X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=suffixtree.cpp;h=fd18109513bea9f59590e16a1c705128f61ca43e;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=2842b366b3360f4b43ad32dd28603073266dcdfa;hpb=63e089e0b3aad1741bab60119ed7ccc784dce347;p=mothur.git

diff --git a/suffixtree.cpp b/suffixtree.cpp
index 2842b36..fd18109 100644
--- a/suffixtree.cpp
+++ b/suffixtree.cpp
@@ -33,9 +33,28 @@ inline bool compareParents(SuffixNode* left, SuffixNode* right){//	this is neces
 	return (left->getParentNode() < right->getParentNode());	//	nodes in order of their parent
 }
 
+//********************************************************************************************************************
+ 
+SuffixTree::SuffixTree(const SuffixTree& st) : root(st.root), activeEndPosition(st.activeEndPosition), activeStartPosition(st.activeStartPosition), activeNode(st.activeNode),
+												nodeCounter(st.nodeCounter), seqName(st.seqName), sequence(st.sequence) { 
+	try {
+		m = MothurOut::getInstance(); 
+		
+		for (int i = 0; i < st.nodeVector.size(); i++) {
+			SuffixNode* temp = new SuffixBranch(*((SuffixBranch*)st.nodeVector[i]));
+			nodeVector.push_back(temp);
+		}
+		
+		
+	}catch(exception& e) {
+		m->errorOut(e, "SuffixTree", "SuffixTree");
+		exit(1);
+	}
+}
+ 
 //********************************************************************************************************************
 
-SuffixTree::SuffixTree(){}
+SuffixTree::SuffixTree(){ m = MothurOut::getInstance(); }
 
 //********************************************************************************************************************
 
@@ -75,7 +94,7 @@ string SuffixTree::getSeqName()	{
 void SuffixTree::print(){
 	vector<SuffixNode*> hold = nodeVector;
 	sort(hold.begin(), hold.end(), compareParents);
-	mothurOut("Address\t\tParent\tNode\tSuffix\tStartC\tEndC\tSuffix"); mothurOutEndLine();
+	m->mothurOut("Address\t\tParent\tNode\tSuffix\tStartC\tEndC\tSuffix"); m->mothurOutEndLine();
 	for(int i=1;i<=nodeCounter;i++){
 		hold[i]->print(sequence, i);
 	}