Java AminoAcidCompound类代码示例

import org.biojava.nbio.core.sequence.compound.AminoAcidCompound; //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;
	}));
}
 

import org.biojava.nbio.core.sequence.compound.AminoAcidCompound; //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();
    }
 

import org.biojava.nbio.core.sequence.compound.AminoAcidCompound; //导入依赖的package包/类
private void testProcessAll(String path) throws Exception {
       ClasspathResource r = new ClasspathResource(path);
       FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = null ;
       try( InputStream inStream = r.getInputStream() ) {
           fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
                   inStream,
                   new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
                   new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
           LinkedHashMap<String, ProteinSequence> sequences = fastaReader.process();
           assertThat(sequences,is(notNullValue()));
           assertThat(sequences.size(),is(1));
           assertThat(sequences.containsKey("P02768"),is(true));
           assertThat(sequences.get("P02768").getLength(),is(609));
       } finally {
           if(fastaReader != null) fastaReader.close();
       }
}
 

import org.biojava.nbio.core.sequence.compound.AminoAcidCompound; //导入依赖的package包/类
/**
 * Selecting lazySequenceLoad=true will parse the Genbank file and figure out the accessionid and offsets and return sequence objects
 * that can in the future read the sequence from the disk. This allows the loading of large Genbank files where you are only interested
 * in one sequence based on accession id.
 * @param file
 * @param lazySequenceLoad
 * @return
 * @throws Exception
 */
public static LinkedHashMap<String, ProteinSequence> readGenbankProteinSequence(File file, boolean lazySequenceLoad) throws Exception {
	if (!lazySequenceLoad) {
		return readGenbankProteinSequence(file);
	}

	GenbankReader<ProteinSequence, AminoAcidCompound> GenbankProxyReader =
			new GenbankReader<ProteinSequence, AminoAcidCompound>(
					file,
					new GenericGenbankHeaderParser<ProteinSequence, AminoAcidCompound>(),
					new FileProxyProteinSequenceCreator(
							file,
							AminoAcidCompoundSet.getAminoAcidCompoundSet(),
							new GenbankSequenceParser<AbstractSequence<AminoAcidCompound>, AminoAcidCompound>()
						)
				);
	return GenbankProxyReader.process();

}
 

import org.biojava.nbio.core.sequence.compound.AminoAcidCompound; //导入依赖的package包/类
private void testProcess1(String path) throws Exception {
    ClasspathResource r = new ClasspathResource(path);
    FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = null ;
    try( InputStream inStream = r.getInputStream() ) {
        fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
                inStream,
                new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
                new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
        LinkedHashMap<String,ProteinSequence> out1 = fastaReader.process(1);
        assertThat(out1,is(notNullValue()));
        assertThat(out1.size(),is(1));
        assertThat(out1.containsKey("P02768"),is(true));
        assertThat(out1.get("P02768").getLength(),is(609));
        LinkedHashMap<String,ProteinSequence> out2 = fastaReader.process(1);
        assertThat(out2,is(nullValue()));
    } finally {
        if(fastaReader != null) fastaReader.close();
    }
}
 

import org.biojava.nbio.core.sequence.compound.AminoAcidCompound; //导入依赖的package包/类
/** test for https://github.com/biojava/biojava/issues/53  */
@Test
public void testHashCollision() throws CompoundNotFoundException{
	Builder builder = new TranscriptionEngine.Builder();
	builder.initMet(false);
	builder.translateNCodons(true);
	builder.trimStop(false);
	TranscriptionEngine engine = builder.build();
	Sequence<AminoAcidCompound> seq=engine.translate(new
			DNASequence("GTNTGTTAGTGT"));
	assertThat("XC*C", is(seq.toString()));
	Sequence<AminoAcidCompound> seq2=engine.translate(new
			DNASequence("ANAANG"));
	assertEquals("XX",seq2.toString());
	assertNotSame("HR",seq2.toString());
}
 

import org.biojava.nbio.core.sequence.compound.AminoAcidCompound; //导入依赖的package包/类
private Map<AminoAcidCompound, Integer> getExtinctAACount(ProteinSequence sequence){
	//Cys => C, Tyr => Y, Trp => W
	int numW = 0;
	int smallW = 0;
	double numC = 0;
	double smallC = 0;
	int numY = 0;
	int smallY = 0;
	for(char aa:sequence.getSequenceAsString().toCharArray()){
		switch(aa){
		case 'W': numW++; break;
		case 'w': smallW++; break;
		case 'C': numC += 0.5; break;
		case 'c': smallC += 0.5; break;
		case 'Y': numY++; break;
		case 'y': smallY++; break;
		}
	}
	AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
	Map<AminoAcidCompound, Integer> extinctAA2Count = new HashMap<AminoAcidCompound, Integer>();
	//Ignore Case is always true
	extinctAA2Count.put(aaSet.getCompoundForString("W"), numW + smallW);
	extinctAA2Count.put(aaSet.getCompoundForString("C"), (int) (numC + smallC));
	extinctAA2Count.put(aaSet.getCompoundForString("Y"), numY + smallY);
	return extinctAA2Count;
}
 

import org.biojava.nbio.core.sequence.compound.AminoAcidCompound; //导入依赖的package包/类
@Override
public double getAvgHydropathy(ProteinSequence sequence) {
	int validLength = 0;
	double total = 0.0;
	AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
	char[] seq = this.getSequence(sequence.toString(), true);
	for(char aa:seq){
		AminoAcidCompound c = aaSet.getCompoundForString(String.valueOf(aa));
		if(Constraints.aa2Hydrophathicity.containsKey(c)){
			total += Constraints.aa2Hydrophathicity.get(c);
			validLength++;
		}
	}
	if (validLength==0) {
		logger.warn("Valid length of sequence is 0, can't divide by 0 to calculate average hydropathy: setting average hydropathy to 0");
		return 0.0;
	}

	return total / validLength;
}
 

import org.biojava.nbio.core.sequence.compound.AminoAcidCompound; //导入依赖的package包/类
private void testProcess2(String path) throws Exception {
    ClasspathResource r = new ClasspathResource(path);
    FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = null ;
    try( InputStream inStream = r.getInputStream() ) {
        fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
                inStream,
                new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
                new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
        LinkedHashMap<String,ProteinSequence> out1 = fastaReader.process(1);
        assertThat(out1,is(notNullValue()));
        assertThat(out1.size(),is(1));
        assertThat(out1.containsKey("P02768"),is(true));
        assertThat(out1.get("P02768").getLength(),is(609));
        LinkedHashMap<String,ProteinSequence> out2 = fastaReader.process(1);
        assertThat(out2,is(notNullValue()));
        assertThat(out2.size(),is(1));
        assertThat(out2.containsKey("P00698"),is(true));
        assertThat(out2.get("P00698").getLength(),is(147));
        LinkedHashMap<String,ProteinSequence> out3 = fastaReader.process(1);
        assertThat(out3,is(nullValue()));
    } finally {
        if(fastaReader != null) fastaReader.close();
    }
}
 

import org.biojava.nbio.core.sequence.compound.AminoAcidCompound; //导入依赖的package包/类
private static LinkedHashMap<String, ProteinSequence> readInputFile(String inputLocation, AminoAcidCompositionTable aaTable) throws Exception{
	FileInputStream inStream = new FileInputStream(inputLocation);
	CompoundSet<AminoAcidCompound>	set;
	if(aaTable == null){
		set = CaseFreeAminoAcidCompoundSet.getAminoAcidCompoundSet();
	}else{
		set = aaTable.getAminoAcidCompoundSet();
	}
	LinkedHashMap<String, ProteinSequence> ret;
	if ( inputLocation.toLowerCase().contains(".gb")) {
		GenbankReader<ProteinSequence, AminoAcidCompound> genbankReader = new GenbankReader<ProteinSequence, AminoAcidCompound>(
				inStream, new GenericGenbankHeaderParser<ProteinSequence, AminoAcidCompound>(),
				new ProteinSequenceCreator(set));
		ret = genbankReader.process();


	} else {
		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
				inStream, new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
				new ProteinSequenceCreator(set));
		ret = fastaReader.process();

	}
	return ret;
}
 

import org.biojava.nbio.core.sequence.compound.AminoAcidCompound; //导入依赖的package包/类
/**
 * Returns a list of codons where the source and target compounds
 * are the same as those given by the parameters.
 *
 * @param nucleotides The nucleotide set to use when building BioJava
 * representations of codons
 * @param aminoAcids The target amino acid compounds objects
 */
		@Override
public List<Codon> getCodons(CompoundSet<NucleotideCompound> nucelotides,
		CompoundSet<AminoAcidCompound> aminoAcids) {

	if (this.codons.isEmpty()) {
		List<String> aminoAcidStrings = aminoAcids();
		List<String> startCodonStrings = startCodons();
		List<List<String>> codonStrings = codonStrings();

		for (int i = 0; i < aminoAcidStrings.size(); i++) {

			List<String> codonString    = codonStrings.get(i);
			NucleotideCompound one      = getCompound(codonString, 0, nucelotides);
			NucleotideCompound two      = getCompound(codonString, 1, nucelotides);
			NucleotideCompound three    = getCompound(codonString, 2, nucelotides);
			boolean start               = ("M".equals(startCodonStrings.get(i)));
			boolean stop                = ("*".equals(aminoAcidStrings.get(i)));
			AminoAcidCompound aminoAcid = aminoAcids
					.getCompoundForString(aminoAcidStrings.get(i));
			codons.add(new Codon(new CaseInsensitiveTriplet(one, two, three), aminoAcid, start, stop));
		}
	}

	return codons;
}
 

import org.biojava.nbio.core.sequence.compound.AminoAcidCompound; //导入依赖的package包/类
public void processing(Callback callback) throws IOException {
   ObjectMapper mapper = new ObjectMapper();

   FileInputStream inStream = new FileInputStream( fastaFile );
   FastaReader<ProteinSequence,AminoAcidCompound> fastaReader =
           new FastaReader<>(
                   inStream,
                   new GenericFastaHeaderParser<>(),
                   new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
   LinkedHashMap<String, ProteinSequence> b = fastaReader.process();

   for (  Map.Entry<String, ProteinSequence> entry : b.entrySet() ) {
       String header = entry.getValue().getOriginalHeader();
       String sequence = entry.getValue().getSequenceAsString();
       String[] parts = header.split("\\|");
       ProteinObj obj = new ProteinObj();

       if (parts.length < 3)
           logger.error("faste parsing error " + header);
       else {
           obj.setAcxn(parts[1]);
           obj.setDefline(parts[2]);
           obj.setSequence(sequence);

           JsonNode node = mapper.valueToTree(obj);
           callback.processSingleJSONRecord(node);
       }

   }
}
 

import org.biojava.nbio.core.sequence.compound.AminoAcidCompound; //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);
}
 

import org.biojava.nbio.core.sequence.compound.AminoAcidCompound; //导入依赖的package包/类
public static void main(String[] args) throws IOException {

        //Try reading with the FastaReader
        FileInputStream inStream = new FileInputStream(BASE_PATH);
        FastaReader<ProteinSequence,AminoAcidCompound> fastaReader =
                new FastaReader<>(inStream,
                        new GenericFastaHeaderParser<ProteinSequence,AminoAcidCompound>(),
                        new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
        LinkedHashMap<String, ProteinSequence> b = fastaReader.process();
        for (  Map.Entry<String, ProteinSequence> entry : b.entrySet() ) {
            System.out.println(entry.getValue().getOriginalHeader());
        }
    }
 

import org.biojava.nbio.core.sequence.compound.AminoAcidCompound; //导入依赖的package包/类
/**
 * Calculate a phylogenetic tree of the MultipleAlignment using Kimura
 * distances and the Neighbor Joining algorithm from forester.
 *
 * @param msta
 *            MultipleAlignment of protein structures
 * @return Phylogeny phylogenetic tree
 * @throws CompoundNotFoundException
 * @throws IOException
 */
public static Phylogeny getKimuraTree(MultipleAlignment msta)
		throws CompoundNotFoundException, IOException {
	MultipleSequenceAlignment<ProteinSequence, AminoAcidCompound> msa = MultipleAlignmentTools
			.toProteinMSA(msta);
	BasicSymmetricalDistanceMatrix distmat = (BasicSymmetricalDistanceMatrix) DistanceMatrixCalculator
			.kimuraDistance(msa);
	Phylogeny tree = TreeConstructor.distanceTree(distmat,
			TreeConstructorType.NJ);
	tree.setName("Kimura Tree");
	return tree;
}