/// <summary>
/// Find the next match of the pattern.
/// </summary>
/// <param name="element">A gap followed by a pattern.</param>
/// <param name="seq">Sequence where the pattern is searched in.</param>
/// <param name="position">Current start position within the sequence.</param>
/// <returns>Returns a match object or null if there is no match with the
/// given similarity or higer. </returns>
private Match NextMatch
(ProfileElement element, Sequence seq, int position)
{
Match match;
int pos;
IPattern pattern = element.Pattern;
while (element.CurrGap <= element.MaxGap)
{
pos = position + element.CurrGap;
match = pattern.Match(seq, pos);
element.CurrGap += pattern.Increment;
if (match != null)
return (match);
}
return (null);
}
/// <summary>
/// Find the match with the highest score for a gap followed by a pattern.
/// </summary>
/// <param name="element">A gap followed by a pattern.</param>
/// <param name="seq">Sequence where the pattern is searched in.</param>
/// <param name="position">Current start position within the sequence.</param>
/// <returns>
/// Returns a match object or null if there is no match with the
/// given similarity or higher.
/// </returns>
private Match MaxMatch
(ProfileElement element, Sequence seq, int position)
{
Match match;
int start = position + element.MinGap;
int end = position + element.MaxGap;
IPattern pattern = element.Pattern;
maxMatch.Set(null, 0, 0, 0, -Double.MaxValue);
for (int pos = start; pos <= end; pos++)
{
do
{
match = pattern.Match(seq, pos);
if (match != null && match.Similarity > maxMatch.Similarity)
maxMatch.Set(match);
} while (pattern.Increment == 0);
}
return (maxMatch.Similarity < Threshold ? null : maxMatch);
}
/// <summary>
/// Getter for the index of the given profile element.
/// </summary>
/// <param name="element">Profile element.</param>
/// <returns>
/// Index of the given profile element within the profile or -1 if
/// the profile element is not part of the profile.
/// </returns>
public int IndexOf(ProfileElement element)
{
return (patternList.IndexOf(element));
}
/// <summary>
/// Adds a pattern preceeded by a gap of variable length to the profile.
/// </summary>
/// <param name="elementIndex">
/// Index to a preceding profile element. If the index
/// smaller than zero it is assumed that there is no preceding profile element.
/// In this case minGap and maxGap must be zero!
/// Please note that the same pattern can not be added twice except it it
/// a copy (with its own internal match object).
/// </param>
/// <param name="alignment">
/// Alignment the gap is based on, e.g. END, START of the
/// the preceding profile element or NONE if there is no preceding profile element
/// or no gap.
/// </param>
/// <param name="minGap"> The min length</param>
/// <param name="maxGap">
/// Maximum gap length. Must be greater than or equal to the
/// minimum gap length.
/// </param>
/// <param name="pattern">Any object which implements the pattern interface.</param>
/// <returns>Returns a reference to the added {ProfileElement}.</returns>
public ProfileElement Add
(int elementIndex, int alignment, int minGap, int maxGap, IPattern pattern)
{
if (IndexOf(pattern) >= 0)
throw new ArgumentException
("The same pattern can not be added twice to a profile!");
ProfileElement element = new ProfileElement
(this[elementIndex], alignment, minGap, maxGap, pattern);
patternList.Add(element);
Matched.Add(pattern.Matched);
return (element);
}
/// <summary>
///
/// Adds a pattern preceeded by a gap of variable length to the profile.
/// </summary>
/// <param name="refElement">
/// refElement Reference to the preceding profile element. Null if there
/// is none. If there is gap then there must be a preceding profile element
/// defined!
/// </param>
/// <param name="alignment">Alignment the gap is based on, e.g. END, START of the
/// the preceding profile element or NONE if there is no preceding profile
/// element or no gap.</param>
/// <param name="minGap">Minimum gap length.</param>
/// <param name="maxGap">Maximum gap length. Must be greater than or equal to the
/// minimum gap length.</param>
/// <param name="pattern">Any object which implements the pattern interface.</param>
/// <returns></returns>
public ProfileElement Add
(ProfileElement refElement, int alignment, int minGap, int maxGap, IPattern pattern)
{
ProfileElement element = new ProfileElement
(refElement, alignment, minGap, maxGap, pattern);
patternList.Add(element);
Matched.Add(pattern.Matched);
return (element);
}
/// <summary>
/// Creates a profile element. A profile element is a pattern with a
/// preceding gap to another profile element.
/// </summary>
/// <param name="refElement">Reference to the preceding profile element. Null if there
/// is none. If there is gap then there must be a preceding profile element
/// defined!
/// </param>
/// <param name="alignment">
/// Alignment the gap is based on, e.g. END, START of the
/// the preceding profile element or NONE if there is no preceding profile element
/// or no gap.
/// </param>
/// <param name="minGap">Minimum gap length.</param>
/// <param name="maxGap">Maximum gap length. Must be greater than or equal to the
/// minimum gap length.</param>
/// <param name="pattern">A pattern.</param>
public ProfileElement
(ProfileElement refElement, int alignment, int minGap, int maxGap, IPattern pattern)
{
if (minGap > maxGap)
throw new ArgumentException
("Minimum gap length is greater than maximum gap length.");
else
if ((refElement == null || alignment == NONE)
&& (minGap != 0 || maxGap != 0))
throw new ArgumentException
("Missing reference or alignment to proceding pattern in gap definition.");
this.RefElement = refElement;
this.Alignment = alignment;
this.MinGap = minGap;
this.CurrGap = minGap;
this.MaxGap = maxGap;
this.Pattern = pattern;
}