/// <summary>
/// Generate IProfileAlignment from a set of aligned sequences
/// </summary>
/// <param name="sequences">aligned sequences</param>
public static IProfileAlignment GenerateProfileAlignment(ICollection <ISequence> sequences)
{
IProfiles profileMatrix = Profiles.GenerateProfiles(sequences);
IProfileAlignment profileAlignment = new ProfileAlignment();
profileAlignment.NumberOfSequences = sequences.Count;
profileAlignment.ProfilesMatrix = profileMatrix;
return(profileAlignment);
}
/// <summary>
/// Generate a profileAlignment from one single sequence
/// The set of sequence items of the seq should be the same as
/// 'static ItemSet' of the IProfiles.
/// </summary>
/// <param name="seq">an input sequence</param>
/// <param name="weight">sequence weight</param>
public static IProfileAlignment GenerateProfileAlignment(ISequence seq, float weight)
{
IProfiles profileMatrix = Profiles.GenerateProfiles(seq, weight);
IProfileAlignment profileAlignment = new ProfileAlignment();
profileAlignment.NumberOfSequences = 1;
profileAlignment.ProfilesMatrix = profileMatrix;
return(profileAlignment);
}
/// <summary>
/// Combine two profileAlignments into one if they are aligned already
/// </summary>
/// <param name="profileAlignmentA">first profile alignment</param>
/// <param name="profileAlignmentB">second profile alignment</param>
public static IProfileAlignment GenerateProfileAlignment(IProfileAlignment profileAlignmentA, IProfileAlignment profileAlignmentB)
{
IProfiles profileMatrix = Profiles.GenerateProfiles(
profileAlignmentA.ProfilesMatrix, profileAlignmentB.ProfilesMatrix,
profileAlignmentA.NumberOfSequences, profileAlignmentB.NumberOfSequences);
IProfileAlignment profileAlignment = new ProfileAlignment();
profileAlignment.NumberOfSequences = profileAlignmentA.NumberOfSequences + profileAlignmentB.NumberOfSequences;
profileAlignment.ProfilesMatrix = profileMatrix;
return(profileAlignment);
}
/// <summary>
/// The profiles of two subsets is extracted from the current multiple alignment.
/// Columns containing no residues, i.e. indels only, are discarded.
///
/// This method is used in alignment refinement, when the guide tree is cut into two,
/// the sequences (leaf nodes) are separated into two subsets. This method generates
/// two profileAlignments for the two subtrees by extracting profiles of the two subsets
/// of sequences.
/// </summary>
/// <param name="alignedSequences">a set of aligned sequences</param>
/// <param name="sequenceIndicesA">the subset sequence indices of subtree A</param>
/// <param name="sequenceIndicesB">the subset sequence indices of subtree B</param>
/// <param name="allIndelPositions">the list of all-indel positions that have been removed when constructing</param>
public static IProfileAlignment[] ProfileExtraction(List <ISequence> alignedSequences,
List <int> sequenceIndicesA, List <int> sequenceIndicesB,
out List <int>[] allIndelPositions)
{
allIndelPositions = new List <int> [2];
IProfiles profileA = Profiles.GenerateProfiles(alignedSequences, sequenceIndicesA, out allIndelPositions[0]);
IProfiles profileB = Profiles.GenerateProfiles(alignedSequences, sequenceIndicesB, out allIndelPositions[1]);
IProfileAlignment profileAlignmentA = new ProfileAlignment();
IProfileAlignment profileAlignmentB = new ProfileAlignment();
profileAlignmentA.ProfilesMatrix = profileA;
profileAlignmentB.ProfilesMatrix = profileB;
profileAlignmentA.NumberOfSequences = sequenceIndicesA.Count;
profileAlignmentB.NumberOfSequences = sequenceIndicesB.Count;
return(new IProfileAlignment[2] {
profileAlignmentA, profileAlignmentB
});
}
/// <summary>
/// Combine two profileAlignments with alignment operation array from dynamic programming.
/// The dynamic programming algorithm returns two arrays containing the alignment operations
/// on the two profiles. This method applies the operation information in the two arrays to
/// the two original profiles, and combine them into a new aligned profile, and put into the
/// newly generated profileAlignment.
/// </summary>
/// <param name="profileAlignmentA">first profile alignment</param>
/// <param name="profileAlignmentB">second profile alignment</param>
/// <param name="aAligned">aligned interger array generated by dynamic programming</param>
/// <param name="bAligned">aligned interger array generated by dynamic programming</param>
/// <param name="gapCode">the gap integer code defined in dynamic programming class</param>
public static IProfileAlignment GenerateProfileAlignment(
IProfileAlignment profileAlignmentA,
IProfileAlignment profileAlignmentB,
int[] aAligned,
int[] bAligned,
int gapCode)
{
IProfiles profileMatrix = Profiles.GenerateProfiles(
profileAlignmentA.ProfilesMatrix, profileAlignmentB.ProfilesMatrix,
profileAlignmentA.NumberOfSequences, profileAlignmentB.NumberOfSequences,
aAligned, bAligned, gapCode);
IProfileAlignment profileAlignment = new ProfileAlignment();
profileAlignment.NumberOfSequences = profileAlignmentA.NumberOfSequences +
profileAlignmentB.NumberOfSequences;
profileAlignment.ProfilesMatrix = profileMatrix;
return(profileAlignment);
}