharPosition;i++){
-		cout << deCodeSequence(sequence[i]);
+		m->mothurOut(toString(deCodeSequence(sequence[i])));
 	}
-	cout << '\'' << endl;
+	m->mothurOut("/");  m->mothurOutEndLine();
 }
 
 //********************************************************************************************************************
@@ -75,14 +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	
+	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
 	
-	cout << '\'';
+	m->mothurOut("/");
 	for(int i=startCharPosition;i<=endCharPosition;i++){
-		cout << deCodeSequence(sequence[i]);
+		m->mothurOut(toString(deCodeSequence(sequence[i])));
 	}
-	cout << '\'' << endl;
+	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