/// <summary>
/// Pairwise alignment of two sequences using an affine gap penalty. The various algorithms in derived classes (NeedlemanWunsch,
/// SmithWaterman, and PairwiseOverlap) all use this general engine for alignment with an affine gap penalty.
/// </summary>
/// <param name="similarityMatrix">Scoring matrix.</param>
/// <param name="gapOpenPenalty">Gap open penalty (by convention, use a negative number for this.)</param>
/// <param name="gapExtensionPenalty">Gap extension penalty (by convention, use a negative number for this.)</param>
/// <param name="aInput">First input sequence.</param>
/// <param name="bInput">Second input sequence.</param>
/// <returns>A list of sequence alignments.</returns>
public IList <IPairwiseSequenceAlignment> Align(
SimilarityMatrix similarityMatrix,
int gapOpenPenalty,
int gapExtensionPenalty,
ISequence aInput,
ISequence bInput)
{
// Initialize and perform validations for alignment
// In addition, initialize gap extension penalty.
SimpleAlignPrimer(similarityMatrix, gapOpenPenalty, aInput, bInput);
_gapExtensionCost = gapExtensionPenalty;
FillMatrixAffine();
////DumpF(); // Writes matrix to application log, used for development and testing
List <byte[]> alignedSequences;
List <int> offsets;
List <int> startOffsets;
List <int> endOffsets;
List <int> insertions;
int optScore = Traceback(out alignedSequences, out offsets, out startOffsets, out endOffsets, out insertions);
return(CollateResults(aInput, bInput, alignedSequences, offsets, optScore, startOffsets, endOffsets, insertions));
}
public void testBug3()
{
//Test on DNA benchmark dataset
ISequenceParser parser = new FastaParser();
string filepath = @"TestUtils\122_raw.afa";
MoleculeType mt = MoleculeType.DNA;
IList <ISequence> orgSequences = parser.Parse(filepath);
List <ISequence> sequences = MsaUtils.UnAlign(orgSequences);
PAMSAMMultipleSequenceAligner.FasterVersion = false;
PAMSAMMultipleSequenceAligner.UseWeights = false;
PAMSAMMultipleSequenceAligner.UseStageB = false;
PAMSAMMultipleSequenceAligner.NumberOfCores = 2;
int gapOpenPenalty = -13;
int gapExtendPenalty = -5;
int kmerLength = 2;
int numberOfDegrees = 2; //Environment.ProcessorCount;
int numberOfPartitions = 16; // Environment.ProcessorCount * 2;
DistanceFunctionTypes distanceFunctionName = DistanceFunctionTypes.EuclideanDistance;
UpdateDistanceMethodsTypes hierarchicalClusteringMethodName = UpdateDistanceMethodsTypes.Average;
ProfileAlignerNames profileAlignerName = ProfileAlignerNames.NeedlemanWunschProfileAligner;
ProfileScoreFunctionNames profileProfileFunctionName = ProfileScoreFunctionNames.InnerProductFast;
SimilarityMatrix similarityMatrix = null;
switch (mt)
{
case (MoleculeType.DNA):
similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.AmbiguousDna);
break;
case (MoleculeType.RNA):
similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.AmbiguousRna);
break;
case (MoleculeType.Protein):
similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum62);
break;
default:
throw new InvalidDataException("Invalid molecular type");
}
//DateTime startTime = DateTime.Now;
PAMSAMMultipleSequenceAligner msa = new PAMSAMMultipleSequenceAligner
(sequences, mt, kmerLength, distanceFunctionName, hierarchicalClusteringMethodName,
profileAlignerName, profileProfileFunctionName, similarityMatrix, gapOpenPenalty, gapExtendPenalty,
numberOfPartitions, numberOfDegrees);
Assert.IsNotNull(msa.AlignedSequences);
((FastaParser)parser).Dispose();
}
/// <summary>
/// Pairwise alignment of two sequences using an affine gap penalty. The various algorithms in derived classes (NeedlemanWunsch,
/// SmithWaterman, and PairwiseOverlap) all use this general engine for alignment with an affine gap penalty.
/// </summary>
/// <param name="localSimilarityMatrix">Scoring matrix.</param>
/// <param name="gapOpenPenalty">Gap open penalty (by convention, use a negative number for this.).</param>
/// <param name="gapExtensionPenalty">Gap extension penalty (by convention, use a negative number for this.).</param>
/// <param name="inputA">First input sequence.</param>
/// <param name="inputB">Second input sequence.</param>
/// <returns>A list of sequence alignments.</returns>
public IList <IPairwiseSequenceAlignment> Align(
SimilarityMatrix localSimilarityMatrix,
int gapOpenPenalty,
int gapExtensionPenalty,
ISequence inputA,
ISequence inputB)
{
// Initialize and perform validations for alignment
// In addition, initialize gap extension penalty.
SimpleAlignPrimer(localSimilarityMatrix, gapOpenPenalty, inputA, inputB);
GapExtensionCost = gapExtensionPenalty;
DynamicProgrammingPairwiseAlignerJob alignerJob = this.CreateAffineAlignmentJob(inputA, inputB);
IList <IPairwiseSequenceAlignment> result = alignerJob.Align();
foreach (IPairwiseSequenceAlignment alignment in result)
{
foreach (PairwiseAlignedSequence sequence in alignment.AlignedSequences)
{
AddSimpleConsensusToResult(sequence);
}
}
return(result);
}
public void testBug()
{
List <ISequence> sequences = new List <ISequence>();
ISequence seq1 = new Sequence(Alphabets.Protein, "MQEPQSELNIDPPLSQETFSELWNLLPENNVLSSELCPAVDELLLPESVVNWLDEDSDDAPRMPATSAP");
ISequence seq2 = new Sequence(Alphabets.Protein, "PLSQETFSDLWNLLPENNLLSSELSAPVDDLLPYTDVATWLDECPNEAPQMPEPSAPAAPPPATPAPATSWPLSSFVPSQKTYPGNYGFRLGF");
ISequence seq3 = new Sequence(Alphabets.Protein, "MEPSSETGMDPPLSQETFEDLWSLLPDPLQTVTCRLDNLSEFPDYPLAADMSVLQEGLMGNAVPTVTSCAPSTDDYAGKYGLQLDFQQNGTAKS");
ISequence seq4 = new Sequence(Alphabets.Protein, "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPRVAPAPAAPTPAAPAPAPSWPLS");
ISequence seq5 = new Sequence(Alphabets.Protein, "MEESQAELGVEPPLSQETFSDLWKLLPENNLLSSELSPAVDDLLLSPEDVANWLDERPDEAPQMPEPPAPAAPTPAAPAPATSWPLSSFVPSQK");
ISequence seq6 = new Sequence(Alphabets.Protein, "MTAMEESQSDISLELPLSQETFSGLWKLLPPEDILPSPHCMDDLLLPQDVEEFFEGPSEALRVSGAPAAQDPVTETPGPVAPAPATPWPLSSFVPSQKTYQGNYGFHLGFLQ");
ISequence seq7 = new Sequence(Alphabets.Protein, "FRLGFLHSGTAKSVTWTYSPLLNKLFCQLAKTCPVQLWVSSPPPPNTCVRAMAIYKKSEFVTEVVRRCPHHERCSDSSDGLAPPQHLIRVEGNLRAKYLDDRNTFRHSVV");
sequences.Add(seq1);
sequences.Add(seq2);
sequences.Add(seq3);
sequences.Add(seq4);
sequences.Add(seq5);
sequences.Add(seq6);
sequences.Add(seq7);
SimilarityMatrix sm = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum50);
PAMSAMMultipleSequenceAligner msa = new PAMSAMMultipleSequenceAligner(sequences,
2, DistanceFunctionTypes.EuclideanDistance, UpdateDistanceMethodsTypes.Average, ProfileAlignerNames.NeedlemanWunschProfileAligner,
ProfileScoreFunctionNames.WeightedEuclideanDistance, sm, -8, -1, 2, 16);
Assert.IsNotNull(msa.AlignedSequences);
}
public void testBug2()
{
//Test on DNA benchmark dataset
string filepath = @"TestUtils\122_raw.afa".TestDir();
FastAParser parser = new FastAParser();
IList <ISequence> orgSequences = parser.Parse(filepath).ToList();
List <ISequence> sequences = MsaUtils.UnAlign(orgSequences);
PAMSAMMultipleSequenceAligner.FasterVersion = false;
PAMSAMMultipleSequenceAligner.UseWeights = false;
PAMSAMMultipleSequenceAligner.UseStageB = false;
PAMSAMMultipleSequenceAligner.NumberOfCores = 2;
int gapOpenPenalty = -13;
int gapExtendPenalty = -5;
int kmerLength = 2;
int numberOfDegrees = 2; //Environment.ProcessorCount;
int numberOfPartitions = 16; // Environment.ProcessorCount * 2;
DistanceFunctionTypes distanceFunctionName = DistanceFunctionTypes.EuclideanDistance;
UpdateDistanceMethodsTypes hierarchicalClusteringMethodName = UpdateDistanceMethodsTypes.Average;
ProfileAlignerNames profileAlignerName = ProfileAlignerNames.NeedlemanWunschProfileAligner;
ProfileScoreFunctionNames profileProfileFunctionName = ProfileScoreFunctionNames.InnerProductFast;
SimilarityMatrix similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.AmbiguousDna);
PAMSAMMultipleSequenceAligner msa = new PAMSAMMultipleSequenceAligner
(sequences, kmerLength, distanceFunctionName, hierarchicalClusteringMethodName,
profileAlignerName, profileProfileFunctionName, similarityMatrix, gapOpenPenalty, gapExtendPenalty,
numberOfPartitions, numberOfDegrees);
Assert.IsNotNull(msa.AlignedSequences);
}
private (int I, int J) FindMostSimilarNodes(SimilarityMatrix matrix)
{
double bestSimilarity = matrix[0, 1];
int bestI = 0;
int bestJ = 1;
for (int i = 0; i < matrix.Dimension; i++)
{
for (int j = 0; j < matrix.Dimension; j++)
{
if (i == j)
{
continue;
}
if (matrix[i, j] > bestSimilarity)
{
bestSimilarity = matrix[i, j];
bestI = i;
bestJ = j;
}
}
}
return(bestI, bestJ);
}
/// <summary>
/// Construct a progressive aligner
/// </summary>
/// <param name="profileAlignerName">ProfileAlignerNames member</param>
/// <param name="similarityMatrix">similarity matrix</param>
/// <param name="gapOpenPenalty">negative gapOpenPenalty</param>
/// <param name="gapExtendPenalty">negative gapExtendPenalty</param>
public ProgressiveAligner(ProfileAlignerNames profileAlignerName,
SimilarityMatrix similarityMatrix,
int gapOpenPenalty,
int gapExtendPenalty)
{
// Get ProfileAligner ready
switch (profileAlignerName)
{
case (ProfileAlignerNames.NeedlemanWunschProfileAligner):
_profileAligner = new NeedlemanWunschProfileAlignerSerial();
break;
case (ProfileAlignerNames.SmithWatermanProfileAligner):
_profileAligner = new SmithWatermanProfileAlignerSerial();
break;
default:
throw new Exception("Invalid profile aligner name");
}
_profileAligner.SimilarityMatrix = similarityMatrix;
_profileAligner.GapOpenCost = gapOpenPenalty;
_profileAligner.GapExtensionCost = gapExtendPenalty;
_alignedSequences = new List <ISequence>();
}
/// <summary>
///
/// </summary>
/// <param name="similarityMatrix"></param>
/// <param name="gapOpenCost"></param>
/// <param name="gapExtensionCost"></param>
/// <param name="aInput"></param>
/// <param name="bInput"></param>
protected DynamicProgrammingPairwiseAlignerJob(SimilarityMatrix similarityMatrix, int gapOpenCost, int gapExtensionCost, ISequence aInput, ISequence bInput)
{
if (aInput == null)
{
throw new ArgumentNullException("aInput");
}
aInput.Alphabet.TryGetDefaultGapSymbol(out gapCode);
// Set Gap Penalty and Similarity Matrix
this.gapOpenCost = gapOpenCost;
this.gapExtensionCost = gapExtensionCost;
// note that _gapExtensionCost is not used for linear gap penalty
this.similarityMatrix = similarityMatrix;
// Convert input strings to 0-based int arrays using similarity matrix mapping
this.sequenceI = aInput;
this.sequenceJ = bInput;
colHeight = sequenceI.Count + 1;
rowWidth = sequenceJ.Count + 1;
gridCols = (int)((rowWidth - 1) / gridStride) + 1;
gridRows = (int)((colHeight - 1) / gridStride) + 1;
}
static void Main(string[] args)
{
//This is a simple driver program
Console.WriteLine("Testing:Driver program for Affinity Propagation clustering algorithm.");
var rnd = new ToyDataset();
Stopwatch s = new Stopwatch();
var data1 = rnd.DataSet();
var sim = SimilarityMatrix.SparseSimilarityMatrix(data1);
Console.WriteLine($"Data size:{data1.Length} ; SimilarityMatrix size:{sim.Length}");
Console.WriteLine($"Start at:{DateTime.Now}");
s.Start();
try
{
AffinityPropagation model = new AffinityPropagation(data1.Length);
var centers = model.Fit(sim);
Print(centers);
ClusterUtility.AssignClusterCenters(data1, centers);
int[] centers_index = new int[model.Centers.Count];
model.Centers.CopyTo(centers_index);
var t = ClusterUtility.GroupClusters(data1, centers, centers_index);
//print the clusters (grouped)
Print(t);
}
catch (Exception e)
{
Console.WriteLine($"\a{e.Message}");
}
s.Stop();
Console.WriteLine($"\nEnding at:{DateTime.Now}");
Console.WriteLine($"Ellapsed time: {s.ElapsedMilliseconds} ms | {s.Elapsed.TotalSeconds} s | {s.Elapsed.TotalMinutes} m");
}
/// <summary>
/// Constructor for NeedlemanWunschProfile Aligner.
/// Sets default similarity matrix, gap penalties, and profile function name.
/// Users will typically reset these using parameters specific to their particular sequences and needs.
/// </summary>
/// <param name="similarityMatrix">similarity matrix</param>
/// <param name="profileScoreFunctionName">enum: profileScoreFunctionName</param>
/// <param name="gapOpenPenalty">negative integer</param>
/// <param name="gapExtensionPenalty">negative integer</param>
/// <param name="numberOfPartitions">positive integer</param>
public NeedlemanWunschProfileAlignerParallel(SimilarityMatrix similarityMatrix,
ProfileScoreFunctionNames profileScoreFunctionName,
int gapOpenPenalty,
int gapExtensionPenalty,
int numberOfPartitions)
: base(similarityMatrix, profileScoreFunctionName, gapOpenPenalty, gapExtensionPenalty, numberOfPartitions)
{
}
public void IupacNASimilarityMatrices()
{
string filename = @"TestUtils\SimilarityMatrices\TestIupacNA.txt";
SimilarityMatrix sm = new SimilarityMatrix(filename);
Assert.IsNotNull(sm.Matrix);
}
/// <summary>
/// Constructor for SmithWatermanProfileAligner.
/// Sets default similarity matrix, gap penalties, and profile function name.
/// Users will typically reset these using parameters specific to their particular sequences and needs.
/// </summary>
/// <param name="similarityMatrix">similarity matrix</param>
/// <param name="profileScoreFunctionName">enum: profileScoreFunctionName</param>
/// <param name="gapOpenPenalty">negative integer</param>
/// <param name="gapExtensionPenalty">negative integer</param>
/// <param name="numberOfPartitions">positive integer</param>
public SmithWatermanProfileAlignerSerial(SimilarityMatrix similarityMatrix,
ProfileScoreFunctionNames profileScoreFunctionName,
int gapOpenPenalty,
int gapExtensionPenalty,
int numberOfPartitions)
: base(similarityMatrix, profileScoreFunctionName, gapOpenPenalty, gapExtensionPenalty, numberOfPartitions)
{
}
public void TestNeedlemanWunschProfileAligner()
{
ISequence templateSequence = new Sequence(Alphabets.DNA, "ATGCSWRYKMBVHDN-");
Dictionary <ISequenceItem, int> itemSet = new Dictionary <ISequenceItem, int>();
for (int i = 0; i < templateSequence.Count; ++i)
{
itemSet.Add(templateSequence[i], i);
}
Profiles.ItemSet = itemSet;
IProfileAligner profileAligner = new NeedlemanWunschProfileAligner();
SimilarityMatrix similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrices.AmbiguousDna);
int gapOpenPenalty = -8;
int gapExtendPenalty = -1;
profileAligner.SimilarityMatrix = similarityMatrix;
profileAligner.GapOpenCost = gapOpenPenalty;
profileAligner.GapExtensionCost = gapExtendPenalty;
ISequence seqA = new Sequence(Alphabets.DNA, "GGGAAAAATCAGATT");
ISequence seqB = new Sequence(Alphabets.DNA, "GGGAATCAAAATCAG");
List <ISequence> sequences = new List <ISequence>();
sequences.Add(seqA);
sequences.Add(seqB);
IProfileAlignment profileAlignmentA = ProfileAlignment.GenerateProfileAlignment(sequences[0]);
IProfileAlignment profileAlignmentB = ProfileAlignment.GenerateProfileAlignment(sequences[1]);
profileAligner.Align(profileAlignmentA, profileAlignmentB);
List <int> eStringSubtree = profileAligner.GenerateEString(profileAligner.AlignedA);
List <int> eStringSubtreeB = profileAligner.GenerateEString(profileAligner.AlignedB);
List <ISequence> alignedSequences = new List <ISequence>();
ISequence seq = profileAligner.GenerateSequenceFromEString(eStringSubtree, sequences[0]);
alignedSequences.Add(seq);
seq = profileAligner.GenerateSequenceFromEString(eStringSubtreeB, sequences[1]);
alignedSequences.Add(seq);
float profileScore = MsaUtils.MultipleAlignmentScoreFunction(alignedSequences, similarityMatrix, gapOpenPenalty, gapExtendPenalty);
ISequence expectedSeqA = new Sequence(Alphabets.DNA, "GGGAA---AAATCAGATT");
ISequence expectedSeqB = new Sequence(Alphabets.DNA, "GGGAATCAAAATCAG---");
Assert.AreEqual(expectedSeqA.ToString(), alignedSequences[0].ToString());
Assert.AreEqual(expectedSeqB.ToString(), alignedSequences[1].ToString());
Assert.AreEqual(40, profileScore);
}
/// <summary>
/// Initializes a new instance of the DynamicProgrammingPairwiseAligner class.
/// Constructor for all the pairwise aligner (NeedlemanWunsch, SmithWaterman, Overlap).
/// Sets default similarity matrix and gap penalties.
/// Users will typically reset these using parameters specific to their particular sequences and needs.
/// </summary>
protected DynamicProgrammingPairwiseAligner()
{
// Set default similarity matrix and gap penalty.
// User will typically choose their own parameters, these defaults are reasonable for many cases.
// Molecule type is set to protein, since this will also work for DNA and RNA in the
// special case of a diagonal similarity matrix.
this.InternalSimilarityMatrix = new DiagonalSimilarityMatrix(2, -2);
GapOpenCost = -8;
GapExtensionCost = -1;
}
public Base(int maxNeighbours, string redisPrefix, IRedisClient redisClient)
{
RedisClient = redisClient;
MaxNeighbours = maxNeighbours;
RedisPrefix = redisPrefix;
InputMatrices = new Dictionary<string, InputMatrix>();
SimilarityMatrix = new SimilarityMatrix(
new Options {Key = "similarities", MaxNeighbours = MaxNeighbours, RedisPrefix = RedisPrefix},
redisClient);
}
public void TestStartNoGapAlgorithm(string matrix, string X, string Y, Func <int, double> penaltyFunc, double evaluation, string resultX, string resultY)
{
var similarityMatrix = new SimilarityMatrix(matrix);
var withGapPenalty = new WithGapPenalty(similarityMatrix, penaltyFunc);
var tuple = withGapPenalty.StartNoGapAlgorithm(X, Y);
Assert.AreEqual(evaluation, tuple.Item1);
Assert.AreEqual(resultX, tuple.Item2.Item1);
Assert.AreEqual(resultY, tuple.Item2.Item2);
}
public void TestStartAlgorithm(string matrix, string X, string Y, string resultX, string resultY)
{
//string matrix = "A G T C\n0 -2 -2 -2 -2\n-2 2 -1 -1 -1\n-2 -1 2 -1 -1\n-2 -1 -1 2 -1\n-2 -1 -1 -1 2";
SimilarityMatrix similarityMatrix = new SimilarityMatrix(matrix);
Hirschberg hirschberg = new Hirschberg(similarityMatrix);
Tuple <string, string> tuple = hirschberg.StartAlgorithm(X, Y);
Assert.AreEqual(resultX, tuple.Item1);
Assert.AreEqual(resultY, tuple.Item2);
}
public override void Summarize(SummaryParameters mySummaryParameters, string newsDirectory, string cacheFileName)
{
Mis = (DegreeCentralityLexRankParameters)mySummaryParameters;
Debug.WriteLine("Starting execution of DegreeCentralityLexRank.");
var startTime = DateTime.Now;
var myTDM = new TDM(newsDirectory, Mis.MyTDMParameters, cacheFileName);
var normalized = ((DegreeCentralityLexRankParameters)mySummaryParameters).SimilarityNormalized;
var mySimilarityMatrix = new SimilarityMatrix(myTDM, cacheFileName, normalized);
var totalPhrases = myTDM.PhrasesList.Count;
var myCosineSimilarities = mySimilarityMatrix.CosineSimilarityBetweenPhrases;
var weights = new double[totalPhrases];
for (var i = 0; i < totalPhrases; i++)
{
var sum = 0.0d;
for (var j = 0; j < totalPhrases; j++)
{
if (myCosineSimilarities[i][j] > Mis.DegreeCentrality)
{
sum++;
}
}
weights[i] = sum;
}
var phrasesList = new List <PositionValue>(); // Save candidate phrases with their weight (relevance)
for (var i = 0; i < totalPhrases; i++)
{
phrasesList.Add(new PositionValue(i, weights[i]));
}
//phrasesList.Sort((x,y) => -1 * x.Value.CompareTo(y.Value)); // The phrases are ordered by their weight
phrasesList.Sort(delegate(PositionValue x, PositionValue y)
{
if (Math.Abs(x.Value - y.Value) < 1e-07)
{
return(myTDM.PhrasesList[x.Position].PositionInDocument.CompareTo(myTDM.PhrasesList[y.Position].PositionInDocument));
}
return(-1 * x.Value.CompareTo(y.Value));
});
TextSummary = Util.SummarizeByCompressionRatio(myTDM, phrasesList, mySummaryParameters.MySummaryType,
Mis.MaximumLengthOfSummaryForRouge, out SummaryByPhrases);
var fin = DateTime.Now - startTime;
Debug.WriteLine("Minutes of DegreeCentralityLexRank: " + fin.TotalMinutes);
}
/// <summary>
/// Pairwise alignment of two sequences using an affine gap penalty. The various algorithms in derived classes (NeedlemanWunsch,
/// SmithWaterman, and PairwiseOverlap) all use this general engine for alignment with an affine gap penalty.
/// </summary>
/// <param name="localSimilarityMatrix">Scoring matrix.</param>
/// <param name="gapOpenPenalty">Gap open penalty (by convention, use a negative number for this.).</param>
/// <param name="gapExtensionPenalty">Gap extension penalty (by convention, use a negative number for this.).</param>
/// <param name="inputA">First input sequence.</param>
/// <param name="inputB">Second input sequence.</param>
/// <returns>A list of sequence alignments.</returns>
public IList <IPairwiseSequenceAlignment> Align(
SimilarityMatrix localSimilarityMatrix,
int gapOpenPenalty,
int gapExtensionPenalty,
ISequence inputA,
ISequence inputB)
{
this.SimilarityMatrix = localSimilarityMatrix;
this.GapOpenCost = gapOpenPenalty;
this.GapExtensionCost = gapExtensionPenalty;
return(DoAlign(inputA, inputB, true));
}
public void PairwiseOverlapProteinSeqAffineGapUseEarth()
{
string sequenceString1 = "HEAGAWGHEE";
string sequenceString2 = "PAWHEAE";
Sequence sequence1 = new Sequence(Alphabets.Protein, sequenceString1);
Sequence sequence2 = new Sequence(Alphabets.Protein, sequenceString2);
SimilarityMatrix sm = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum50);
int gapPenalty = -8;
PairwiseOverlapAligner overlap = new PairwiseOverlapAligner();
overlap.SimilarityMatrix = sm;
overlap.GapOpenCost = gapPenalty;
overlap.UseEARTHToFillMatrix = true;
overlap.GapExtensionCost = -1;
IList <IPairwiseSequenceAlignment> result = overlap.Align(sequence1, sequence2);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"{0}, Affine; Matrix {1}; GapOpenCost {2}; GapExtenstionCost {3}",
overlap.Name, overlap.SimilarityMatrix.Name, overlap.GapOpenCost, overlap.GapExtensionCost));
foreach (IPairwiseSequenceAlignment sequenceResult in result)
{
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"score {0}", sequenceResult.PairwiseAlignedSequences[0].Score));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"input 0 {0}", sequenceResult.FirstSequence.ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"input 1 {0}", sequenceResult.SecondSequence.ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"result 0 {0}", sequenceResult.PairwiseAlignedSequences[0].FirstSequence.ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"result 1 {0}", sequenceResult.PairwiseAlignedSequences[0].SecondSequence.ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"consesus {0}", sequenceResult.PairwiseAlignedSequences[0].Consensus.ToString()));
}
IList <IPairwiseSequenceAlignment> expectedOutput = new List <IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
PairwiseAlignedSequence alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.Protein, "GAWGHEE");
alignedSeq.SecondSequence = new Sequence(Alphabets.Protein, "PAW-HEA");
alignedSeq.Consensus = new Sequence(Alphabets.AmbiguousProtein, "XAWGHEX");
alignedSeq.Score = 25;
alignedSeq.FirstOffset = 0;
alignedSeq.SecondOffset = 3;
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
Assert.IsTrue(CompareAlignment(result, expectedOutput));
}
public override void Summarize(SummaryParameters mySummaryParameters, string newsDirectory, string cacheFileName)
{
MyParameters = (FSPParameters)mySummaryParameters;
MyTDM = new TDM(newsDirectory, MyParameters.MyTDMParameters, cacheFileName);
MyExternalMDS = new SimilarityMatrix(MyTDM, cacheFileName);
SolutionSize = MyTDM.PhrasesList.Count;
var phrasesList = Execute();
TextSummary = Util.SummarizeByCompressionRatio(MyTDM, phrasesList, mySummaryParameters.MySummaryType,
MyParameters.MaximumLengthOfSummaryForRouge, out SummaryByPhrases);
}
public void SmithWatermanProteinSeqSimpleGap()
{
string sequenceString1 = "HEAGAWGHEE";
string sequenceString2 = "PAWHEAE";
Sequence sequence1 = new Sequence(Alphabets.Protein, sequenceString1);
Sequence sequence2 = new Sequence(Alphabets.Protein, sequenceString2);
SimilarityMatrix sm = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum50);
int gapPenalty = -8;
SmithWatermanAligner sw = new SmithWatermanAligner();
sw.SimilarityMatrix = sm;
sw.GapOpenCost = gapPenalty;
IList <IPairwiseSequenceAlignment> result = sw.AlignSimple(sequence1, sequence2);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"{0}, Simple; Matrix {1}; GapOpenCost {2}", sw.Name, sw.SimilarityMatrix.Name, sw.GapOpenCost));
foreach (IPairwiseSequenceAlignment sequenceResult in result)
{
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"score {0}", sequenceResult.PairwiseAlignedSequences[0].Score));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"input 0 {0}", sequenceResult.FirstSequence.ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"input 1 {0}", sequenceResult.SecondSequence.ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"result 0 {0}", sequenceResult.PairwiseAlignedSequences[0].FirstSequence.ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"result 1 {0}", sequenceResult.PairwiseAlignedSequences[0].SecondSequence.ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"consesus {0}", sequenceResult.PairwiseAlignedSequences[0].Consensus.ToString()));
}
IList <IPairwiseSequenceAlignment> expectedOutput = new List <IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
PairwiseAlignedSequence alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.Protein, "AWGHE");
alignedSeq.SecondSequence = new Sequence(Alphabets.Protein, "AW-HE");
alignedSeq.Consensus = new Sequence(Alphabets.Protein, "AWGHE");
alignedSeq.Score = 28;
alignedSeq.FirstOffset = 0;
alignedSeq.SecondOffset = 3;
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
Assert.IsTrue(CompareAlignment(result, expectedOutput));
}
public void NeedlemanWunschProteinSeqAffineGap()
{
string sequenceString1 = "HEAGAWGHEE";
string sequenceString2 = "PAWHEAE";
Sequence sequence1 = new Sequence(Alphabets.Protein, sequenceString1);
Sequence sequence2 = new Sequence(Alphabets.Protein, sequenceString2);
SimilarityMatrix sm = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum50);
int gapPenalty = -8;
NeedlemanWunschAligner nw = new NeedlemanWunschAligner();
nw.SimilarityMatrix = sm;
nw.GapOpenCost = gapPenalty;
nw.GapExtensionCost = -1;
IList <IPairwiseSequenceAlignment> result = nw.Align(sequence1, sequence2);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"{0}, Affine; Matrix {1}; GapOpenCost {2}; GapExtenstionCost {3}",
nw.Name, nw.SimilarityMatrix.Name, nw.GapOpenCost, nw.GapExtensionCost));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"score {0}", result[0].PairwiseAlignedSequences[0].Score));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"input 0 {0}", result[0].FirstSequence.ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"input 1 {0}", result[0].SecondSequence.ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"result 0 {0}", result[0].PairwiseAlignedSequences[0].FirstSequence.ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"result 1 {0}", result[0].PairwiseAlignedSequences[0].SecondSequence.ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"consesus {0}", result[0].PairwiseAlignedSequences[0].Consensus));
IList <IPairwiseSequenceAlignment> expectedOutput = new List <IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
PairwiseAlignedSequence alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.Protein, "HEAGAWGHE-E");
alignedSeq.SecondSequence = new Sequence(Alphabets.Protein, "---PAW-HEAE");
alignedSeq.Consensus = new Sequence(AmbiguousProteinAlphabet.Instance, "HEAXAWGHEAE");
alignedSeq.Score = 14;
alignedSeq.FirstOffset = 0;
alignedSeq.SecondOffset = 3;
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
Assert.IsTrue(CompareAlignment(result, expectedOutput));
}
/// <summary>
/// Performs initializations and validations required
/// before carrying out sequence alignment.
/// Initializes only gap open penalty. Initialization for
/// gap extension, if required, has to be done separately.
/// </summary>
/// <param name="similarityMatrix">Scoring matrix.</param>
/// <param name="gapPenalty">Gap open penalty (by convention, use a negative number for this.).</param>
/// <param name="inputA">First input sequence.</param>
/// <param name="inputB">Second input sequence.</param>
private void SimpleAlignPrimer(SimilarityMatrix similarityMatrix, int gapPenalty, ISequence inputA, ISequence inputB)
{
InitializeAlign(inputA);
// Set Gap Penalty and Similarity Matrix
GapOpenCost = gapPenalty;
// note that _gapExtensionCost is not used for linear gap penalty
this.InternalSimilarityMatrix = similarityMatrix;
ValidateAlignInput(inputA, inputB); // throws exception if input not valid
// Convert input strings to 0-based int arrays using similarity matrix mapping
this.FirstInputSequence = inputA;
this.SecondInputSequence = inputB;
}
public void TestProgressiveAligner()
{
ISequence templateSequence = new Sequence(Alphabets.DNA, "ATGCSWRYKMBVHDN-");
Dictionary <ISequenceItem, int> itemSet = new Dictionary <ISequenceItem, int>();
for (int i = 0; i < templateSequence.Count; ++i)
{
itemSet.Add(templateSequence[i], i);
}
Profiles.ItemSet = itemSet;
SimilarityMatrix similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrices.AmbiguousDna);
int gapOpenPenalty = -8;
int gapExtendPenalty = -1;
int kmerLength = 3;
ISequence seqA = new Sequence(Alphabets.DNA, "GGGAAAAATCAGATT");
ISequence seqB = new Sequence(Alphabets.DNA, "GGGAATCAAAATCAG");
ISequence seqC = new Sequence(Alphabets.DNA, "GGGACAAAATCAG");
List <ISequence> sequences = new List <ISequence>();
sequences.Add(seqA);
sequences.Add(seqB);
sequences.Add(seqC);
KmerDistanceMatrixGenerator kmerDistanceMatrixGenerator =
new KmerDistanceMatrixGenerator(sequences, kmerLength, MoleculeType.DNA);
kmerDistanceMatrixGenerator.GenerateDistanceMatrix(sequences);
IHierarchicalClustering hierarchicalClustering = new HierarchicalClusteringSerial(kmerDistanceMatrixGenerator.DistanceMatrix);
BinaryGuideTree tree = new BinaryGuideTree(hierarchicalClustering);
IProgressiveAligner progressiveAligner = new ProgressiveAligner(ProfileAlignerNames.NeedlemanWunschProfileAligner, similarityMatrix, gapOpenPenalty, gapExtendPenalty);
progressiveAligner.Align(sequences, tree);
ISequence expectedSeqA = new Sequence(Alphabets.DNA, "GGGA---AAAATCAGATT");
ISequence expectedSeqB = new Sequence(Alphabets.DNA, "GGGAATCAAAATCAG---");
ISequence expectedSeqC = new Sequence(Alphabets.DNA, "GGGA--CAAAATCAG---");
Assert.AreEqual(expectedSeqA.ToString(), progressiveAligner.AlignedSequences[0].ToString());
Assert.AreEqual(expectedSeqB.ToString(), progressiveAligner.AlignedSequences[1].ToString());
Assert.AreEqual(expectedSeqC.ToString(), progressiveAligner.AlignedSequences[2].ToString());
}
/// <summary>
/// Performs initializations and validations required
/// before carrying out sequence alignment.
/// Initializes only gap open penalty. Initialization for
/// gap extension, if required, has to be done seperately.
/// </summary>
/// <param name="similarityMatrix">Scoring matrix.</param>
/// <param name="gapPenalty">Gap open penalty (by convention, use a negative number for this.)</param>
/// <param name="aInput">First input sequence.</param>
/// <param name="bInput">Second input sequence.</param>
private void SimpleAlignPrimer(SimilarityMatrix similarityMatrix, int gapPenalty, ISequence aInput, ISequence bInput)
{
InitializeAlign(aInput);
ResetSpecificAlgorithmMemberVariables();
// Set Gap Penalty and Similarity Matrix
_gapOpenCost = gapPenalty;
// note that _gapExtensionCost is not used for simple gap penalty
_similarityMatrix = similarityMatrix;
ValidateAlignInput(aInput, bInput); // throws exception if input not valid
// Convert input strings to 0-based int arrays using similarity matrix mapping
_a = similarityMatrix.ToByteArray(aInput.ToString());
_b = similarityMatrix.ToByteArray(bInput.ToString());
}
/// <summary>
/// The execution method for the activity.
/// </summary>
/// <param name="executionContext">The execution context.</param>
/// <returns>The execution status.</returns>
protected override ActivityExecutionStatus Execute(ActivityExecutionContext executionContext)
{
if (MatrixName.Equals("Blosum45", StringComparison.InvariantCultureIgnoreCase))
{
Matrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum45);
}
else if (MatrixName.Equals("Blosum50", StringComparison.InvariantCultureIgnoreCase))
{
Matrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum50);
}
else if (MatrixName.Equals("Blosum62", StringComparison.InvariantCultureIgnoreCase))
{
Matrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum62);
}
else if (MatrixName.Equals("Blosum80", StringComparison.InvariantCultureIgnoreCase))
{
Matrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum80);
}
else if (MatrixName.Equals("Blosum90", StringComparison.InvariantCultureIgnoreCase))
{
Matrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum90);
}
else if (MatrixName.Equals("Pam250", StringComparison.InvariantCultureIgnoreCase))
{
Matrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Pam250);
}
else if (MatrixName.Equals("Pam30", StringComparison.InvariantCultureIgnoreCase))
{
Matrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Pam30);
}
else if (MatrixName.Equals("Pam70", StringComparison.InvariantCultureIgnoreCase))
{
Matrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Pam70);
}
else if (MatrixName.Equals("AmbiguousDna", StringComparison.InvariantCultureIgnoreCase))
{
Matrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.AmbiguousDna);
}
else if (MatrixName.Equals("AmbiguousRna", StringComparison.InvariantCultureIgnoreCase))
{
Matrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.AmbiguousRna);
}
return(ActivityExecutionStatus.Closed);
}
/// <summary>
///
/// </summary>
public NucmerPairwiseAligner()
{
// Set the default Similarity Matrix
SimilarityMatrix = new SimilarityMatrix(
SimilarityMatrix.StandardSimilarityMatrix.DiagonalScoreMatrix);
// Set the defaults
GapOpenCost = DefaultGapOpenCost;
GapExtensionCost = DefaultGapExtensionCost;
LengthOfMUM = DefaultLengthOfMUM;
// Set the ClusterBuilder properties to defaults
FixedSeparation = ClusterBuilder.DefaultFixedSeparation;
MaximumSeparation = ClusterBuilder.DefaultMaximumSeparation;
MinimumScore = ClusterBuilder.DefaultMinimumScore;
SeparationFactor = ClusterBuilder.DefaultSeparationFactor;
BreakLength = ModifiedSmithWaterman.DefaultBreakLength;
}
public static void BasicTest()
{
BidirectionalGraph gA = new BidirectionalGraph(false);
BidirectionalGraph gB = new BidirectionalGraph(false);
IVertex a1 = gA.AddVertex();
IVertex a2 = gA.AddVertex();
IVertex a3 = gA.AddVertex();
IVertex a4 = gA.AddVertex();
gA.AddEdge(a1,a2);
gA.AddEdge(a2,a3);
gA.AddEdge(a3,a1);
gA.AddEdge(a3,a4);
SimilarityMatrix similarity = new SimilarityMatrix(gA);
WriteMatrix(similarity.Matrix);
}
/// <summary>
/// Pairwise alignment of two sequences using a linear gap penalty. The various algorithms in derived classes (NeedlemanWunsch,
/// SmithWaterman, and PairwiseOverlap) all use this general engine for alignment with a linear gap penalty.
/// </summary>
/// <param name="localSimilarityMatrix">Scoring matrix.</param>
/// <param name="gapPenalty">Gap penalty (by convention, use a negative number for this.).</param>
/// <param name="inputA">First input sequence.</param>
/// <param name="inputB">Second input sequence.</param>
/// <returns>A list of sequence alignments.</returns>
public IList <IPairwiseSequenceAlignment> AlignSimple(SimilarityMatrix localSimilarityMatrix, int gapPenalty, ISequence inputA, ISequence inputB)
{
// Initialize and perform validations for simple alignment
SimpleAlignPrimer(localSimilarityMatrix, gapPenalty, inputA, inputB);
DynamicProgrammingPairwiseAlignerJob alignerJob = this.CreateSimpleAlignmentJob(inputA, inputB);
IList <IPairwiseSequenceAlignment> result = alignerJob.Align();
foreach (IPairwiseSequenceAlignment alignment in result)
{
foreach (PairwiseAlignedSequence sequence in alignment.AlignedSequences)
{
AddSimpleConsensusToResult(sequence);
}
}
return(result);
}
public void TestMuscleMultipleSequenceAlignment()
{
ISequence templateSequence = new Sequence(Alphabets.DNA, "ATGCSWRYKMBVHDN-");
Dictionary <ISequenceItem, int> itemSet = new Dictionary <ISequenceItem, int>();
for (int i = 0; i < templateSequence.Count; ++i)
{
itemSet.Add(templateSequence[i], i);
}
Profiles.ItemSet = itemSet;
SimilarityMatrix similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrices.AmbiguousDna);
int gapOpenPenalty = -8;
int gapExtendPenalty = -1;
int kmerLength = 3;
ISequence seqA = new Sequence(Alphabets.DNA, "GGGAAAAATCAGATT");
ISequence seqB = new Sequence(Alphabets.DNA, "GGGAATCAAAATCAG");
ISequence seqC = new Sequence(Alphabets.DNA, "GGGACAAAATCAG");
List <ISequence> sequences = new List <ISequence>();
sequences.Add(seqA);
sequences.Add(seqB);
sequences.Add(seqC);
DistanceFunctionTypes distanceFunctionName = DistanceFunctionTypes.EuclieanDistance;
UpdateDistanceMethodsTypes hierarchicalClusteringMethodName = UpdateDistanceMethodsTypes.Aaverage;
ProfileAlignerNames profileAlignerName = ProfileAlignerNames.NeedlemanWunschProfileAligner;
ProfileScoreFunctionNames profileProfileFunctionName = ProfileScoreFunctionNames.WeightedInnerProduct;
MuscleMultipleSequenceAlignment msa = new MuscleMultipleSequenceAlignment
(sequences, MoleculeType.DNA, kmerLength, distanceFunctionName, hierarchicalClusteringMethodName,
profileAlignerName, profileProfileFunctionName, similarityMatrix, gapOpenPenalty, gapExtendPenalty);
ISequence expectedSeqA = new Sequence(Alphabets.DNA, "GGGA---AAAATCAGATT");
ISequence expectedSeqB = new Sequence(Alphabets.DNA, "GGGAATCAAAATCAG---");
ISequence expectedSeqC = new Sequence(Alphabets.DNA, "GGGA--CAAAATCAG---");
Assert.AreEqual(expectedSeqA.ToString(), msa.AlignedSequences[0].ToString());
Assert.AreEqual(expectedSeqB.ToString(), msa.AlignedSequences[1].ToString());
Assert.AreEqual(expectedSeqC.ToString(), msa.AlignedSequences[2].ToString());
Assert.AreEqual(46, msa.AlignmentScore);
}
public static void BasicTest()
{
BidirectionalGraph gA = new BidirectionalGraph(false);
BidirectionalGraph gB = new BidirectionalGraph(false);
IVertex a1 = gA.AddVertex();
IVertex a2 = gA.AddVertex();
IVertex a3 = gA.AddVertex();
IVertex a4 = gA.AddVertex();
gA.AddEdge(a1, a2);
gA.AddEdge(a2, a3);
gA.AddEdge(a3, a1);
gA.AddEdge(a3, a4);
SimilarityMatrix similarity = new SimilarityMatrix(gA);
WriteMatrix(similarity.Matrix);
}
