/// <summary>
/// Traverse the suffix tree, following the longest path from the root that matches a prefix of words[wordNum].
/// This allows the caller to skip over these duplicate characters, and process only the part of the coming word.
/// </summary>
/// <param name="active">The current active suffix</param>
/// <param name="endIndex">The number of characters skipped</param>
/// <param name="wordNum">The index of the current word begin processed</param>
/// <seealso cref="http://www.cs.uku.fi/~kilpelai/BSA05/lectures/slides08.pdf">
/// The first 10 slides of this slideshow by Pekka Kilpeläinen
/// have useful tips on creating a generalized suffix tree.
/// </seealso>
/// <remarks>
/// TODO: Note: The following method is WORK IN PROGRESS, and does not yet work.
/// </remarks>
private void skipDuplicateInitialSubstring(ref GstSuffix active, ref int endIndex, int wordNum)
{
GstNode curNode = root;
GstEdge nextEdge = null;
GstEdge curEdge = null;
// Traverse matching edges
while (
(endIndex < wordDict[wordNum].Length) &&
((nextEdge = curNode.GetChildEdge(GetWordChar(wordNum, endIndex))) != null)
)
{
int strLen = nextEdge.Span(0) + 1;
// edgeStr = String in next edge
string edgeStr = nextEdge.GetText();
// wordStr = next segment of upcoming word that corresponds to edgeStr
string wordStr = wordDict[wordNum].Substring(endIndex, Math.Min(strLen, wordDict[wordNum].Length - endIndex));
bool foundMismatch = false;
int numCharsMatched = 0;
// Traverse matching characters within edge
for (int i = 0; i < strLen; i++)
{
if (edgeStr[i] == wordStr[i])
{
numCharsMatched++;
}
else
{
foundMismatch = true; break;
}
}
if (foundMismatch)
{
GstUtil.WriteLine(GstVerbosityLevel.Verbose, String.Format(
" skipDuplicateInitialSubstring: Word #{0:d} does not cover existing edge #{1:d}",
wordNum, nextEdge.Id));
active.OriginNode = nextEdge.ParentNode;
active.EndIndex = active.BeginIndex;
break;
}
else
{
nextEdge.SetBeginIndex(wordNum, endIndex);
nextEdge.SetEndIndex(wordNum, endIndex + strLen - 1);
GstUtil.WriteLine(GstVerbosityLevel.Verbose, String.Format(
" skipDuplicateInitialSubstring: Word #{0:d} covers existing edge #{1:d} ({2:s})",
wordNum, nextEdge.Id, nextEdge.ToString(wordNum)));
active.OriginNode = nextEdge.ChildNode;
active.BeginIndex += numCharsMatched;
active.EndIndex = active.BeginIndex;
}
endIndex += numCharsMatched;
// Set up next iteration of loop
curEdge = nextEdge;
curNode = curEdge.ChildNode;
}
}
/// <summary>
/// Rule #1 (Ukkonen's first group of t_i-transitions): Try to find matching edge for the parent node.
/// </summary>
/// <param name="parentNode">This is a member of active. It is kept separate for clarity.</param>
private ExtensionResult extendSuffixByRuleOne(
ref GstSuffix active, ref GstNode parentNode, int endIndex, int wordNum)
{
if (active.IsExplicit)
{
GstEdge edge = active.OriginNode.GetChildEdge(GetWordChar(wordNum, endIndex));
if (edge != null && edge.IsSet())
{
return(ExtensionResult.Done);
}
}
else // active suffix is implicit
{
GstEdge edge = active.OriginNode.GetChildEdge(GetWordChar(wordNum, active.BeginIndex));
int span = active.EndIndex - active.BeginIndex;
if (edge != null)
{
int extantWordNum = edge.GetExtantWordNum();
if (GetWordChar(extantWordNum, edge.GetBeginIndex(extantWordNum) + span + 1)
== GetWordChar(wordNum, endIndex))
{
return(ExtensionResult.Done);
}
GstUtil.WriteLine(GstVerbosityLevel.Verbose, String.Format(
" Rule #1: About to split edge E{0:d} (\"{1:s}\") at suffix {2:s}",
edge.Id, edge.GetText(), active.ToString()));
parentNode = edge.Split(active);
}
}
return(ExtensionResult.NotDone);
}
public GstEdge GetChildEdge(char c)
{
GstEdge childEdge = null;
childEdges.TryGetValue(c, out childEdge);
return(childEdge);
}
public void MoveFromTo(GstNode oldParentNode, char oldFirstChar, GstNode newParentNode, char newFirstChar)
{
GstEdge self = oldParentNode.GetChildEdge(oldFirstChar);
if (self != this)
{
throw new ArgumentException("Error: MoveTo called with incorrect parent node and/or first char arguments");
}
oldParentNode.RemoveChildEdge(oldFirstChar);
newParentNode.AddChildEdge(newFirstChar, this);
}
private string toStringEdgeTable(int wordNum,
bool doAddIds = true,
bool doAddTree = true)
{
StringBuilder sb = new StringBuilder();
string edgesBanner = toStringEdgeBanner(wordDict.Values.Select(w => w.Length).Max());
string addIdsSpacer = " Id ";
int[] wordNums = (wordNum == GSuffixTree.NoWordNum)
? wordDict.Keys.ToArray()
: new int[] { wordNum };
if (doAddIds)
{
sb.Append(addIdsSpacer);
}
sb.AppendLine(edgesBanner);
foreach (DepthTaggedGstEdge dtEdge in DepthTaggedEdges())
{
GstEdge edge = dtEdge.Edge;
string formatStr = " {0,-11:d}{1,-11:d}{2,-11:s}{3,-11:d}{4,-11:d}{5,-9:d}{6,-"
+ Math.Max(7, wordDict.Values.Select(w => 1 + w.Length).Max()).ToString()
+ ":s}";
for (int i = 0; i < wordNums.Length; i++)
{
if (!edge.HasWordNum(wordNums[i]))
{
continue;
}
if (doAddIds)
{
sb.Append(String.Format(" {0,-4:d}", edge.Id));
}
sb.Append(String.Format(formatStr,
edge.ParentNode.Id, edge.ChildNode.Id,
(edge.ChildNode.SuffixNode == null ? "null" : edge.ChildNode.SuffixNode.Id.ToString()),
wordNums[i],
edge.GetBeginIndex(wordNums[i]), edge.GetEndIndex(wordNums[i]),
(new String(' ', edge.GetBeginIndex(wordNums[i]))) +
GetRangeString(wordNums[i], edge.GetBeginIndex(wordNums[i]), edge.GetEndIndex(wordNums[i]))
));
if (doAddTree)
{
string depthStr = new String(' ', 2 * dtEdge.Depth - 1) + "*";
sb.AppendLine(depthStr);
}
}
}
return(sb.ToString());
}
/// <summary>
/// Rule #2 (Ukkonen's second group of t_i-transitions):
/// Create a new edge and add it to the tree at the parent's position.
// Part of this is inserting the new edge into the hash table,
// and creating a suffix link to the new node from the last one visited.
/// </summary>
/// <param name="parentNode">This is a member of active. It is kept separate for clarity.</param>
private void extendSuffixByRuleTwo(
ref GstSuffix active, GstNode parentNode, ref GstNode prevParentNode, int endIndex, int wordNum)
{
GstEdge newEdge = new GstEdge(this, parentNode, wordNum, endIndex, GetWord(wordNum).Length - 1);
newEdge.Add();
GstUtil.WriteLine(GstVerbosityLevel.Verbose, String.Format(
" Rule #2: New edge E{0:d} (\"{1:s}\") connects N{2:d} (old parent) to N{3:d} (new child)",
newEdge.Id,
newEdge.GetText(),
newEdge.ParentNode.Id,
newEdge.ChildNode.Id
));
setSuffixLink(prevParentNode, parentNode);
prevParentNode = parentNode;
}
public GstNode Split(GstSuffix s)
{
// Create new edge
int wordNum = s.WordNum;
GstEdge newEdge;
if (this.HasWordNum(s.WordNum))
{
newEdge = new GstEdge(tree, s.OriginNode, wordNum, GetBeginIndex(wordNum), GetBeginIndex(wordNum) + s.Span);
}
else
{
newEdge = new GstEdge(tree, s.OriginNode, wordNum, s.BeginIndex, s.EndIndex);
}
foreach (int n in beginIndexes.Keys)
{
newEdge.SetBeginIndex(n, beginIndexes[n]);
}
foreach (int n in endIndexes.Keys)
{
newEdge.SetEndIndex(n, beginIndexes[n] + s.Span);
}
newEdge.ChildNode.SuffixNode = s.OriginNode;
char oldFirstChar = GetFirstChar();
// Modify old edge
int [] wordNums = beginIndexes.Keys.ToArray();
foreach (int n in wordNums)
{
IncBeginIndex(n, s.Span + 1);
}
// Perform switch
MoveFromTo(ParentNode, oldFirstChar, newEdge.ChildNode, GetFirstChar());
ParentNode = newEdge.ChildNode;
newEdge.Add();
GstUtil.WriteLine(GstVerbosityLevel.Normal, String.Format(
" Split E{0:d} into E{1:d} + E{0:d} = \"{2:s}\" + \"{3:s}\"",
Id, newEdge.Id,
newEdge.GetText(),
this.GetText()
));
return(newEdge.ChildNode);
}
public IEnumerable <GstEdge> Edges()
{
Stack <GstEdge> edges = new Stack <GstEdge>();
foreach (GstEdge edge in root.ChildEdges())
{
edges.Push(edge);
}
while (edges.Count > 0)
{
GstEdge edge = edges.Pop();
foreach (GstEdge childEdge in edge.ChildNode.ChildEdges())
{
edges.Push(childEdge);
}
yield return(edge);
}
yield break;
}
/// <remarks>
/// Constraint: Implicit suffixes must have BeginIndex < words[wordNum].Length
/// </remarks>
public void Canonicalize()
{
if (IsImplicit)
{
bool haveValuesChanged = false;
StringBuilder sb = new StringBuilder();
sb.AppendLine(" Canonicalize: Entering");
// sb.AppendLine(tree.ToString());
int origNodeId, begin, end;
origNodeId = this.OriginNode.Id;
begin = this.beginIndex;
end = this.endIndex;
GstEdge edge = OriginNode.GetChildEdge(tree.GetWordChar(WordNum, BeginIndex));
while (edge.Span() <= Span)
{
sb.Append(String.Format(
" Canonicalize: Active suffix changed from {0:s}",
ToSuffixString(origNodeId, begin, end)));
this.beginIndex += edge.Span() + 1;
this.OriginNode = edge.ChildNode;
haveValuesChanged = true;
sb.AppendLine(String.Format(" to {0:s}",
ToSuffixString(OriginNode.Id, beginIndex, endIndex)));
if (Span >= 0)
{
edge = edge.ChildNode.GetChildEdge(tree.GetWordChar(0, BeginIndex));
}
}
sb.AppendLine(" Canonicalize: Exiting");
if (haveValuesChanged)
{
GstUtil.Write(GstVerbosityLevel.Verbose, sb.ToString());
}
}
}
public DepthTaggedGstEdge(GstEdge e, int d)
{
Edge = e;
Depth = d;
}
private static bool validateSuffixStrings(
GSuffixTree tree,
out List <int> failedLeafNodeIds)
{
var edgeStringDicts = new Stack <EdgeStringDict>();
// Step 1: Populate edgeStrings with data from child edges of the root node.
// Track any leaves that are immediate children of the root node.
var leafEdgeStringDicts = new List <EdgeStringDict>();
foreach (GstEdge edge in tree.Root.ChildEdges())
{
var edgeStringDict = new EdgeStringDict(edge, new Dictionary <int, string>());
foreach (int wordNum in edge.WordNums())
{
edgeStringDict.Item2[wordNum] = edge.GetText();
edgeStringDicts.Push(edgeStringDict);
}
if (!edge.ChildNode.HasChildEdges())
{
Console.WriteLine(String.Format(
"SuffixTreeTest: Found a leaf edge adjacent to the root: E{0:d}",
edge.Id));
leafEdgeStringDicts.Add(edgeStringDict);
}
}
// Step 2: Walk the tree, adding the remaining edges. Keep track of leaf edges.
// Also keep a running record of accumulated text for each edge.
while (edgeStringDicts.Count > 0)
{
EdgeStringDict edgeStringDict = edgeStringDicts.Pop();
foreach (GstEdge childEdge in edgeStringDict.Item1.ChildNode.ChildEdges())
{
EdgeStringDict newEdgeStringDict = new EdgeStringDict(childEdge, new Dictionary <int, string>());
foreach (int wordNum in childEdge.WordNums())
{
newEdgeStringDict.Item2[wordNum] = edgeStringDict.Item2[wordNum] + childEdge.GetText();
}
edgeStringDicts.Push(newEdgeStringDict);
if (!childEdge.ChildNode.HasChildEdges())
{
Console.WriteLine(String.Format(
"SuffixTreeTest: Found a leaf not adjacent to the root: E{0:s}",
newEdgeStringDict.Item1.Id));
leafEdgeStringDicts.Add(newEdgeStringDict);
}
}
}
// Step 3: Inspect the leaf edge content (i.e., strings). Keep track of failed leaf nodes
failedLeafNodeIds = new List <int>();
foreach (var leafEdgeStringDict in leafEdgeStringDicts)
{
// Accumulated string should equal the corresponding substring of tree.Text.
GstEdge edge = leafEdgeStringDict.Item1;
foreach (int wordNum in leafEdgeStringDict.Item2.Keys)
{
int len = leafEdgeStringDict.Item2[wordNum].Length;
string pathStr = leafEdgeStringDict.Item2[wordNum];
string textStr = tree.GetRangeString(wordNum,
tree.GetWord(wordNum).Length - len, tree.GetWord(wordNum).Length - 1);
string formatSpec2 = "{2" /* + "," + tree.GetWord(0).Length.ToString() */ + ":s}";
string formatSpec3 = "{3" /* + "," + tree.GetWord(0).Length.ToString() */ + ":s}";
string formatStr = "SuffixTreeTest: Leaf edge #{0:d}, word#{1:d}. "
+ String.Format("Comparing \"{0:s}\" with \"{1:s}\"", formatSpec2, formatSpec3);
Console.WriteLine(formatStr, edge.Id, wordNum, pathStr, textStr);
if (pathStr != textStr)
{
failedLeafNodeIds.Add(leafEdgeStringDict.Item1.ChildNode.Id);
break;
}
}
}
return(failedLeafNodeIds.Count() == 0);
}
public void AddChildEdge(char c, GstEdge edge)
{
childEdges.Add(c, edge);
}
