本文整理汇总了Java中org.biojava.nbio.alignment.SimpleGapPenalty类的典型用法代码示例。如果您正苦于以下问题:Java SimpleGapPenalty类的具体用法?Java SimpleGapPenalty怎么用?Java SimpleGapPenalty使用的例子?那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
SimpleGapPenalty类属于org.biojava.nbio.alignment包,在下文中一共展示了SimpleGapPenalty类的20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,您的评价将有助于我们的系统推荐出更棒的Java代码示例。
示例1: filterSequenceSimilar
import org.biojava.nbio.alignment.SimpleGapPenalty; //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;
}));
}
开发者ID:biojava,项目名称:biojava-spark,代码行数:27,代码来源:BiojavaSparkUtils.java
示例2: swAlignment
import org.biojava.nbio.alignment.SimpleGapPenalty; //导入依赖的package包/类
private void swAlignment() throws CompoundNotFoundException {
ProteinSequence s1 = new ProteinSequence(query);
s1.setAccession(new AccessionID("Query"));
ProteinSequence s2 = new ProteinSequence(subject);
s2.setAccession(new AccessionID("Subject"));
SubstitutionMatrix<AminoAcidCompound> matrix
= SimpleSubstitutionMatrix.getBlosum62();
alignment = Alignments.getPairwiseAlignment(s1, s2,
Alignments.PairwiseSequenceAlignerType.LOCAL,
new SimpleGapPenalty(), matrix);
FractionalSimilarityScorer<ProteinSequence, AminoAcidCompound> scorer =
new FractionalSimilarityScorer<>(alignment);
score = scorer.getScore();
}
开发者ID:CameronTolooee,项目名称:Mendel,代码行数:21,代码来源:SmithWaterman.java
示例3: setUpBefore
import org.biojava.nbio.alignment.SimpleGapPenalty; //导入依赖的package包/类
@BeforeClass
public static void setUpBefore() throws URISyntaxException {
sf_matrix = new SimpleSubstitutionMatrix<>(AmbiguityDNACompoundSet.getDNACompoundSet(), (short)sf_m, (short)-sf_m);
sf_gapPenalty = new SimpleGapPenalty(5, 3); // and sf_m==2, so they're all coprime
sf_gop = sf_gapPenalty.getOpenPenalty();
sf_gep = sf_gapPenalty.getExtensionPenalty();
}
开发者ID:dmyersturnbull,项目名称:sequence-alignment,代码行数:8,代码来源:SequenceAlignerTest.java
示例4: testAdjacentGaps
import org.biojava.nbio.alignment.SimpleGapPenalty; //导入依赖的package包/类
@Test // TODO Biojava is even more wrong
public void testAdjacentGaps() throws Exception {
DNASequence a = new DNASequence("AAATTT CCCATTT".replaceAll(" ", ""));
DNASequence b = new DNASequence("AAA GGGCCCATTT".replaceAll(" ", ""));
GapPenalty gapPenalty = new SimpleGapPenalty(0, 0);
@SuppressWarnings("unchecked")
SequenceAligner<DNASequence, NucleotideCompound> aligner = new SequenceAligner.Builder<>(sf_matrix, Alignments.PairwiseSequenceAlignerType.GLOBAL, DNASequence::new).setGapPenalty(gapPenalty).build();
int scoreA = aligner.align(a, b).getScore();
assertEquals(sf_m * "AAA".length() + sf_m * "CCCATTT".length() + 2 * sf_gop - 5 * sf_gep, scoreA);
int score = aligner.alignFast(a, b);
assertEquals(sf_m * "AAA".length() + sf_m * "CCCATTT".length() + 2 * sf_gop - 5 * sf_gep, score);
}
开发者ID:dmyersturnbull,项目名称:sequence-alignment,代码行数:13,代码来源:SequenceAlignerTest.java
示例5: call
import org.biojava.nbio.alignment.SimpleGapPenalty; //导入依赖的package包/类
@Override
public double[] call() throws Exception
{
List<ProteinSequence> sequences = Lists.newArrayList(new ProteinSequence(pair_.getQuery().getValue()),
new ProteinSequence(pair_.getTarget().getValue()));
return Alignments.getAllPairsScores(sequences, PairwiseSequenceScorerType.LOCAL, new SimpleGapPenalty(), getBlosum65());
}
开发者ID:alessandroleite,项目名称:dohko,代码行数:9,代码来源:LocalPairsScoreCallable.java
示例6: alignPairLocal
import org.biojava.nbio.alignment.SimpleGapPenalty; //导入依赖的package包/类
private static void alignPairLocal(String id1, String id2) throws Exception {
ProteinSequence s1 = new ProteinSequence("METSSSLPLSPISIEPEQPSHRDYDITTRRGVGTTGNPIELCTNHFNVSVRQPDVVFYQY" +
"TVSITTENGDAVDGTGISRKLMDQLFKTYSSDLDGKRLAYDGEKTLYTVGPLPQNEFDFL" +
"VIVEGSFSKRDCGVSDGGSSSGTCKRSKRSFLPRSYKVQIHYAAEIPLKTVLGTQRGAYT" +
"PDKSAQDALRVLDIVLRQQAAERGCLLVRQAFFHSDGHPMKVGGGVIGIRGLHSSFRPTH" +
"GGLSLNIDVSTTMILEPGPVIEFLKANQSVETPRQIDWIKAAKMLKHMRVKATHRNMEFK" +
"IIGLSSKPCNQQLFSMKIKDGEREVPIREITVYDYFKQTYTEPISSAYFPCLDVGKPDRP" +
"NYLPLEFCNLVSLQRYTKPLSGRQRVLLVESSRQKPLERIKTLNDAMHTYCYDKDPFLAG" +
"CGISIEKEMTQVEGRVLKPPMLKFGKNEDFQPCNGRWNFNNKMLLEPRAIKSWAIVNFSF" +
"PCDSSHISRELISCGMRKGIEIDRPFALVEEDPQYKKAGPVERVEKMIATMKLKFPDPPH" +
"FILCILPERKTSDIYGPWKKICLTEEGIHTQCICPIKISDQYLTNVLLKINSKLGGINSL" +
"LGIEYSYNIPLINKIPTLILGMDVSHGPPGRADVPSVAAVVGSKCWPLISRYRAAVRTQS" +
"PRLEMIDSLFQPIENTEKGDNGIMNELFVEFYRTSRARKPKQIIIFRDGVSESQFEQVLK" +
"IEVDQIIKAYQRLGESDVPKFTVIVAQKNHHTKLFQAKGPENVPAGTVVDTKIVHPTNYD" +
"FYMCAHAGKIGTSRPAHYHVLLDEIGFSPDDLQNLIHSLSYVNQRSTTATSIVAPVRYAH" +
"LAAAQVAQFTKFEGISEDGKVPELPRLHENVEGNMFFC");
ProteinSequence s2 = new ProteinSequence("MDLLDKVMGEMGSKPGSTAKKPATSASSTPRTNVWGTAKKPSSQQQPPKPLFTTPGSQQG" +
"SLGGRIPKREHTDRTGPDPKRKPLGGLSVPDSFNNFGTFRVQMNAWNLDISKMDERISRI" +
"MFRATLVHTDGRRFELSLGVSAFSGDVNRQQRRQAQCLLFRAWFKRNPELFKGMTDPAIA" +
"AYDAAETIYVGCSFFDVELTEHVCHLTEADFSPQEWKIVSLISRRSGSTFEIRIKTNPPI" +
"YTRGPNALTLENRSELTRIIEAITDQCLHNEKFLLYSSGTFPTKGGDIASPDEVTLIKSG" +
"FVKTTKIVDRDGVPDAIMTVDTTKSPFYKDTSLLKFFTAKMDQLTNSGGGPRGHNGGRER" +
"RDGGGNSRKYDDRRSPRDGEIDYDERTVSHYQRQFQDERISDGMLNTLKQSLKGLDCQPI" +
"HLKDSKANRSIMIDEIHTGTADSVTFEQKLPDGEMKLTSITEYYLQRYNYRLKFPHLPLV" +
"TSKRAKCYDFYPMELMSILPGQRIKQSHMTVDIQSYMTGKMSSLPDQHIKQSKLVLTEYL" +
"KLGDQPANRQMDAFRVSLKSIQPIVTNAHWLSPPDMKFANNQLYSLNPTRGVRFQTNGKF" +
"VMPARVKSVTIINYDKEFNRNVDMFAEGLAKHCSEQGMKFDSRPNSWKKVNLGSSDRRGT" +
"KVEIEEAIRNGVTIVFGIIAEKRPDMHDILKYFEEKLGQQTIQISSETADKFMRDHGGKQ" +
"TIDNVIRKLNPKCGGTNFLIDVPESVGHRVVCNNSAEMRAKLYAKTQFIGFEMSHTGART" +
"RFDIQKVMFDGDPTVVGVAYSLKHSAQLGGFSYFQESRLHKLTNLQEKMQICLNAYEQSS" +
"SYLPETVVVYRVGSGEGDYPQIVNEVNEMKLAARKKKHGYNPKFLVICTQRNSHIRVFPE" +
"HINERGKSMEQNVKSGTCVDVPGASHGYEEFILCCQTPLIGTVKPTKYTIIVNDCRWSKN" +
"EIMNVTYHLAFAHQVSYAPPAIPNVSYAAQNLAKRGHNNYKTHTKLVDMNDYSYRIKEKH" +
"EEIISSEEVDDILMRDFIETVSNDLNAMTINGRNFWA");
SubstitutionMatrix<AminoAcidCompound> matrix = SimpleSubstitutionMatrix.getBlosum62();
SequencePair<ProteinSequence, AminoAcidCompound> pair = Alignments.getPairwiseAlignment(s1, s2,
Alignments.PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(), matrix);
System.out.printf("%n%s vs %s%n%s", pair.getQuery().getAccession(), pair.getTarget().getAccession(), pair);
}
开发者ID:CameronTolooee,项目名称:Mendel,代码行数:40,代码来源:ProteinAlignment.java
示例7: setup
import org.biojava.nbio.alignment.SimpleGapPenalty; //导入依赖的package包/类
@Before
public void setup() throws CompoundNotFoundException {
query = new ProteinSequence("ARND");
target = new ProteinSequence("RDG");
gaps = new SimpleGapPenalty(10, 1);
blosum62 = SubstitutionMatrixHelper.getBlosum62();
alignment = new GuanUberbacher<ProteinSequence, AminoAcidCompound>(query, target, gaps, blosum62);
self = new GuanUberbacher<ProteinSequence, AminoAcidCompound>(query, query, gaps, blosum62);
}
开发者ID:biojava,项目名称:biojava,代码行数:10,代码来源:GuanUberbacherTest.java
示例8: should_align_shorter_query
import org.biojava.nbio.alignment.SimpleGapPenalty; //导入依赖的package包/类
/**
* @author Daniel Cameron
*/
@Test
public void should_align_shorter_query() throws CompoundNotFoundException {
DNASequence query = new DNASequence("A", AmbiguityDNACompoundSet.getDNACompoundSet());
DNASequence target = new DNASequence("AT", AmbiguityDNACompoundSet.getDNACompoundSet());
GuanUberbacher<DNASequence, NucleotideCompound> aligner = new GuanUberbacher<DNASequence, NucleotideCompound>(query, target, new SimpleGapPenalty((short)5, (short)2), SubstitutionMatrixHelper.getNuc4_4());
assertEquals(String.format("A-%nAT%n"), aligner.getPair().toString());
}
开发者ID:biojava,项目名称:biojava,代码行数:11,代码来源:GuanUberbacherTest.java
示例9: should_align_shorter_target
import org.biojava.nbio.alignment.SimpleGapPenalty; //导入依赖的package包/类
/**
* @author Daniel Cameron
*/
@Test
public void should_align_shorter_target() throws CompoundNotFoundException {
DNASequence query = new DNASequence("AT", AmbiguityDNACompoundSet.getDNACompoundSet());
DNASequence target = new DNASequence("A", AmbiguityDNACompoundSet.getDNACompoundSet());
GuanUberbacher<DNASequence, NucleotideCompound> aligner = new GuanUberbacher<DNASequence, NucleotideCompound>(query, target, new SimpleGapPenalty((short)5, (short)2), SubstitutionMatrixHelper.getNuc4_4());
assertEquals(String.format("AT%nA-%n"), aligner.getPair().toString());
}
开发者ID:biojava,项目名称:biojava,代码行数:11,代码来源:GuanUberbacherTest.java
示例10: should_align_multiple_cuts
import org.biojava.nbio.alignment.SimpleGapPenalty; //导入依赖的package包/类
/**
* @author Daniel Cameron
*/
@Test
public void should_align_multiple_cuts() throws CompoundNotFoundException {
DNASequence query = new DNASequence("AAT", AmbiguityDNACompoundSet.getDNACompoundSet());
DNASequence target = new DNASequence("AATG", AmbiguityDNACompoundSet.getDNACompoundSet());
GuanUberbacher<DNASequence, NucleotideCompound> aligner = new GuanUberbacher<DNASequence, NucleotideCompound>(query, target, new SimpleGapPenalty((short)0, (short)2), SubstitutionMatrixHelper.getNuc4_4());
aligner.setCutsPerSection(2); // 3 bases with 2 cuts
assertEquals(String.format("AAT-%nAATG%n"), aligner.getPair().toString());
}
开发者ID:biojava,项目名称:biojava,代码行数:12,代码来源:GuanUberbacherTest.java
示例11: setup
import org.biojava.nbio.alignment.SimpleGapPenalty; //导入依赖的package包/类
@Before
public void setup() throws CompoundNotFoundException {
protein1 = new ProteinSequence("ARND");
protein2 = new ProteinSequence("ARND");
protein3 = new ProteinSequence("HILK");
protein4 = new ProteinSequence("ANDR");
gaps = new SimpleGapPenalty((short) 2, (short) 1);
blosum62 = SubstitutionMatrixHelper.getBlosum62();
pair1 = new NeedlemanWunsch<ProteinSequence, AminoAcidCompound>(protein1, protein2, gaps, blosum62).getPair();
pair2 = new NeedlemanWunsch<ProteinSequence, AminoAcidCompound>(protein3, protein4, gaps, blosum62).getPair();
}
开发者ID:biojava,项目名称:biojava,代码行数:12,代码来源:SimpleProfilePairTest.java
示例12: smithWaterman
import org.biojava.nbio.alignment.SimpleGapPenalty; //导入依赖的package包/类
@GET
@Produces(MediaType.APPLICATION_JSON)
@Path("/verse/algin/sw/{chapterNo}/{verseNo}/{threshold}")
public Response smithWaterman(@PathParam("chapterNo") int chapterNo, @PathParam("verseNo") int verseNo, @PathParam("threshold") int threshold) {
int MATCH_SCORE = 3;
ResultList<Verse, Double> scores = new ResultList<>();
Verse verse = managersSet.getVerseManager().get(chapterNo, verseNo);
List<Root> mainRootList = VerseUtils.getRootList(verse);
Verse nextVerse = verse.getSuccessor();
while (nextVerse != null) {
List<Root> secondRootList = VerseUtils.getRootList(nextVerse);
RootCompoundSet cs = new RootCompoundSet(mainRootList, secondRootList);
SmithWaterman sw = new SmithWaterman();
sw.setQuery(new ArrayListSequenceReader(cs.getCompounds(0), cs));
sw.setTarget(new ArrayListSequenceReader(cs.getCompounds(1), cs));
GapPenalty penalty = new SimpleGapPenalty(2, 1);
sw.setGapPenalty(penalty);
RootSubstitutionMatrix matrix = new RootSubstitutionMatrix(cs, (short) MATCH_SCORE, (short) -4);
sw.setSubstitutionMatrix(matrix);
Double score = sw.getScore();
if (score >= (MATCH_SCORE * threshold)) {
scores.add(new ResultItem<Verse, Double>(nextVerse, score));
// System.out.println(nextVerse.getAddress() + "***" + score);
}
nextVerse = nextVerse.getNextInQuran();
}
scores.descendSort();
String json = getJson("verses", scores);
return getOkResponse(json);
}
开发者ID:vahidooo,项目名称:quranic-graph,代码行数:43,代码来源:RootWS.java
示例13: main
import org.biojava.nbio.alignment.SimpleGapPenalty; //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());
}
开发者ID:biojava,项目名称:biojava,代码行数:63,代码来源:TestDNANeedlemanWunsch.java
示例14: mergeSequence
import org.biojava.nbio.alignment.SimpleGapPenalty; //导入依赖的package包/类
/**
* Merges the other SubunitCluster into this one if their representatives
* sequences are similar (according to the criteria in params).
* <p>
* The sequence alignment is performed using linear {@link SimpleGapPenalty} and
* BLOSUM62 as scoring matrix.
*
* @param other
* SubunitCluster
* @param params
* SubunitClustererParameters, with information whether to use local
* or global alignment, sequence identity and coverage thresholds.
* Threshold values lower than 0.7 are not recommended.
* Use {@link #mergeStructure} for lower values.
* @return true if the SubunitClusters were merged, false otherwise
* @throws CompoundNotFoundException
*/
public boolean mergeSequence(SubunitCluster other, SubunitClustererParameters params) throws CompoundNotFoundException {
PairwiseSequenceAlignerType alignerType = PairwiseSequenceAlignerType.LOCAL;
if (params.isUseGlobalMetrics()) {
alignerType = PairwiseSequenceAlignerType.GLOBAL;
}
return mergeSequence(other, params,alignerType
, new SimpleGapPenalty(),
SubstitutionMatrixHelper.getBlosum62());
}
开发者ID:biojava,项目名称:biojava,代码行数:28,代码来源:SubunitCluster.java
示例15: alignProtein
import org.biojava.nbio.alignment.SimpleGapPenalty; //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();
}
开发者ID:biojava,项目名称:biojava,代码行数:11,代码来源:EntityFinder.java
示例16: alignDNA
import org.biojava.nbio.alignment.SimpleGapPenalty; //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();
}
开发者ID:biojava,项目名称:biojava,代码行数:11,代码来源:EntityFinder.java
示例17: alignRNA
import org.biojava.nbio.alignment.SimpleGapPenalty; //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();
}
开发者ID:biojava,项目名称:biojava,代码行数:11,代码来源:EntityFinder.java
示例18: main
import org.biojava.nbio.alignment.SimpleGapPenalty; //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));
}
开发者ID:biojava,项目名称:biojava,代码行数:29,代码来源:DemoAlignProteins.java
示例19: call
import org.biojava.nbio.alignment.SimpleGapPenalty; //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);
}
开发者ID:biojava,项目名称:biojava-spark,代码行数:68,代码来源:PairwiseSequenceComparison.java
示例20: call
import org.biojava.nbio.alignment.SimpleGapPenalty; //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);
}
开发者ID:biojava,项目名称:biojava-spark,代码行数:56,代码来源:PairwiseSequenceComparison.java
注:本文中的org.biojava.nbio.alignment.SimpleGapPenalty类示例整理自Github/MSDocs等源码及文档管理平台,相关代码片段筛选自各路编程大神贡献的开源项目,源码版权归原作者所有,传播和使用请参考对应项目的License;未经允许,请勿转载。 |
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