public void LongestCommonSubstring(SuffixNode node, int length, int len1)
{
length += node.end.endIndex - node.startIndex + 1;
bool firstLeaf = false;
bool secondLeaf = false;
for (int i = 0; i < node.child.Length; i++)
{
var childNode = node.child[i];
if (childNode != null)
{
if (childNode.startIndex <= len1)
{
firstLeaf = true;
}
else
{
secondLeaf = true;
}
LongestCommonSubstring(childNode, length, len1);
}
}
if (firstLeaf && secondLeaf)
{
if (this.deepestLength < length)
{
this.deepestLength = length;
this.deepestNode = node;
}
}
}
public SuffixNode(int si, End e, int ind, SuffixNode linkNode)
{
this.startIndex = si;
this.end = e;
this.index = ind;
this.suffixLink = linkNode;
}
private char nextCharInTree(int index)
{
SuffixNode activeEdgeNode = this.active.activeNode.child[this.str[this.active.activeEdge]]; // current edge in the direction of current char.
int activeEdgeLength = (activeEdgeNode.end.endIndex - activeEdgeNode.startIndex) + 1;
if (activeEdgeLength > this.active.activeLength)
{
return(this.str[activeEdgeNode.startIndex + this.active.activeLength]);
}
else if (activeEdgeLength == this.active.activeLength)
{
if (activeEdgeNode.child[this.str[index]] != null)
{
return(this.str[index]);
}
else
{
throw new OverflowException();
}
}
else
{
this.active.activeNode = activeEdgeNode;
this.active.activeLength = this.active.activeLength - activeEdgeLength;
this.active.activeEdge = this.active.activeEdge + activeEdgeLength;
return(nextCharInTree(index));
}
}
private SuffixTreeImpl()
{
this.theRoot = new SuffixNode()
{
Parent = null
};
}
public int LongestRepeatedSubstring(SuffixNode node, int si)
{
int nodeLength = node.end.endIndex - si + 1;
int maxL = 0;
bool hi = false;
for (int i = 0; i < node.child.Length; i++)
{
if (node.child[i] != null && node.child[i].index == -1)
{
hi = true;
int temp = LongestRepeatedSubstring(node.child[i], si);
if (temp > maxL)
{
maxL = temp;
node = node.child[i];
}
}
}
if (maxL > 0)
{
return(maxL);
}
if (hi)
{
return(nodeLength);
}
return(0);
}
/// <summary>
/// C'tor
/// </summary>
/// <param name="text"></param>
private SuffixTreeImpl(string text)
{
this.theRoot = new SuffixNode()
{
Parent = null
};
this.Text = text;
}
/// <summary>
/// match routine
/// </summary>
/// <param name="node">node to start matching from</param>
/// <param name="edges">set of edges to be matched tree edges against</param>
/// <param name="childNode">on return should contain the node reached by the matching routing</param>
/// <param name="unmatchedEdgeCursor">if matching didn't finish at an internal node, it contains the first unmatched char index</param>
/// <returns>true if matching ended at node; false if matching finished inside an edge</returns>
private bool Match(SuffixNode node, IEdgeLabel[] edges, out SuffixNode childNode, out int unmatchedEdgeCursor)
{
if (node == null)
{
throw new ArgumentNullException("parent");
}
if (edges == null || edges.Length <= 0)
{
throw new ArgumentException("invalid argument", "edges");
}
unmatchedEdgeCursor = -1;
var matchingEdgeIndex = 0;
var matchingEdgeCursor = edges[matchingEdgeIndex].Start;
var matchingEdgeEnd = edges[matchingEdgeIndex].End;
childNode = this.TraverseEdge(node, matchingEdgeCursor);
var treeEdgeLength = this.GetEdgeLength(childNode.Edge);
do
{
var diff = matchingEdgeEnd - matchingEdgeCursor + 1 - treeEdgeLength;
if (diff > 0)
{
matchingEdgeCursor += treeEdgeLength;
}
else
{
if (++matchingEdgeIndex < edges.Length)
{
matchingEdgeCursor = edges[matchingEdgeIndex].Start;
matchingEdgeEnd = edges[matchingEdgeIndex].End;
}
else
{
// nothing more to match ..
if (diff < 0) //unmatched = -diff
{
unmatchedEdgeCursor = (childNode.Edge.End == -1 ? (this.CurrentPhase - 1) : childNode.Edge.End) + diff + 1;
}
break;
}
}
if (diff >= 0)
{
node = childNode;
childNode = this.TraverseEdge(node, matchingEdgeCursor);
treeEdgeLength = this.GetEdgeLength(childNode.Edge);
}
} while (true);
return(unmatchedEdgeCursor == -1);
}
private int EdgeLength([NotNull] SuffixNode node)
{
var stop = Math.Min(node.End, _text.Count);
if (node.Start == stop)
{
return(1);
}
return(stop - node.Start);
}
private SuffixNode TraverseEdge(SuffixNode parent, int matchingStart)
{
SuffixNode child = parent.GetEdge(this.GetCharFromIndex(matchingStart));
if (child == null)
{
throw new ApplicationException("unexpected!");
}
return(child);
}
private int AddNode(int start, int end)
{
var node = new SuffixNode {
Start = start,
End = end,
SuffixLink = 0
};
_tree.Add(node);
return(_tree.Count - 1);
}
private SuffixNode TraverseEdge(SuffixNode parent, int matchingStart)
{
SuffixNode child = parent.GetEdge(this.GetCharFromIndex(matchingStart));
if (child != null)
{
return(child);
}
else
{
throw new ArgumentException("invalid argument", "matchingStart");
}
}
private void FixupLeaves(SuffixNode p, int endIndex)
{
if (!p.IsLeaf)
{
foreach (var c in p.Children)
{
this.FixupLeaves(c.Value as SuffixNode, endIndex);
}
}
else
{
p.Edge.End = endIndex;
}
}
/// <summary>
/// pre-match routine
/// </summary>
/// <param name="p">node to start pre-matching from</param>
/// <param name="target">if method returns true, this value will be ignored; otherwise, upon return, it contains the node to start the next matching from</param>
/// <param name="edges">if method returns true, this will be ignored; otherwise, upon return, it contains the set of edges to be matched next,
/// or null (if no further matching should be performed next</param>
/// <returns>true if the next match should be started from root node, false otherwise</returns>
private bool PreMatch(SuffixNode p, out SuffixNode target, out IEdgeLabel[] edges)
{
Debug.Assert(p != this.theRoot);
target = null;
edges = null;
bool goDownFromRoot = true;
var v = p.Parent;
if (p.Link != null)
{
target = p.Link;
edges = null;
goDownFromRoot = false;
}
else if (v != this.theRoot)
{
if (v.Link == null)
{
var w = v.Parent;
if (w != this.theRoot)
{
Debug.Assert(w.Link != null);
edges = new EdgeLabel[2] {
EdgeLabel.Create(v.Edge.Start, v.Edge.End == -1 ? (this.CurrentPhase - 1) : v.Edge.End),
EdgeLabel.Create(p.Edge.Start, p.Edge.End == -1 ? (this.CurrentPhase - 1) : p.Edge.End)
};
target = w.Link;
goDownFromRoot = false;
}
}
else
{
Debug.Assert(v.Link != null);
edges = new EdgeLabel[1] {
EdgeLabel.Create(p.Edge.Start, p.Edge.End == -1 ? (this.CurrentPhase - 1) : p.Edge.End)
};
target = v.Link;
goDownFromRoot = false;
}
}
return(goDownFromRoot);
}
public void BuildSuffixTree(string inputStr)
{
this.str = inputStr + '$';
this.root = new SuffixNode(-1, null, -1, this.root);
remSuffix = 0;
globalEnd = new End(-1);
active = new ActivePoint(this.root, -1, 0);
for (int i = 0; i < str.Length; i++)
{
this.StartPhase(i);
}
}
public SuffixNode AddEdge(string text, int startCharIndex, int endCharIndex)
{
Debug.Assert(endCharIndex == -1 || (0 <= startCharIndex && startCharIndex <= endCharIndex && endCharIndex < text.Length));
Debug.Assert(!this.Children.ContainsKey(text[startCharIndex]));
var newChild = new SuffixNode()
{
Edge = EdgeLabel.Create(startCharIndex, endCharIndex),
Parent = this,
Link = null,
IsLeaf = false
};
this.Children.Add(text[startCharIndex], newChild);
return(newChild);
}
[NotNull] private int[] NodeEdgeData([NotNull] SuffixNode node)
{
var stop = Math.Min(node.End, _text.Count);
if (node.Start == stop)
{
return(new int[0]);
}
var sb = new int[stop - node.Start];
var j = 0;
for (int i = node.Start; i < stop; i++)
{
sb[j++] = _text[i];
}
return(sb);
}
public void DFSToPopulateStartIndexAtLeaves(SuffixNode node, int sLength, List <SuffixNode> leaveNodes)
{
bool isLeaf = true;
sLength += node.end.endIndex - node.startIndex + 1;
for (int i = 0; i < node.child.Length; i++)
{
if (node.child[i] != null)
{
isLeaf = false;
DFSToPopulateStartIndexAtLeaves(node.child[i], sLength, leaveNodes);
}
}
if (isLeaf)
{
node.index = node.end.endIndex - sLength + 1;
leaveNodes.Add(node);
}
}
public string LongestCommonSubstring(int len1)
{
this.deepestNode = null;
this.deepestLength = 0;
for (int i = 0; i < this.root.child.Length; i++)
{
if (this.root.child[i] != null)
{
LongestCommonSubstring(this.root.child[i], 0, len1);
}
}
if (this.deepestNode != null)
{
return(this.str.Substring(deepestNode.end.endIndex - deepestLength + 1, deepestLength));
}
return(string.Empty);
}
public void AddEdge(string text, SuffixNode newChild)
{
this.Children.Add(text[newChild.Edge.Start], newChild);
}
public static SuffixTreeImpl <ChildrenCollectionType> Create(string text)
{
if (string.IsNullOrEmpty(text))
{
return(null);
}
var tree = new SuffixTreeImpl <ChildrenCollectionType>();
tree.Text = text;
var root = tree.theRoot;
int m = text.Length;
var deep = root.AddEdge(tree.Text, 0, -1);
deep.SetLeaf(0);
SuffixNode prevExtEnd = deep;
int lastCreatedLeaf = -1;
for (int i = 1; i < m; i++)
{
tree.CurrentPhase = i;
bool skipRemaining = false;
SuffixNode internCreatedPrevExt = null;
for (int j = 1; j < i && !skipRemaining; j++)
{
if (j < lastCreatedLeaf)
{
continue;
}
List <EdgeLabel> edges = null;
SuffixNode found = null;
int edgecursor = -1;
bool matchEndedAtNode;
if (j == lastCreatedLeaf && j > 1)
{
if (!prevExtEnd.IsLeaf)
{
edges = new List <EdgeLabel>(new EdgeLabel[] { EdgeLabel.Create(i - 1, i - 1) });
matchEndedAtNode = tree.Match(prevExtEnd, edges, out found, out edgecursor);
}
else
{
found = prevExtEnd;
matchEndedAtNode = true;
}
}
if (found == null)
{
SuffixNode target = null;
if (tree.PreMatch(prevExtEnd, out target, out edges))
{
edges = new List <EdgeLabel>(new EdgeLabel[] { EdgeLabel.Create(j, i - 1) });
matchEndedAtNode = tree.Match(tree.theRoot, edges, out found, out edgecursor);
}
else
{
if (edges != null)
{
matchEndedAtNode = tree.Match(target, edges, out found, out edgecursor);
}
else
{
found = target;
matchEndedAtNode = true;
}
}
}
else
{
matchEndedAtNode = true;
}
if (!matchEndedAtNode)
{
if (tree.Text[edgecursor] == tree.Text[i])
{
skipRemaining = true;
break;
}
else
{
var foundParent = found.Parent;
// there's no node here .. better create one..
foundParent.RemoveEdge(tree.GetCharFromIndex(found.Edge.Start));
// create new node..
var internalNode = foundParent.AddEdge(tree.Text, found.Edge.Start, edgecursor - 1);
// massage old node and add it back..
found.Parent = internalNode;
found.Edge.Start = edgecursor;
internalNode.AddEdge(tree.Text, found);
// fix up links if we need to ..
if (internCreatedPrevExt != null)
{
internCreatedPrevExt.Link = internalNode;
}
internCreatedPrevExt = internalNode;
// create a new leaf and hang it here..
var newLeaf = internalNode.AddEdge(tree.Text, i, -1);
newLeaf.SetLeaf(j);
lastCreatedLeaf = j;
prevExtEnd = internalNode;
}
}
else
{
if (found.IsLeaf)
{
prevExtEnd = found;
}
else
{
if (internCreatedPrevExt != null)
{
internCreatedPrevExt.Link = found;
}
internCreatedPrevExt = found.Link == null ? found : null;
if (found.GetEdge(tree.GetCharFromIndex(i)) == null)
{
var newLeaf = found.AddEdge(tree.Text, i, -1);
newLeaf.SetLeaf(j);
lastCreatedLeaf = j;
prevExtEnd = found;
}
else
{
skipRemaining = true;
break;
}
}
}
}
if (!skipRemaining)
{
var parent = root;
var child = parent.GetEdge(tree.GetCharFromIndex(i));
if (child == null)
{
var newLeaf = parent.AddEdge(tree.Text, i, -1);
newLeaf.SetLeaf(i);
lastCreatedLeaf = i;
prevExtEnd = newLeaf;
}
if (internCreatedPrevExt != null)
{
internCreatedPrevExt.Link = parent;
internCreatedPrevExt = null;
}
}
}
tree.FixupLeaves(tree.theRoot, tree.Text.Length - 1);
return(tree);
}
private bool Match(SuffixNode p, List <EdgeLabel> edges, out SuffixNode child, out int firstUnmachedEdgeIndex)
{
if (edges == null || edges.Count <= 0)
{
throw new ArgumentException();
}
firstUnmachedEdgeIndex = -1;
int matchingToDo = 0;
for (int i = 0; i < edges.Count; i++)
{
matchingToDo += this.GetEdgeLength(edges[i]);
}
int matchingDone = 0;
var parent = p;
child = null;
int matchingEdgeIndex = 0;
var matchingEdge = edges[matchingEdgeIndex];
int cursorNext = matchingEdge.Start;
int edgeEnd = matchingEdge.End;
child = this.TraverseEdge(parent, cursorNext);
var treeEdgeLen = this.GetEdgeLength(child.Edge);
do
{
if (cursorNext + treeEdgeLen - 1 < edgeEnd)
{
matchingDone += treeEdgeLen;
cursorNext += treeEdgeLen;
Debug.Assert(matchingDone < matchingToDo);
parent = child;
child = this.TraverseEdge(parent, cursorNext);
treeEdgeLen = this.GetEdgeLength(child.Edge);
}
else if (cursorNext + treeEdgeLen - 1 == edgeEnd)
{
matchingDone += treeEdgeLen;
if (matchingEdgeIndex + 1 < edges.Count)
{
matchingEdge = edges[++matchingEdgeIndex];
cursorNext = matchingEdge.Start;
edgeEnd = matchingEdge.End;
parent = child;
child = this.TraverseEdge(parent, cursorNext);
treeEdgeLen = this.GetEdgeLength(child.Edge);
}
}
else
{
matchingDone += edgeEnd - cursorNext + 1;
var deltaUnmatched = cursorNext + treeEdgeLen - 1 - edgeEnd;
if (matchingEdgeIndex + 1 < edges.Count)
{
matchingEdge = edges[++matchingEdgeIndex];
cursorNext = matchingEdge.Start;
edgeEnd = matchingEdge.End;
treeEdgeLen = deltaUnmatched;
}
else
{
firstUnmachedEdgeIndex = (child.Edge.End == -1 ? (this.CurrentPhase - 1) : child.Edge.End) - deltaUnmatched + 1;
}
}
}while (matchingDone < matchingToDo);
return(firstUnmachedEdgeIndex == -1);
}
public ActivePoint(SuffixNode node)
{
this.ActiveNode = node;
this.ActiveEdge = -1;
this.ActiveLength = 0;
}
private void StartPhase(int index)
{
++remSuffix;
++globalEnd.endIndex; //Handling Rule 1 extension.
SuffixNode LastCreatedInternalNode = null;
while (remSuffix > 0)
{
int ch = (int)this.str[index]; // ascii of next character in input to compare.
if (active.activeLength == 0) // active node will be Root if Aactive length is 0.No Need to traverse edge. Check directly on active node.
{
if (active.activeNode.child[ch] == null) // If edge in current char direction doesn't exists.
{
SuffixNode node = new SuffixNode(index, globalEnd, -1, root); // New node start index will be current index.
active.activeNode.child[ch] = node; // Create and assign new Edge in current char direction.
--remSuffix; // As a new leaf node is created, so one remaning suffix is handled.
}
else
{
++active.activeLength;
active.activeEdge = active.activeNode.child[ch].startIndex; // Set Active edge and increase active length.
break;
}
}
else
{
try
{
char nextChInTree = nextCharInTree(index);
SuffixNode activeEdgeNode = active.activeNode.child[this.str[active.activeEdge]]; // current edge in the direction of current char.
if (nextChInTree == this.str[index]) // If current char matches Next Char after active length. Rule 3 Extension
{
// walk down and jump active node if required while increasing active length
int activeEdgeLength = activeEdgeNode.end.endIndex - activeEdgeNode.startIndex + 1;
if (active.activeLength >= activeEdgeLength)
{
active.activeNode = activeEdgeNode;
active.activeLength = 1;
active.activeEdge = active.activeNode.startIndex + activeEdgeLength;
}
else
{
++active.activeLength;
}
break; // Ends of phase as Rule 3 occurred.
}
else // If current char does not match next char after active length. Rule 2 Extension.
{
SuffixNode newInternalNode = new SuffixNode( // Two new leaf nodes will be created and current node will become internal node.
activeEdgeNode.startIndex,
new End(activeEdgeNode.startIndex + active.activeLength - 1),
-1,
this.root);
SuffixNode newLeafNode = new SuffixNode(
index,
globalEnd,
-1,
this.root);
activeEdgeNode.startIndex = activeEdgeNode.startIndex + active.activeLength;
newInternalNode.child[this.str[activeEdgeNode.startIndex]] = activeEdgeNode;
newInternalNode.child[this.str[newLeafNode.startIndex]] = newLeafNode;
active.activeNode.child[this.str[newInternalNode.startIndex]] = newInternalNode;
--remSuffix;
if (active.activeNode != this.root)
{
active.activeNode = active.activeNode.suffixLink;
}
else
{
active.activeLength--;
active.activeEdge++;
}
if (LastCreatedInternalNode != null)
{
LastCreatedInternalNode.suffixLink = newInternalNode; // Suffix link pointed to the internal node created in the same phase;
}
LastCreatedInternalNode = newInternalNode;
}
}
catch (OverflowException)
{
SuffixNode activeEdgeNode = this.active.activeNode.child[this.str[this.active.activeEdge]]; // current edge in the direction of current char.
activeEdgeNode.child[this.str[index]] = new SuffixNode(index, this.globalEnd, -1, this.root); // Rule 2 extension happens.
if (active.activeNode != this.root)
{
this.active.activeNode = this.active.activeNode.suffixLink;
}
this.active.activeEdge++;
this.active.activeLength--;
this.remSuffix--;
}
}
}
}
public ActivePoint(SuffixNode an, int ae, int al)
{
activeNode = an;
activeEdge = ae;
activeLength = al;
}