本文整理汇总了Java中org.biojava.nbio.alignment.template.PairwiseSequenceAligner类的典型用法代码示例。如果您正苦于以下问题：Java PairwiseSequenceAligner类的具体用法？Java PairwiseSequenceAligner怎么用？Java PairwiseSequenceAligner使用的例子？那么, 这里精选的类代码示例或许可以为您提供帮助。
PairwiseSequenceAligner类属于org.biojava.nbio.alignment.template包，在下文中一共展示了PairwiseSequenceAligner类的13个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Java代码示例。
示例1: filterSequenceSimilar
import org.biojava.nbio.alignment.template.PairwiseSequenceAligner; //导入依赖的package包/类
/**
* Filter the {@link SegmentDataRDD} based on minimum sequence similarity to a reference sequence.
* @param inputSequence the reference sequence to compare
* @param minSimilarity the minimum similarity (as a double between 0.00 and 1.00)
* @return the {@link SegmentDataRDD} after being filtered
* @throws CompoundNotFoundException if Biojava cannot accurately convert the String sequence to a {@link ProteinSequence}
*/
public static SegmentDataRDD filterSequenceSimilar(SegmentDataRDD segmentDataRDD, String inputSequence, double minSimilarity) throws CompoundNotFoundException {
ProteinSequence proteinSequence = new ProteinSequence(inputSequence);
// First set up the environment
int gop = 8;
int extend = 1;
GapPenalty penalty = new SimpleGapPenalty();
penalty.setOpenPenalty(gop);
penalty.setExtensionPenalty(extend);
SubstitutionMatrix<AminoAcidCompound> matrix = SubstitutionMatrixHelper.getBlosum65();
return new SegmentDataRDD(segmentDataRDD.getSegmentRDD().filter(t -> {
ProteinSequence otherSequence = new ProteinSequence(t._2.getSequence());
PairwiseSequenceAligner<ProteinSequence, AminoAcidCompound> smithWaterman =
Alignments.getPairwiseAligner(proteinSequence, otherSequence, PairwiseSequenceAlignerType.LOCAL, penalty, matrix);
if(smithWaterman.getSimilarity()<minSimilarity){
return false;
}
return true;
}));
}
示例2: testComplex
import org.biojava.nbio.alignment.template.PairwiseSequenceAligner; //导入依赖的package包/类
@Test
public void testComplex() throws Exception {
short match = 2, gop = -5, gep = -3; // 2, 5, and 3 are coprime; -2 is the mismatch score
SimpleSubstitutionMatrix<NucleotideCompound> mx = new SimpleSubstitutionMatrix<NucleotideCompound>(new DNACompoundSet(), match, (short)-match);
DNASequence a = new DNASequence("CGTAT ATATCGCGCGCGCGATATATATATCT TCTCTAAAAAAA".replaceAll(" ", ""));
DNASequence b = new DNASequence("GGTATATATATCGCGCGCACGAT TATATATCTCTCTCTAAAAAAA".replaceAll(" ", ""));
// --CGTATATATCGCGCGCGCGATATATATATCT-TCTCTAAAAAAA
// GGTATATATATCGCGCGCACGAT-TATATATCTCTCTCTAAAAAAA
// mismatches: ^ ^
// The two alignments should have the same score. The bottom one is the one the aligner found.
PairwiseSequenceAligner<DNASequence, NucleotideCompound> aligner = Alignments.getPairwiseAligner(a, b, Alignments.PairwiseSequenceAlignerType.GLOBAL, new SimpleGapPenalty(gop, gep), mx);
SequencePair<DNASequence, NucleotideCompound> pair = aligner.getPair();
int nMatches = "--CGTATATATCGCGCGCGCGATATATATATCT-TCTCTAAAAAAA".length() - 2 - 4;
double expectedScore = nMatches * match
- 2 * match // there are two mismatches
+ 3 * gop + 4 * gep; // there are 3 gap opens and either 1 or 4 extensions, depending on the def
assertEquals(expectedScore, aligner.getScore(), 0.00000001);
}
示例3: align
import org.biojava.nbio.alignment.template.PairwiseSequenceAligner; //导入依赖的package包/类
@Nonnull
public SequenceAlignment<S, C> align(@Nonnull S a, @Nonnull S b) {
PairwiseSequenceAligner<S, C> aligner = Alignments.getPairwiseAligner(a, b, m_type, m_gapPenalty, m_matrix);
//noinspection ConstantConditions
if (aligner == null) {
throw new RuntimeException("Couldn't create aligner; something is wrong in Biojava");
}
// this actually performs the alignment; do it first
SequencePair<S, C> pair = aligner.getPair();
return new SequenceAlignment<>(toIntExact(aligner.getScore()), aligner.getSimilarity(), pair);
}
示例4: shouldAllowZeroLengthMatches
import org.biojava.nbio.alignment.template.PairwiseSequenceAligner; //导入依赖的package包/类
@Test
public void shouldAllowZeroLengthMatches() throws CompoundNotFoundException {
DNASequence query = new DNASequence("C", DNACompoundSet.getDNACompoundSet());
DNASequence target = new DNASequence("A", DNACompoundSet.getDNACompoundSet());
SubstitutionMatrix<NucleotideCompound> matrix = SubstitutionMatrixHelper.getNuc4_4();
SimpleGapPenalty gapP = new SimpleGapPenalty((short)5, (short)2);
PairwiseSequenceAligner<DNASequence, NucleotideCompound> result = Alignments.getPairwiseAligner(query, target, PairwiseSequenceAlignerType.LOCAL, gapP, matrix);
assertEquals(0, result.getScore(), PRECISION);
assertEquals(0, result.getProfile().getLength());
}
示例5: testNoAlignedBases
import org.biojava.nbio.alignment.template.PairwiseSequenceAligner; //导入依赖的package包/类
/**
* @author Daniel Cameron
*/
public void testNoAlignedBases() throws CompoundNotFoundException {
DNASequence target = new DNASequence("A", DNACompoundSet.getDNACompoundSet());
DNASequence query = new DNASequence("T", DNACompoundSet.getDNACompoundSet());
SubstitutionMatrix<NucleotideCompound> matrix = SubstitutionMatrixHelper.getNuc4_4();
SimpleGapPenalty gapP = new SimpleGapPenalty((short)0, (short)1);
PairwiseSequenceAligner<DNASequence, NucleotideCompound> aligner = Alignments.getPairwiseAligner(query, target, PairwiseSequenceAlignerType.GLOBAL, gapP, matrix);
assertEquals(2, aligner.getPair().getLength());
}
示例6: testLinearAlignment
import org.biojava.nbio.alignment.template.PairwiseSequenceAligner; //导入依赖的package包/类
/**
* @author Daniel Cameron
*/
public void testLinearAlignment() throws CompoundNotFoundException {
DNASequence query = new DNASequence("GTAAAAG", DNACompoundSet.getDNACompoundSet());
DNASequence target = new DNASequence("GAAAACGTTTTTTTTTT", DNACompoundSet.getDNACompoundSet());
SubstitutionMatrix<NucleotideCompound> matrix = SubstitutionMatrixHelper.getNuc4_4();
SimpleGapPenalty gapP = new SimpleGapPenalty((short)0, (short)3);
PairwiseSequenceAligner<DNASequence, NucleotideCompound> aligner = Alignments.getPairwiseAligner(query, target, PairwiseSequenceAlignerType.GLOBAL, gapP, matrix);
assertEquals(String.format("GTAAAA-G----------%nG-AAAACGTTTTTTTTTT%n"), aligner.getPair().toString());;
}
示例7: main
import org.biojava.nbio.alignment.template.PairwiseSequenceAligner; //导入依赖的package包/类
public static void main(String[] args) throws Exception {
String query = "AGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGTGAAGCCCAGCTTGCTGGGTGGATCA" +
"GTGGCGAACGGGTGAGTAACACGTGAGCAACCTGCCCCTGACTCTGGGATAAGCGCTGGAAACGGTGTCT" +
"AATACTGGATATGAGCTACCACCGCATGGTGAGTGGTTGGAAAGATTTTTCGGTTGGGGATGGGCTCGCG" +
"GCCTATCAGCTTGTTGGTGAGGTAATGGCTCACCAAGGCGTCGACGGGTAGCCGGCCTGAGAGGGTGACC" +
"GGCCACACTGGGACTGAGACACGGCCCAGACTCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGC" +
"GGAAGCCTGATGCAGCAACGCCGCGTGAGGGACGACGGCTTCGGGTTGTAAACCTCTTTTAGCAGGGAAG" +
"AAGCGAGAGTGACGGTACCTGCAGAAAAAGCGCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAG" +
"GGCGCAAGCGTTATCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGTTTGTCGCGTCTGCTGTGAAAA" +
"CCCGAGGCTCAACCTNNGGGCTGCAGTGGGTACGGGCAGACTAGAGTGCGGTAGGGGAGATTGGAATTCC" +
"TGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGATCTCTGGGCCGTAAC" +
"TGACGCTGAGGAGCGAAAGGGTGGGGAGCAAACAGGCTTAGATACCCTGGTAGTCCACCCCGTAAACGTT" +
"GGGAACTAGTTGTGGGGTCCTTTCCACGGATTCCGTGACGCACGTAACGCATTAAGTTCCCCGCCTGGGG" +
"AGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGCGGAGCATGCGGATTA" +
"AATCGATGCAACGCGAAGAACCTTACCAAGGCTTGACATACACGAGAACGCTGCAGAAATGTAGAACTCT" +
"TTGGACACTCGTGAACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCG" +
"CAACGAGCGCAACCCTCGTTCTATGTTGCCAGCACGTAATGGTGGGAACTCATGGGATACTGCCGGGGTC" +
"AACTCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGTCTTGGGCTTCACGCATGCTACA" +
"ATGGCCGGTACAAAGGGCTGCAATACCGTGAGGTGGAGCGAATCCCAAAAAGCCGGTCCCAGTTCGGATT" +
"GAGGTCTGCAACTCGACCTCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATA" +
"CGTTCCCGGGTCTTGTACACACCGCCCGTCAAGTCATGAAAGTCGGTAACACCTGAAGCCGGTGGCCTAA" +
"CCCTTGTGGAGGGAGCCGGTAATTAAA";
String target = "CTGGCCGCCTGCTTAACACATCCAAGTCGAACGGTGAAGCCCCANCTTACTGGGTGGATCAGTGCCGAAC" +
"GGGTGAGTAACACGTGAGCAACCTCCCCCTGACTCTGGGATAAGCGCTGGAANCGGTGTCTAATACTGGA" +
"TATGAGCTACCACCGCATGGTGAGTGGTTGGAAAGATTTTTCGGTTGGGGATGGGCTCGCGCCCTATGAG" +
"CTTGTTGGTGAGGTAATGGCTCACCAAGCCGTCGACGGGTAGCCGGCCTGAGAGGGTGACCGNCCACACT" +
"GGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGGAAGCCT" +
"GATTCANCAACCCCGCGTGAGGGACGACGGCCTTCGGGTTGTAAACCTCTTTTAGCAGGGAAGAAGCGAG" +
"AGTGACGGTACCTGCAGAAAAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGCGCAA" +
"GCGTTATCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGTTTGTCGCGTCTGCTGTGAAAACCCGAGG" +
"CTCAACCTCGGGCCTGCAGTGGGTACGGGCAGACTAGAGTGCGGTAGGGGAGATTGGAATTCCTGGTGTA" +
"GCGGTGGAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGATCTCTGGGCCGTAACTGACGCT" +
"GAGGAGCGAAAGGGTGGGGAGCAAACAGGCTTAGATACCCTGGTAGTCCACCCCGTAAACGTTGGGAACT" +
"AGTTGTGGGGTCCTTTCCACGGATTCCGTGACGCAGCTAACGCATTAAGTTCCCCGCCTGGGGAGTACGG" +
"CCGCAAGGCTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGCGGAGCATGCGGATTAATTCGAT" +
"GCAACGCGAAGAACCTTACCAAGGCTTGACATACACGAGAACGCTGCAGAAATGTAGAACTCTTTGGACA" +
"CTCGTGAACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAG" +
"CGCAACCCTCGTTCTATGTTGCCAGCACGTAATGGTGGGAACTCATGGGATACTGCCGGGGTCAACTCGG" +
"AGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGTCTTGGGCTTCACGCATGCTACAATGGCCG" +
"GTACAAAGGGCTGCAATACCGTGAGGTGGAGCGAATCCCAAAAAGCCGGTCCCAGTTCGGATTGAGGTCT" +
"GCAACTCGACCTCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCC" +
"GGGTCTTGTACACACCGCCCGTCAAGTCATGAAAGTCGGTAACACCTGAAGCCGGTGGCCCAACCCTTGT" +
"GGAGGGAGCCGTCGAAGGTGGGATCGGTAATTAGGACTAAGTCGTAACAAGGTAGCCGTACC";
GapPenalty penalty = new SimpleGapPenalty(-14, -4);
PairwiseSequenceAligner<DNASequence, NucleotideCompound> aligner = Alignments.getPairwiseAligner(
new DNASequence(query, AmbiguityDNACompoundSet.getDNACompoundSet()),
new DNASequence(target, AmbiguityDNACompoundSet.getDNACompoundSet()),
PairwiseSequenceAlignerType.GLOBAL,
penalty, SubstitutionMatrixHelper.getNuc4_4());
SequencePair<DNASequence, NucleotideCompound>
alignment = aligner.getPair();
System.out.println("Alignment: "+ alignment);
int identical = alignment.getNumIdenticals();
System.out.println("Number of identical residues: "+ identical);
System.out.println("% identical query: "+ identical / (float) query.length());
System.out.println("% identical target: "+ identical / (float) target.length());
}
示例8: alignProtein
import org.biojava.nbio.alignment.template.PairwiseSequenceAligner; //导入依赖的package包/类
private static SequencePair<ProteinSequence, AminoAcidCompound> alignProtein(ProteinSequence s1, ProteinSequence s2) {
SubstitutionMatrix<AminoAcidCompound> matrix = SubstitutionMatrixHelper.getIdentity();
GapPenalty penalty = new SimpleGapPenalty(8, 1);
PairwiseSequenceAligner<ProteinSequence, AminoAcidCompound> nw =
Alignments.getPairwiseAligner(s1, s2, PairwiseSequenceAlignerType.GLOBAL, penalty, matrix);
return nw.getPair();
}
示例9: alignDNA
import org.biojava.nbio.alignment.template.PairwiseSequenceAligner; //导入依赖的package包/类
private static SequencePair<DNASequence, NucleotideCompound> alignDNA(DNASequence s1, DNASequence s2) {
SubstitutionMatrix<NucleotideCompound> matrix = SubstitutionMatrixHelper.getNuc4_4();
GapPenalty penalty = new SimpleGapPenalty(8, 1);
PairwiseSequenceAligner<DNASequence, NucleotideCompound> nw =
Alignments.getPairwiseAligner(s1, s2, PairwiseSequenceAlignerType.GLOBAL, penalty, matrix);
return nw.getPair();
}
示例10: alignRNA
import org.biojava.nbio.alignment.template.PairwiseSequenceAligner; //导入依赖的package包/类
private static SequencePair<RNASequence, NucleotideCompound> alignRNA(RNASequence s1, RNASequence s2) {
SubstitutionMatrix<NucleotideCompound> matrix = SubstitutionMatrixHelper.getNuc4_4();
GapPenalty penalty = new SimpleGapPenalty(8, 1);
PairwiseSequenceAligner<RNASequence, NucleotideCompound> nw =
Alignments.getPairwiseAligner(s1, s2, PairwiseSequenceAlignerType.GLOBAL, penalty, matrix);
return nw.getPair();
}
示例11: main
import org.biojava.nbio.alignment.template.PairwiseSequenceAligner; //导入依赖的package包/类
public static void main(String[] args) throws Exception {
String uniprotID1 = "P69905";
String uniprotID2 = "P68871";
ProteinSequence s1 = getSequenceForId(uniprotID1);
ProteinSequence s2 = getSequenceForId(uniprotID2);
SubstitutionMatrix<AminoAcidCompound> matrix = SubstitutionMatrixHelper.getBlosum65();
GapPenalty penalty = new SimpleGapPenalty();
int gop = 8;
int extend = 1;
penalty.setOpenPenalty(gop);
penalty.setExtensionPenalty(extend);
PairwiseSequenceAligner<ProteinSequence, AminoAcidCompound> smithWaterman =
Alignments.getPairwiseAligner(s1, s2, PairwiseSequenceAlignerType.LOCAL, penalty, matrix);
SequencePair<ProteinSequence, AminoAcidCompound> pair = smithWaterman.getPair();
System.out.println(pair.toString(60));
}
示例12: call
import org.biojava.nbio.alignment.template.PairwiseSequenceAligner; //导入依赖的package包/类
@Override
public Tuple5<String,String,Float,Float,Float> call(Tuple2<Tuple2<String,String>,Tuple2<String,String>> tuple) throws Exception {
Tuple2<String,String> p1 = tuple._1();
Tuple2<String,String> p2 = tuple._2();
SubstitutionMatrix matrix = SubstitutionMatrixHelper.getBlosum65();
GapPenalty penalty = new SimpleGapPenalty();
penalty.setOpenPenalty(8);
penalty.setExtensionPenalty(1);
ProteinSequence prot1 = new ProteinSequence(p1._2());
ProteinSequence prot2 = new ProteinSequence(p2._2());
try {
PairwiseSequenceAligner<ProteinSequence, AminoAcidCompound> smithWaterman =
Alignments.getPairwiseAligner(
prot1,
prot2,
Alignments.PairwiseSequenceAlignerType.LOCAL,
penalty,
matrix);
SequencePair<ProteinSequence, AminoAcidCompound> alignment = smithWaterman.getPair();
if ( debug )
System.out.println(alignment.toString(60));
int numIdenticals = alignment.getNumIdenticals();
int aligLength = alignment.getLength();
float percentIdenticals = (numIdenticals / (float) aligLength);
// test overlaps
int l1 = prot1.getLength();
int l2 = prot2.getLength();
int size = alignment.getLength();
AlignedSequence alignedSequence1 = alignment.getAlignedSequence(1);
AlignedSequence alignedSequence2 = alignment.getAlignedSequence(2);
String alignedSeq1 = alignedSequence1.getSequenceAsString().replaceAll("-","");
String alignedSeq2 = alignedSequence2.getSequenceAsString().replaceAll("-","");
int size1 = alignedSeq1.length();
int size2 = alignedSeq2.length();
float overlap1 = size1 / (float) l1;
float overlap2 = size2 / (float) l2;
if ( debug )
System.out.println(p1._1() + " " + p2._1() + " size:" + size + " l1: " + l1 + " l2: " + l2 + " overlap1 " + overlap1 + " overlap2 " + overlap2 + " %id: " + percentIdenticals);
return new Tuple5<String, String, Float,Float,Float>(p1._1(),p2._1(),overlap1,overlap2,percentIdenticals);
} catch (Exception e) {
System.err.println("Could not align " + p1._1() + " vs." + p2._1());
}
return new Tuple5<String, String, Float,Float,Float>(p1._1(),p2._1(),0f,0f,0f);
}
示例13: call
import org.biojava.nbio.alignment.template.PairwiseSequenceAligner; //导入依赖的package包/类
@Override
public Tuple5<String,String,Float,Float,Float> call(Tuple2<Tuple2<String,String>,Tuple2<String,String>> tuple) throws Exception {
Tuple2<String,String> p1 = tuple._1();
Tuple2<String,String> p2 = tuple._2();
SubstitutionMatrix<AminoAcidCompound> matrix = SubstitutionMatrixHelper.getBlosum65();
GapPenalty penalty = new SimpleGapPenalty();
penalty.setOpenPenalty(8);
penalty.setExtensionPenalty(1);
ProteinSequence prot1 = new ProteinSequence(p1._2());
ProteinSequence prot2 = new ProteinSequence(p2._2());
try {
PairwiseSequenceAligner<ProteinSequence, AminoAcidCompound> smithWaterman = Alignments.getPairwiseAligner(prot1,
prot2,
Alignments.PairwiseSequenceAlignerType.LOCAL, penalty, matrix);
SequencePair<ProteinSequence, AminoAcidCompound> alignment = smithWaterman.getPair();
if ( debug )
System.out.println(alignment.toString(60));
int numIdenticals = alignment.getNumIdenticals();
int aligLength = alignment.getLength();
float percentIdenticals = (numIdenticals / (float) aligLength);
// test overlaps
int l1 = prot1.getLength();
int l2 = prot2.getLength();
int size = alignment.getLength();
float overlap1 = l1 / (float) size;
float overlap2 = l2 / (float) size;
if ( debug )
System.out.println(p1._1() + " " + p2._1() + " size:" + size + " l1: " + l1 + " l2: " + l2 + " overlap1 " + overlap1 + " overlap2 " + overlap2 + " %id: " + percentIdenticals);
return new Tuple5<String, String, Float,Float,Float>(p1._1(),p2._1(),overlap1,overlap2,percentIdenticals);
} catch (Exception e) {
e.printStackTrace();
}
return new Tuple5<String, String, Float,Float,Float>(p1._1(),p2._1(),0f,0f,0f);
}