/// <summary> Returns the alignment of two sequences based on the passed array of pointers</summary> /// <param name="s1">sequence #1 </param> /// <param name="s2">sequence #2 </param> /// <param name="m">scoring matrix </param> /// <param name="cell">The cell where the traceback starts. </param> /// <returns> <see cref="Alignment"/> with the two aligned sequences and alignment score. </returns> /// <seealso cref="Cell"/> /// <seealso cref="Alignment"/> private Alignment Traceback(Sequence s1, Sequence s2, Matrix m, byte[] pointers, Cell cell, short[] sizesOfVerticalGaps, short[] sizesOfHorizontalGaps) { char[] a1 = s1.ToArray(); char[] a2 = s2.ToArray(); float[,] scores = m.Scores; int n = s2.Length + 1; Alignment alignment = new Alignment(); alignment.Score = cell.Score; int maxlen = s1.Length + s2.Length; // maximum length after the // aligned sequences char[] reversed1 = new char[maxlen]; // reversed sequence #1 char[] reversed2 = new char[maxlen]; // reversed sequence #2 char[] reversed3 = new char[maxlen]; // reversed markup int len1 = 0; // length of sequence #1 after alignment int len2 = 0; // length of sequence #2 after alignment int len3 = 0; // length of the markup line int identity = 0; // count of identitcal pairs int similarity = 0; // count of similar pairs int gaps = 0; // count of gaps char c1, c2; int i = cell.Row; // traceback start row int j = cell.Column; // traceback start col int k = i * n; bool stillGoing = true; // traceback flag: true -> continue & false // -> stop while (stillGoing) { switch (pointers[k + j]) { case Directions.UP: for (int l = 0, len = sizesOfVerticalGaps[k + j]; l < len; l++) { reversed1[len1++] = a1[--i]; reversed2[len2++] = Alignment.GAP; reversed3[len3++] = Markups.GAP; k -= n; gaps++; } break; case Directions.DIAGONAL: c1 = a1[--i]; c2 = a2[--j]; k -= n; reversed1[len1++] = c1; reversed2[len2++] = c2; if (c1 == c2) { reversed3[len3++] = Markups.IDENTITY; identity++; similarity++; } else if (scores[c1,c2] > 0) { reversed3[len3++] = Markups.SIMILARITY; similarity++; } else { reversed3[len3++] = Markups.MISMATCH; } break; case Directions.LEFT: for (int l = 0, len = sizesOfHorizontalGaps[k + j]; l < len; l++) { reversed1[len1++] = Alignment.GAP; reversed2[len2++] = a2[--j]; reversed3[len3++] = Markups.GAP; gaps++; } break; case Directions.STOP: stillGoing = false; break; } } alignment.Sequence1 = Reverse(reversed1, len1); alignment.Start1 = i; alignment.Sequence2 = Reverse(reversed2, len2); alignment.Start2 = j; alignment.MarkupLine = Reverse(reversed3, len3); alignment.Identity = identity; alignment.Gaps = gaps; alignment.Similarity = similarity; return alignment; }
/// <summary> Constructs directions matrix for the traceback </summary> /// <param name="s1">sequence #1 </param> /// <param name="s2">sequence #2 </param> /// <param name="matrix">scoring matrix </param> /// <param name="o">open gap penalty </param> /// <param name="e">extend gap penalty </param> /// <returns> The cell where the traceback starts. </returns> private Cell Construct(Sequence s1, Sequence s2, float[,] matrix, float o, float e, byte[] pointers, short[] sizesOfVerticalGaps, short[] sizesOfHorizontalGaps) { char[] a1 = s1.ToArray(); char[] a2 = s2.ToArray(); int m = s1.Length + 1; int n = s2.Length + 1; float f; // score of alignment x1...xi to y1...yi if xi aligns to yi float[] g = new float[n]; // score if xi aligns to a gap after yi float h; // score if yi aligns to a gap after xi float[] v = new float[n]; // best score of alignment x1...xi to y1...yi float vDiagonal; g[0] = float.NegativeInfinity; h = float.NegativeInfinity; v[0] = 0; for (int j = 1; j < n; j++) { g[j] = float.NegativeInfinity; v[j] = 0; } float similarityScore, g1, g2, h1, h2; Cell cell = new Cell(); for (int i = 1, k = n; i < m; i++, k += n) { h = float.NegativeInfinity; vDiagonal = v[0]; for (int j = 1, l = k + 1; j < n; j++, l++) { similarityScore = matrix[a1[i - 1], a2[j - 1]]; // Fill the matrices f = vDiagonal + similarityScore; g1 = g[j] - e; g2 = v[j] - o; if (g1 > g2) { g[j] = g1; sizesOfVerticalGaps[l] = (short) (sizesOfVerticalGaps[l - n] + 1); } else { g[j] = g2; } h1 = h - e; h2 = v[j - 1] - o; if (h1 > h2) { h = h1; sizesOfHorizontalGaps[l] = (short) (sizesOfHorizontalGaps[l - 1] + 1); } else { h = h2; } vDiagonal = v[j]; v[j] = Max(f, g[j], h, 0); // Determine the traceback direction if (v[j] == 0) { pointers[l] = Directions.STOP; } else if (v[j] == f) { pointers[l] = Directions.DIAGONAL; } else if (v[j] == g[j]) { pointers[l] = Directions.UP; } else { pointers[l] = Directions.LEFT; } // Set the traceback start at the current cell i, j and score if (v[j] > cell.Score) { cell.Set(i, j, v[j]); } } } return cell; }