X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=suffixtree.cpp;h=fd18109513bea9f59590e16a1c705128f61ca43e;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=0dbe2c0e41e6bd68df024f411c0883bdd306fe8b;hpb=02909d6cae9963ba00dc746969a370fa8ca934fc;p=mothur.git

diff --git a/suffixtree.cpp b/suffixtree.cpp
index 0dbe2c0..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);
-	cout << "Address\t\tParent\tNode\tSuffix\tStartC\tEndC\tSuffix" << endl;
+	m->mothurOut("Address\t\tParent\tNode\tSuffix\tStartC\tEndC\tSuffix"); m->mothurOutEndLine();
 	for(int i=1;i<=nodeCounter;i++){
 		hold[i]->print(sequence, i);
 	}
@@ -125,7 +144,46 @@ int SuffixTree::countSuffixes(string compareSequence, int& minValue){	//	here we
 	return numSuffixes;											//	change the value and return the number of suffixes
 	
 }
+//********************************************************************************************************************
 
+int SuffixTree::countSuffixes(string compareSequence){	//	here we count the number of suffix parts 
+															//	we need to rewrite a user supplied sequence.  if the 
+	int numSuffixes = 0;									//	count exceeds the supplied minValue, bail out.  The
+	int seqLength = compareSequence.length();				//	time complexity should be O(L)
+	int position = 0;
+	
+	int presentNode = 0;
+	
+	while(position < seqLength){		//	while the position in the query sequence isn't at the end...
+		
+		int newNode = nodeVector[presentNode]->getChild(compareSequence[position]);	//	see if the current node has a
+																//	child that matches the next character in the query
+		if(newNode == -1){										
+			if(presentNode == 0){	position++;		}			//	if not, go back to the root and increase the count
+			numSuffixes++;										//	by one.
+			presentNode = 0;
+		}
+		else{													//	if there is, move to that node and see how far down
+			presentNode = newNode;								//	it we can get
+			
+			for(int i=nodeVector[newNode]->getStartCharPos(); i<=nodeVector[newNode]->getEndCharPos(); i++){
+				if(compareSequence[position] == sequence[i]){
+					position++;									//	as long as the query and branch agree, keep going
+				}
+				else{
+					numSuffixes++;								//	if there is a mismatch, increase the number of 
+					presentNode = 0;							//	suffixes and go back to the root
+					break;
+				}
+			}
+		}
+		//	if we get all the way through the node we'll go to the top of the while loop and find the child node
+		//	that corresponds to what we are interested in		
+	}
+	numSuffixes--;												//	the method puts an extra count on numSuffixes
+	
+	return numSuffixes;											//	change the value and return the number of suffixes
+}
 //********************************************************************************************************************
 
 void SuffixTree::canonize(){	//	if you have to ask how this works, you don't really want to know and this really