public static void AlignSequences(ref Alignment alignmentObject, SubstitutionMatrix.SubstitutionMatrixSeries subMatrix, ref double[,] similarityMatrix, ReadOnlyCollection <Tree.GuideTree <AlignedMacromolecule> .TreeLeaf> leavesList, ReadOnlyCollection <Tuple <ReadOnlyCollection <AlignedMacromolecule>, ReadOnlyCollection <AlignedMacromolecule>, double> > steps)
{
IMultipleAlignmentAlgorithm alignmentAlgorithm = new MyersMillerProfileAlign();
int numSteps = steps.Count();
// Here, Clustal checks the similarity matrix and looks up the most closely-related sequence
// for each sequence.
// But it could have used the distance matrix and found the minimum distance. Consider switching to avoid unnecessary calculations
foreach (Tuple <ReadOnlyCollection <AlignedMacromolecule>, ReadOnlyCollection <AlignedMacromolecule>, double> step in steps)
{
// Here, Clustal would check to make sure that at least one pair of sequences isn't too divergent.
// It also records which ones are too divergent so that the alignment doesn't use them.
double score = alignmentAlgorithm.Align(ref alignmentObject, subMatrix, step);
}
}
char[] residueCodes = Routines.nucleotideCodesPlusGaps; // should be one with gaps, need to do programatically
public double Align(ref Alignment alignmentObject, SubstitutionMatrix.SubstitutionMatrixSeries subMatrixClass, Tuple <ReadOnlyCollection <AlignedMacromolecule>, ReadOnlyCollection <AlignedMacromolecule>, double> step)
{
bool switchGroups;
ReadOnlyCollection <AlignedMacromolecule> group1;
ReadOnlyCollection <AlignedMacromolecule> group2;
double meanSimilarity = step.Item3;
int numSeqs1 = step.Item1.Count();
int numSeqs2 = step.Item2.Count();
int numSeqs = alignmentObject.NumberMacromolecules;
if (numSeqs1 == 0 || numSeqs2 == 0)
// If one of the groups has no alignable sequences, can't do anything!
{
return(0);
}
// Make the group with the most sequences group 1
// Figure out the structure penalties here
if (switchGroups = numSeqs2 > numSeqs1)
{
group1 = step.Item2;
group2 = step.Item1;
}
else
{
group1 = step.Item1;
group2 = step.Item2;
}
// Make the first group
int group1MaxLength = 0;
foreach (AlignedMacromolecule macromolecule in group1)
{
group1MaxLength = Math.Max(group1MaxLength, macromolecule.AlignedPositions.Last() + 1);
}
// Make the second group
int group2MaxLength = 0;
foreach (AlignedMacromolecule macromolecule in group2)
{
group2MaxLength = Math.Max(group2MaxLength, macromolecule.AlignedPositions.Last() + 1);
}
maxLength = group1MaxLength + group2MaxLength + 2; // Clustal sets the Alignment parameter here.
displ = new int[maxLength + 1];
alnPath1 = new int[maxLength + 1];
alnPath2 = new int[maxLength + 1];
// Calculate the real length of profiles, removing gaps:
int group1NoGapsLength = 0;
foreach (AlignedMacromolecule macromolecule in group1)
{
group1NoGapsLength += macromolecule.Sequence.Length;
}
group1NoGapsLength = (int)(group1NoGapsLength / (double)numSeqs1);
int group2NoGapsLength = 0;
foreach (AlignedMacromolecule macromolecule in group2)
{
group2NoGapsLength += macromolecule.Sequence.Length;
}
group2NoGapsLength = (int)(group2NoGapsLength / (double)numSeqs2);
int minNoGapsLength = Math.Min(group1NoGapsLength, group2NoGapsLength);
int maxNoGapsLength = Math.Max(group1NoGapsLength, group2NoGapsLength);
// I'm just going to reproduce the Clustal code directly. May recode later once I fully understand what it does.
// There is quite literally no point to the scaleVals.scale value, and no point to setting this here.
// Tuple<double, double> scaleVals = Tuple.Create(1.0, 100.0); // scaleVals.scale and scaleVals.intScale, respectively.
double gapOpeningCoefficient, gapExtensionCoefficient;
double gapOpenPenalty = 10.0; // Will be user selectable parameter
double gapExtendPenalty = 0.2; // Will be user selectable parameter
//Will be user option
bool useNegative = false;
SubstitutionMatrix.SubstitutionMatrix subMatrix = subMatrixClass.GetMatrix(meanSimilarity, minNoGapsLength, useNegative);
double gapPenaltyScaleFactor = subMatrixClass.GetScaleFactor(meanSimilarity, useNegative);
// Then it sets DNA vs. Protein parameters
if (alignmentObject.IsNucleicAcid)
{
gapOpeningCoefficient = 100.0 * gapOpenPenalty * gapPenaltyScaleFactor;
gapExtensionCoefficient = 100.0 * gapExtendPenalty * gapPenaltyScaleFactor;
}
else
{
gapOpeningCoefficient = CalculateProteinGapOpeningCoefficient(gapOpenPenalty, group1NoGapsLength, group2NoGapsLength, subMatrix.AverageScore, gapPenaltyScaleFactor);
gapExtensionCoefficient = 100.0 * gapExtendPenalty;
}
// We need one profile with substitution matrix information and one without!
// But this will change when we have the LE scoring function. (Whatever that is.)
// Calculate the profile arrays. The first group, but not the second, incorporates substitution information.
group1Profile = Profile.Calculate(group1, group1MaxLength, gapOpeningCoefficient, gapExtensionCoefficient, subMatrix);
group2Profile = Profile.Calculate(group2, group2MaxLength, gapOpeningCoefficient, gapExtensionCoefficient, null); //new SubstitutionMatrix());
// User Myers and Miller to align the two sequences
double score = ProgDiff(0, 0, group1MaxLength, group2MaxLength, group1Profile.GapOpeningPenalties[0], group1Profile.GapExtensionPenalties[0]);
alignmentLength = ProgTracepath();
addGGaps();
group1MaxLength = alignmentLength;
if (true) // Clustal: DoRemoveFirstIteration() == TREE ???
{
// Combine the sequences and submit for iterations
}
return(0);
}
