/// <returns> FASTA format of the input alignment</returns>
public override string Format(Alignment alignment)
{
System.Text.StringBuilder buffer = new System.Text.StringBuilder();
System.Text.StringBuilder s1 = new System.Text.StringBuilder();
System.Text.StringBuilder s2 = new System.Text.StringBuilder();
s1.Append(alignment.Sequence1);
s2.Append(alignment.Sequence2);
buffer.Append(Format(new Sequence(s1.ToString(), alignment.Name1, "", SequenceType.Protein)));
buffer.Append(Format(new Sequence(s2.ToString(), alignment.Name2, "", SequenceType.Protein)));
return buffer.ToString();
}
/// <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> Returns CLUSTAL format of the alignment</summary>
public override string Format(Alignment alignment)
{
string[] sequences = new string[] {new string(alignment.Sequence1), new string(alignment.Sequence2)};
string[] names = new string[] {alignment.Name1, alignment.Name2};
return Format(names, sequences);
}
/// <summary> Formats alignment</summary> /// <returns> formatted alignment </returns> public abstract string Format(Alignment 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> Formats an alignment object to the Pair_FORMAT format</summary>
/// <param name="alignment">alignment object to be formated </param>
/// <returns> string of the alignment pair-formatted </returns>
public override string Format(Alignment alignment)
{
char[] sequence1 = alignment.Sequence1;
char[] sequence2 = alignment.Sequence2;
char[] markup = alignment.MarkupLine;
int length = sequence1.Length > sequence2.Length ? sequence2.Length : sequence1.Length;
string name1 = AdjustName(alignment.Name1);
string name2 = AdjustName(alignment.Name2);
StringBuilder buffer = new StringBuilder();
StringBuilder preMarkup = new StringBuilder();
for (int j = 0; j < NAME_WIDTH + 1 + POSITION_WIDTH + 1; j++)
{
preMarkup.Append(BLANK);
}
int oldPosition1, position1 = 1 + alignment.Start1;
int oldPosition2, position2 = 1 + alignment.Start2;
char[] subsequence1;
char[] subsequence2;
char[] submarkup;
int line;
char c1, c2;
for (int i = 0; i*SEQUENCE_WIDTH < length; i++)
{
oldPosition1 = position1;
oldPosition2 = position2;
line = ((i + 1)*SEQUENCE_WIDTH) < length ? (i + 1)*SEQUENCE_WIDTH : length;
subsequence1 = new char[line - i*SEQUENCE_WIDTH];
subsequence2 = new char[line - i*SEQUENCE_WIDTH];
submarkup = new char[line - i*SEQUENCE_WIDTH];
for (int j = i*SEQUENCE_WIDTH, k = 0; j < line; j++, k++)
{
subsequence1[k] = sequence1[j];
subsequence2[k] = sequence2[j];
submarkup[k] = markup[j];
c1 = subsequence1[k];
c2 = subsequence2[k];
if (c1 == c2)
{
position1++;
position2++;
}
else if (c1 == Alignment.GAP)
{
position2++;
}
else if (c2 == Alignment.GAP)
{
position1++;
}
else
{
position1++;
position2++;
}
}
buffer.Append(name1);
buffer.Append(BLANK);
buffer.Append(AdjustPosition((oldPosition1).ToString()));
buffer.Append(BLANK);
buffer.Append(subsequence1);
buffer.Append(BLANK);
buffer.Append(AdjustPosition(((position1 - 1)).ToString()));
buffer.Append(Commons.LineSeparator);
buffer.Append(preMarkup);
buffer.Append(submarkup);
buffer.Append(Commons.LineSeparator);
buffer.Append(name2);
buffer.Append(BLANK);
buffer.Append(AdjustPosition((oldPosition2).ToString()));
buffer.Append(BLANK);
buffer.Append(subsequence2);
buffer.Append(BLANK);
buffer.Append(AdjustPosition(((position2 - 1)).ToString()));
buffer.Append(Commons.LineSeparator);
buffer.Append(Commons.LineSeparator);
}
return buffer.ToString();
}