/// <summary> Returns the name, description and sequence combined in one string.
/// The length of each line in the sequence is FASTA.LINE_LENGTH</summary>
public virtual string Format(Sequence sequence)
{
StringBuilder buffer = new StringBuilder(">");
buffer.Append(sequence.Id == null ? "" : sequence.Id);
buffer.Append("\n");
for (int i = 0, n = sequence.Length; i*LINE_WIDTH < n; i++)
{
for (int j = i*LINE_WIDTH, m = (i + 1)*LINE_WIDTH < n ? (i + 1)*LINE_WIDTH : n; j < m; j++)
{
buffer.Append(sequence.Subsequence(j, 1));
}
buffer.Append("\n");
}
return buffer.ToString();
}
/// <summary> Aligns two sequences by Smith-Waterman algorithm</summary>
/// <param name="s1">sequene #1 </param>
/// <param name="s2">sequene #2 </param>
/// <param name="matrix">scoring matrix </param>
/// <param name="o">open gap penalty </param>
/// <param name="e">extend gap penalty </param>
/// <returns> alignment object contains the two aligned sequences,
/// the alignment score and alignment statistics</returns>
/// <seealso cref="Sequence"/>
/// <seealso cref="Matrix"/>
public static Alignment Align(Sequence s1, Sequence s2, Matrix matrix, float o, float e)
{
float[,] scores = matrix.Scores;
SmithWatermanGotoh sw = new SmithWatermanGotoh();
int m = s1.Length + 1;
int n = s2.Length + 1;
byte[] pointers = new byte[m * n];
// Initializes the boundaries of the traceback matrix to STOP.
for (int i = 0, k = 0; i < m; i++, k += n)
{
pointers[k] = Directions.STOP;
}
for (int j = 1; j < n; j++)
{
pointers[j] = Directions.STOP;
}
short[] sizesOfVerticalGaps = new short[m * n];
short[] sizesOfHorizontalGaps = new short[m * n];
for (int i = 0, k = 0; i < m; i++, k += n)
{
for (int j = 0; j < n; j++)
{
sizesOfVerticalGaps[k + j] = sizesOfHorizontalGaps[k + j] = 1;
}
}
Cell cell = sw.Construct(s1, s2, scores, o, e, pointers,
sizesOfVerticalGaps, sizesOfHorizontalGaps);
Alignment alignment = sw.Traceback(s1, s2, matrix, pointers, cell,
sizesOfVerticalGaps, sizesOfHorizontalGaps);
alignment.Name1 = s1.Id;
alignment.Name2 = s2.Id;
alignment.Matrix = matrix;
alignment.Open = o;
alignment.Extend = e;
return alignment;
}
/// <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;
}
/// <summary> Returns a <see cref="Sequence"/> parsed and loaded from a file</summary>
/// <param name="file">to parse </param>
/// <returns> parsed sequence </returns>
public static Sequence Parse(FileInfo file)
{
string sequenceName = null;
string sequenceDescription = null;
StreamReader reader = new StreamReader(file.FullName);
StringBuilder buffer = new StringBuilder();
// Read & parse the first line
string line = reader.ReadLine();
if (line.StartsWith(">"))
{
// FASTA sequence
line = line.Substring(1).Trim();
int index = 0;
for (int i = 0; i < line.Length && line[i] != ' ' && line[i] != '\t'; i++, index++)
{
// Skip white spaces
}
sequenceName = line.Substring(0, (index) - (0));
sequenceDescription = index + 1 > line.Length ? "" : line.Substring(index + 1);
}
else
{
// Plain sequence
buffer.Append(PrepareAndValidate(line));
}
// Read the remaining the file (the actual sequence)
while ((line = reader.ReadLine()) != null)
{
buffer.Append(PrepareAndValidate(line));
}
reader.Close();
Sequence s = new Sequence(buffer.ToString(), sequenceName, sequenceDescription, SequenceType.Protein);
return s;
}
/// <summary> Returns a parsed Sequence from a FASTA string.</summary>
/// <param name="stringToParse">FASTA string to parse</param>
public static Sequence Parse(string stringToParse)
{
stringToParse = stringToParse.Replace("\r\n", "\n");
string sequenceName = null;
string sequenceDescription = null;
if (stringToParse.StartsWith(">"))
{
// FASTA format
int index = stringToParse.IndexOf("\n");
if (index == - 1)
{
throw new System.Exception("Invalid sequence");
}
string first = stringToParse.Substring(1, (index) - (1));
stringToParse = stringToParse.Substring(index);
index = 0;
for (int i = 0; i < first.Length && first[i] != ' ' && first[i] != '\t'; i++, index++)
{
// Skip white spaces
}
sequenceName = first.Substring(0, (index) - (0));
sequenceDescription = index + 1 > first.Length ? "" : first.Substring(index + 1);
}
else
{
// Plain format ... nothing to do here
}
Sequence s = new Sequence(PrepareAndValidate(stringToParse), sequenceName, sequenceDescription, SequenceType.Protein);
return s;
}
