/// <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;
}
}
private void incrSuffix(ref GstSuffix active, int wordNum)
{
int origNodeId, begin, end;
origNodeId = active.OriginNode.Id;
begin = active.BeginIndex;
end = active.EndIndex;
if (active.OriginNode.IsRoot())
{
active.BeginIndex++;
}
else
{
active.OriginNode = active.OriginNode.SuffixNode;
}
active.Canonicalize();
if (origNodeId != active.OriginNode.Id ||
begin != active.BeginIndex ||
end != active.EndIndex)
{
GstUtil.WriteLine(GstVerbosityLevel.Verbose, String.Format(
" incrSuffix: Active suffix changed from {0:s} to {1:s}",
GstSuffix.ToSuffixString(origNodeId, begin, end),
GstSuffix.ToSuffixString(active.OriginNode.Id, active.BeginIndex, active.EndIndex)));
}
}
private void setSuffixLink(GstNode node, GstNode suffixNode)
{
if ((node != null) && (node != root))
{
if (node.SuffixNode == null)
{
GstUtil.WriteLine(GstVerbosityLevel.Verbose, String.Format(
" New suffix link from N{0:d} to N{1:d}",
node.Id, suffixNode.Id));
}
else
{
if (node.SuffixNode.Id == suffixNode.Id)
{
GstUtil.WriteLine(GstVerbosityLevel.Verbose, String.Format(
" Suffix link (N{0:d} to N{1:d}) retaining same value",
node.Id, node.SuffixNode.Id));
}
else
{
GstUtil.WriteLine(GstVerbosityLevel.Verbose, String.Format(
" Suffix link (N{0:d} to N{1:d}) set to new value (N{0:d} to N{2:d})",
node.Id, node.SuffixNode.Id, suffixNode.Id));
}
}
node.SuffixNode = suffixNode;
}
}
/// <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);
}
private bool AddWord(string word, bool doConsoleVerbose = false)
{
if (word == null || word.Length == 0)
{
return(false);
}
GstUtil.WriteLine(GstVerbosityLevel.Verbose, new String('-', 40));
int wordNum = wordCount++;
wordDict[wordNum] = word;
GstUtil.WriteLine(GstVerbosityLevel.Verbose, String.Format(
"Adding word #{0:d} (\"{1:s}\") to the suffix tree",
wordNum, wordDict[wordNum]));
GstSuffix active = new GstSuffix(this, root, wordNum, 0, GSuffixTree.InfiniteIndex);
GstUtil.WriteLine(GstVerbosityLevel.Verbose, String.Format(
"Created active (longest proper) suffix pointer: {0:s}",
active.ToString()));
int endIndex = 0;
if (wordNum > 0)
{
skipDuplicateInitialSubstring(ref active, ref endIndex, wordNum);
if (endIndex > 0)
{
GstUtil.WriteLine(GstVerbosityLevel.Verbose, String.Format(
"The first {0:d} letter(s) of word #{1:d} are already in the suffix tree",
endIndex, wordNum));
}
}
for ( ; endIndex < wordDict[wordNum].Length; endIndex++)
{
GstUtil.WriteLine(GstVerbosityLevel.Verbose, this.ToString());
GstUtil.WriteLine(GstVerbosityLevel.Verbose, String.Format(
"Calling extendSuffixes() for word #{0:d}, with endIndex = {1:d} ('{2:c}') and active suffix = {3:s}",
wordNum, endIndex, GetWordChar(wordNum, endIndex), active.ToString()));
extendSuffixes(ref active, endIndex, wordNum);
}
if (doConsoleVerbose)
{
string logStr = String.Format("Done adding word #{0:d} (\"{1:s}\") to the suffix tree",
wordNum, wordDict[wordNum]);
GstUtil.WriteLine(GstVerbosityLevel.Verbose, logStr);
Console.WriteLine(logStr);
Console.WriteLine(this.ToString());
}
return(true);
}
/// <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);
}
/// <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 GSuffixTree(IEnumerable <string> words, bool doConsoleVerbose = false)
{
if (words == null || words.Count() == 0)
{
throw new ArgumentException("Error: A new GSuffixTree must be constructed with at least one word");
}
this.wordDict = new Dictionary <int, string>();
this.root = new GstNode(this, null);
foreach (string word in words.Where(w => w.Length > 0))
{
if (AddWord(word, doConsoleVerbose))
{
GstUtil.WriteLine(GstVerbosityLevel.Verbose, String.Format(
"Added word (\"{0:s}\") to suffix tree", word));
}
else
{
GstUtil.WriteLine(GstVerbosityLevel.Quiet, String.Format(
"Error: Failed to add word (\"{0:s}\") to suffix tree", word));
}
}
// GstUtil.Write(GstVerbosityLevel.Normal, this.ToString());
}
public static void WriteLine(GstVerbosityLevel v, string message)
{
GstUtil.Write(v, message + Environment.NewLine);
}
// For debugging. Currently unused
public static void Exiting()
{
TraceDepth--;
Console.WriteLine(Indentation + String.Format("Exiting {0:s}....", GstUtil.GetCurrentMethodName(2)));
}
// For debugging. Currently unused
public static void Entering()
{
Console.WriteLine(Indentation + String.Format("Entering {0:s}....", GstUtil.GetCurrentMethodName(2)));
TraceDepth++;
}
