/// <summary>
/// The implementation ensures that
/// a match fails for a given position if there is no match. Otherwise the
/// matcher might return a match at a different position.
/// <see cref="QUT.Bio.BioPatML.Patterns.IPattern">IPattern Match(Sequence, int) method</see>
/// </summary>
/// <param name="sequence"> The sequence for comparing</param>
/// <param name="position"> Matching position</param>
/// <returns></returns>
public override Match Match(BioPatML.Sequences.Sequence sequence, int position)
{
while (Index < base.Count)
{
IPattern pattern = this[Index++];
Match match = pattern.Match(sequence, position);
// store minimum increment
int inc = pattern.Increment;
if (inc < Min_inc)
Min_inc = inc;
if (match != null && (match.Similarity >= Threshold))
{
increment = 0;
return match;
}
}
Index = 0;
increment = Min_inc;
Min_inc = int.MaxValue;
return null;
}
/// <summary>
/// The implementation ensures that
/// a match fails for a given position if there is no match. Otherwise the
/// matcher might return a match at a different position.
/// <see cref="QUT.Bio.BioPatML.Patterns.IPattern">IPattern Match(Sequence, int) method</see>
/// </summary>
/// <param name="sequence"> The sequence for comparing</param>
/// <param name="position"> Matching position</param>
/// <returns></returns>
public override Match Match(BioPatML.Sequences.Sequence sequence, int position)
{
Match match = Matched;
Match bestMatch = match.Clone();
Match nextMatch = null;
int patternNumber = Patterns.Count;
int index = 0;
bestMatch.Similarity = -1.0;
while (index >= 0)
{
IPattern pattern = this[index];
position = index > 0 ? match.GetSubMatch(index - 1).End + 1 : position;
nextMatch = pattern.Match(sequence, position);
if (nextMatch == null)
{
while (--index >= 0 && this[index].Increment != 0) ;
continue;
}
pattern.Matched.Set(nextMatch);
index++;
if (index == patternNumber)
{
while (--index >= 0 && this[index].Increment != 0) ;
match.CalcSimilarity();
if (match.Similarity >= Threshold
&& match.Similarity > bestMatch.Similarity)
bestMatch.Set(match);
}
}
if (bestMatch.Similarity < 0)
return (null);
match.Set(bestMatch);
match.CalcStartEnd();
match.Strand = sequence.Strand;
match.SetSequence(sequence);
return (match);
}
/// <summary>
/// The implementation ensures that
/// a match fails for a given position if there is no match. Otherwise the
/// matcher might return a match at a different position.
/// <see cref="QUT.Bio.BioPatML.Patterns.IPattern">IPattern Match(Sequence, int) method</see>
/// </summary>
/// <param name="sequence"> the sequence for matching</param>
/// <param name="position"> position used for matching</param>
/// <returns>The matched</returns>
public override Match Match(BioPatML.Sequences.Sequence sequence, int position)
{
Match match = Matched;
Match nextMatch = null;
int patternNumber = Patterns.Count;
while (Index >= 0)
{
IPattern pattern = this[Index];
position = Index > 0 ? match.GetSubMatch(Index - 1).End + 1 : position;
nextMatch = pattern.Match(sequence, position);
if (nextMatch == null)
{
while (--Index >= 0 && this[Index].Increment > 0) ;
continue;
}
pattern.Matched.Set(nextMatch);
Index++;
if (Index == patternNumber)
{
while (--Index >= 0 && this[Index].Increment > 0) ;
increment = 0;
match.CalcSimilarity();
if (match.Similarity < Threshold)
return null;
match.CalcStartEnd();
match.Strand = sequence.Strand;
match.SetSequence(sequence);
return (match);
}
}
increment = base.Increment;
Index = 0;
return (null);
}
/// <summary>
/// Implementation of the pattern interface. A match is successful if
/// every pattern of the profile matches successfully and the mean
/// similarity is higher or equal than the profile similarity threshold.
/// This matching method trys to match all possibilities which are
/// allowed be the profile patterns and the gaps in between.
/// <see cref="QUT.Bio.BioPatML.Patterns.IMatcher">IMatcher Match Method</see>
/// </summary>
/// <param name="sequence"></param>
/// <param name="position"></param>
/// <returns></returns>
public override Match Match(BioPatML.Sequences.Sequence sequence, int position)
{
Match match = Matched;
Match nextMatch = null;
int patternNumber = Count; //patternList.Count;
increment = 0;
while (Index >= 0)
{
ProfileElement element = this[Index];
position = Index > 0 ? element.GapStart : position;
nextMatch = NextMatch(element, sequence, position);
if (nextMatch == null)
{
element.ResetGap();
Index--;
continue;
}
element.Pattern.Matched.Set(nextMatch);
Index++;
if (Index >= patternNumber)
{
Index = patternNumber - 1;
match.CalcSimilarity();
if (match.Similarity < Threshold)
return (null);
match.CalcStartEnd();
match.Strand = sequence.Strand;
match.SetSequence(sequence);
return (match);
}
}
increment = base.Increment;
Index = 0;
return (null);
}
/// <summary>
/// Implementation of the pattern interface. A match is successful if
/// every pattern of the profile matches successfully and the mean
/// similarity is higher or equal than the profile similarity threshold
/// <see cref="QUT.Bio.BioPatML.Patterns.IMatcher">IMatcher Match Method</see>
/// </summary>
/// <param name="sequence"></param>
/// <param name="position"></param>
/// <returns></returns>
public override Match Match(BioPatML.Sequences.Sequence sequence, int position)
{
Match match = Matched;
Match maxMatch = null;
int patternNumber = patternList.Count;
for (int index = 0; index < patternNumber; index++)
{
ProfileElement element = this[index];
position = index > 0 ? element.GapStart : position;
maxMatch = MaxMatch(element, sequence, position);
if (maxMatch == null)
return (null);
element.Pattern.Matched.Set(maxMatch);
}
match.CalcSimilarity();
if (match.Similarity < Threshold)
return (null);
match.CalcStartEnd();
match.Strand = sequence.Strand;
match.SetSequence(sequence);
return (match);
}
