[Test] public void Align2()
{
string matrixPath = @"../../matrices/TEST1";
if (!File.Exists(matrixPath))
{
matrixPath = @"TEST1";
}
Matrix customMatrix = Matrix.Load(matrixPath);
Sequence seq1 = Sequence.Parse(@"AACCC");
Sequence seq2 = Sequence.Parse(@"CCACC");
float opengap = 2.0f;
float extendgap = 1.0f;
Alignment alignment = SmithWatermanGotoh.Align(seq1, seq2, customMatrix, opengap, extendgap);
Assert.AreEqual(alignment.Sequence1.Length, 3, "#A00 Unexpected aligment");
Assert.AreEqual(alignment.Sequence2.Length, 3, "#A01 Unexpected aligment");
Assert.AreEqual(alignment.Sequence1[0], 'A', "#A02 Unexpected alignement");
Assert.AreEqual(alignment.Sequence1[1], 'C', "#A03 Unexpected alignement");
Assert.AreEqual(alignment.Sequence1[2], 'C', "#A04 Unexpected alignement");
Assert.AreEqual(alignment.Sequence2[0], 'A', "#A05 Unexpected alignement");
Assert.AreEqual(alignment.Sequence2[1], 'C', "#A06 Unexpected alignement");
Assert.AreEqual(alignment.Sequence2[2], 'C', "#A07 Unexpected alignement");
Assert.AreEqual(15.0f, alignment.Score, "#A08 Unexpected score.");
}
[Test] public void Align()
{
string matrixPath = @"../../matrices/PAM250";
if (!File.Exists(matrixPath))
{
matrixPath = @"PAM250";
}
Matrix pam250 = Matrix.Load(matrixPath);
float opengap = 15.0f;
float extendgap = 3.0f;
string str1 = @">100K_RAT 100 kDa protein (EC 6.3.2.-)." + NL +
"MMSARGDFLN YALSLMRSHN DEHSDVLPVL DVCSLKHVAY VFQALIYWIK AMNQQTTLDT" +
"PQLERKRTRE LLELGIDNED SEHENDDDTS QSATLNDKDD ESLPAETGQN HPFFRRSDSM" +
"TFLGCIPPNP FEVPLAEAIP LADQPHLLQP NARKEDLFGR PSQGLYSSSA GSGKCLVEVT" +
"MDRNCLEVLP TKMSYAANLK NVMNMQNRQK KAGEDQSMLA EEADSSKPGP SAHDVAAQLK" +
"SSLLAEIGLT ESEGPPLTSF RPQCSFMGMV ISHDMLLGRW RLSLELFGRV FMEDVGAEPG" +
"SILTELGGFE VKESKFRREM EKLRNQQSRD LSLEVDRDRD LLIQQTMRQL NNHFGRRCAT" +
"TPMAVHRVKV TFKDEPGEGS GVARSFYTAI AQAFLSNEKL PNLDCIQNAN KGTHTSLMQR" +
"LRNRGERDRE REREREMRRS SGLRAGSRRD RDRDFRRQLS IDTRPFRPAS EGNPSDDPDP" +
"LPAHRQALGE RLYPRVQAMQ PAFASKITGM LLELSPAQLL LLLASEDSLR ARVEEAMELI" +
"VAHGRENGAD SILDLGLLDS SEKVQENRKR HGSSRSVVDM DLDDTDDGDD NAPLFYQPGK" +
"RGFYTPRPGK NTEARLNCFR NIGRILGLCL LQNELCPITL NRHVIKVLLG RKVNWHDFAF" +
"FDPVMYESLR QLILASQSSD ADAVFSAMDL AFAVDLCKEE GGGQVELIPN GVNIPVTPQN" +
"VYEYVRKYAE HRMLVVAEQP LHAMRKGLLD VLPKNSLEDL TAEDFRLLVN GCGEVNVQML" +
"ISFTSFNDES GENAEKLLQF KRWFWSIVER MSMTERQDLV YFWTSSPSLP ASEEGFQPMP" +
"SITIRPPDDQ HLPTANTCIS RLYVPLYSSK QILKQKLLLA IKTKNFGFV";
string str2 = @">104K_THEPA 104 kDa microneme-rhoptry antigen." + NL +
"MKFLILLFNI LCLFPVLAAD NHGVGPQGAS GVDPITFDIN SNQTGPAFLT AVEMAGVKYL" +
"QVQHGSNVNI HRLVEGNVVI WENASTPLYT GAIVTNNDGP YMAYVEVLGD PNLQFFIKSG" +
"DAWVTLSEHE YLAKLQEIRQ AVHIESVFSL NMAFQLENNK YEVETHAKNG ANMVTFIPRN" +
"GHICKMVYHK NVRIYKATGN DTVTSVVGFF RGLRLLLINV FSIDDNGMMS NRYFQHVDDK" +
"YVPISQKNYE TGIVKLKDYK HAYHPVDLDI KDIDYTMFHL ADATYHEPCF KIIPNTGFCI" +
"TKLFDGDQVL YESFNPLIHC INEVHIYDRN NGSIICLHLN YSPPSYKAYL VLKDTGWEAT" +
"THPLLEEKIE ELQDQRACEL DVNFISDKDL YVAALTNADL NYTMVTPRPH RDVIRVSDGS" +
"EVLWYYEGLD NFLVCAWIYV SDGVASLVHL RIKDRIPANN DIYVLKGDLY WTRITKIQFT" +
"QEIKRLVKKS KKKLAPITEE DSDKHDEPPE GPGASGLPPK APGDKEGSEG HKGPSKGSDS" +
"SKEGKKPGSG KKPGPAREHK PSKIPTLSKK PSGPKDPKHP RDPKEPRKSK SPRTASPTRR" +
"PSPKLPQLSK LPKSTSPRSP PPPTRPSSPE RPEGTKIIKT SKPPSPKPPF DPSFKEKFYD" +
"DYSKAASRSK ETKTTVVLDE SFESILKETL PETPGTPFTT PRPVPPKRPR TPESPFEPPK" +
"DPDSPSTSPS EFFTPPESKR TRFHETPADT PLPDVTAELF KEPDVTAETK SPDEAMKRPR" +
"SPSEYEDTSP GDYPSLPMKR HRLERLRLTT TEMETDPGRM AKDASGKPVK LKRSKSFDDL" +
"TTVELAPEPK ASRIVVDDEG TEADDEETHP PEERQKTEVR RRRPPKKPSK SPRPSKPKKP" +
"KKPDSAYIPS ILAILVVSLI VGIL";
Sequence seq1 = Sequence.Parse(str1);
Sequence seq2 = Sequence.Parse(str2);
Alignment alignment = SmithWatermanGotoh.Align(seq1, seq2, pam250, opengap, extendgap);
Assert.AreEqual(98.0f, alignment.Score, "Unexpected score.");
}
/// <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> 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);
}
[Test] public void Align2()
{
string matrixPath = @"../../matrices/TEST1";
if (!File.Exists(matrixPath))
{
matrixPath = @"TEST1";
}
Matrix customMatrix = Matrix.Load(matrixPath);
Sequence seq1 = Sequence.Parse(@"AACCC");
Sequence seq2 = Sequence.Parse(@"CCACC");
float opengap = 2.0f;
float extendgap = 1.0f;
Alignment alignment = SmithWatermanGotoh.Align(seq1, seq2, customMatrix, opengap, extendgap);
Assert.AreEqual(14.0f, alignment.Score, "Unexpected score.");
}