Examples with NucleotidePositionRange org.nextprot.api.commons.utils.NucleotidePositionRange used on opensource projects

Example 1 with NucleotidePositionRange

use of org.nextprot.api.commons.utils.NucleotidePositionRange in project nextprot-api by calipho-sib.

the class SequencePositionMapper method getCodonPositionOnMaster.

/**
 * Get the codon position on gene master that corresponds to the given amino-acid position on isoform
 *
 * @param isoformPos the aa position on isoform
 * @param isoformMasterMapping the list of isoform to gene master mapping
 * @return the codon position on gene master
 */
static GeneMasterCodonPosition getCodonPositionOnMaster(int isoformPos, List<NucleotidePositionRange> isoformMasterMapping) {
    int firstNucPos = isoformPos * 3 - 3;
    // if (debug) System.out.println("nu1Num:" + nu1Num);
    int lowNum = 0;
    GeneMasterCodonPosition result = new GeneMasterCodonPosition();
    for (NucleotidePositionRange range : isoformMasterMapping) {
        int firstRangeNucPos = range.getLower();
        int lastRangeNucPos = range.getUpper();
        int highNum = lowNum + lastRangeNucPos - firstRangeNucPos;
        // if (debug) System.out.println("nu1Pos:"+ nu1Pos + " nu2Pos:" + nu2Pos + " lowNum:" + lowNum + " highNum:" + highNum);
        while (true) {
            int nuIndex = result.size();
            int nuNum = firstNucPos + nuIndex;
            // if (debug) System.out.println("nuNum:" + nuNum);
            if (nuNum < lowNum || nuNum > highNum)
                break;
            result.addNucleotidePosition(firstRangeNucPos + nuNum - lowNum);
            if (result.size() == 3)
                return result;
        }
        lowNum = highNum + 1;
    }
    return result;
}

Example 2 with NucleotidePositionRange

use of org.nextprot.api.commons.utils.NucleotidePositionRange in project nextprot-api by calipho-sib.

the class SequencePositionMapperTest method geneCodonPosTest.

@Test
public void geneCodonPosTest() {
    // represent two coding regions of DNA (gene,master) mapped to an isoform sequence
    List<NucleotidePositionRange> ranges = new ArrayList<NucleotidePositionRange>();
    ranges.add(new NucleotidePositionRange(100, 104));
    ranges.add(new NucleotidePositionRange(201, 204));
    /*
    	 * 
    	 * nuNum      0   1   2   3   4            5   6   7   8
    	 * exons     |---- exon1 ------|          |-- exon 2 ---|
    	 * nuPos     100 101 102 103 104          201 202 203 204
    	 * codons    |--codon1--|-------codon2-------|--codon3--|
    	 * 
    	 * 
    	 */
    GeneMasterCodonPosition result;
    // get gene position of each nucl of the codon coding for aa of isoform at pos 1
    result = SequencePositionMapper.getCodonPositionOnMaster(1, ranges);
    assertEquals(new Integer(100), result.getNucleotidePosition(0));
    assertEquals(new Integer(101), result.getNucleotidePosition(1));
    assertEquals(new Integer(102), result.getNucleotidePosition(2));
    assertEquals(true, result.isValid());
    // get gene position of each nucl of the codon coding for aa of isoform at pos 2
    result = SequencePositionMapper.getCodonPositionOnMaster(2, ranges);
    assertEquals(new Integer(103), result.getNucleotidePosition(0));
    assertEquals(new Integer(104), result.getNucleotidePosition(1));
    assertEquals(new Integer(201), result.getNucleotidePosition(2));
    assertEquals(true, result.isValid());
    // get gene position of each nucl of the codon coding for aa of isoform at pos 3
    result = SequencePositionMapper.getCodonPositionOnMaster(3, ranges);
    assertEquals(new Integer(202), result.getNucleotidePosition(0));
    assertEquals(new Integer(203), result.getNucleotidePosition(1));
    assertEquals(new Integer(204), result.getNucleotidePosition(2));
    assertEquals(true, result.isValid());
    // get gene position of each nucl of the codon coding for aa of isoform at pos 0 (out of range)
    result = SequencePositionMapper.getCodonPositionOnMaster(0, ranges);
    assertEquals(0, result.size());
    assertEquals(false, result.isValid());
    // get gene position of each nucl of the codon coding for aa of isoform at pos 4 (out of range)
    result = SequencePositionMapper.getCodonPositionOnMaster(4, ranges);
    assertEquals(0, result.size());
    assertEquals(false, result.isValid());
}

Example 3 with NucleotidePositionRange

use of org.nextprot.api.commons.utils.NucleotidePositionRange in project nextprot-api by calipho-sib.

the class SequencePositionMapperTest method geneIsoformPosTest.

@Test
public void geneIsoformPosTest() {
    // represent two coding regions of DNA mapped to an isoform sequence
    List<NucleotidePositionRange> genePosRanges = new ArrayList<NucleotidePositionRange>();
    genePosRanges.add(new NucleotidePositionRange(100, 104));
    genePosRanges.add(new NucleotidePositionRange(201, 204));
    /*
    	 * nuNum      0   1   2   3   4            5   6   7   8
    	 * exons     |---- exon1 ------|          |-- exon 2 ---|
    	 * nuPos     100 101 102 103 104          201 202 203 204
    	 * codons    |--codon1--|-------codon2-------|--codon3--|
    	 */
    CodonNucleotideIndices result;
    GeneMasterCodonPosition codonNuPos = new GeneMasterCodonPosition();
    // get isoform pos of aa corresponding to codon with nu at pos 202 203 204
    codonNuPos.clear();
    codonNuPos.addNucleotidePosition(202);
    codonNuPos.addNucleotidePosition(203);
    codonNuPos.addNucleotidePosition(204);
    result = SequencePositionMapper.getCodonNucleotideIndices(codonNuPos, genePosRanges);
    assertEquals(true, result.has3Nucleotides());
    assertEquals(new Integer(3), result.getAminoAcidPosition());
    // get isoform position of aa corresponding to codon with nucleotides at position 100,101,102
    codonNuPos.clear();
    codonNuPos.addNucleotidePosition(100);
    codonNuPos.addNucleotidePosition(101);
    codonNuPos.addNucleotidePosition(102);
    result = SequencePositionMapper.getCodonNucleotideIndices(codonNuPos, genePosRanges);
    assertEquals(new Integer(1), result.getAminoAcidPosition());
    // get isoform position of aa corresponding to codon with nucleotides at position 103 104 201
    codonNuPos.clear();
    codonNuPos.addNucleotidePosition(103);
    codonNuPos.addNucleotidePosition(104);
    codonNuPos.addNucleotidePosition(201);
    result = SequencePositionMapper.getCodonNucleotideIndices(codonNuPos, genePosRanges);
    assertEquals(new Integer(2), result.getAminoAcidPosition());
    // get isoform position of aa corresponding to codon with nucleotides at position 202 203 204
    codonNuPos.clear();
    codonNuPos.addNucleotidePosition(202);
    codonNuPos.addNucleotidePosition(203);
    codonNuPos.addNucleotidePosition(204);
    result = SequencePositionMapper.getCodonNucleotideIndices(codonNuPos, genePosRanges);
    assertEquals(new Integer(3), result.getAminoAcidPosition());
    // trying to find a codon position having NON consecutive nucleotides i.e. at pos 201 203 204
    codonNuPos.clear();
    codonNuPos.addNucleotidePosition(201);
    codonNuPos.addNucleotidePosition(203);
    codonNuPos.addNucleotidePosition(204);
    result = SequencePositionMapper.getCodonNucleotideIndices(codonNuPos, genePosRanges);
    assertEquals(false, result.areConsecutive());
    assertEquals(null, result.getAminoAcidPosition());
    // trying to find a codon position having nucleotide positions that are not in frame (3 nucl of same codon)
    // i.e. at pos 101 102 103
    codonNuPos.clear();
    codonNuPos.addNucleotidePosition(101);
    codonNuPos.addNucleotidePosition(102);
    codonNuPos.addNucleotidePosition(103);
    result = SequencePositionMapper.getCodonNucleotideIndices(codonNuPos, genePosRanges);
    assertEquals(false, result.areInFrame());
    assertEquals(null, result.getAminoAcidPosition());
    // trying to find a codon position having nucleotide positions that are not in frame (3 nucl of same codon)
    // i.e. at pos 102 103 104
    codonNuPos.clear();
    codonNuPos.addNucleotidePosition(102);
    codonNuPos.addNucleotidePosition(103);
    codonNuPos.addNucleotidePosition(104);
    result = SequencePositionMapper.getCodonNucleotideIndices(codonNuPos, genePosRanges);
    assertEquals(false, result.areInFrame());
    assertEquals(null, result.getAminoAcidPosition());
    // trying to find a codon having nucleotide positions out of the gene mapping ranges
    // i.e. at pos  77,78,79
    codonNuPos.clear();
    codonNuPos.addNucleotidePosition(77);
    codonNuPos.addNucleotidePosition(78);
    codonNuPos.addNucleotidePosition(79);
    result = SequencePositionMapper.getCodonNucleotideIndices(codonNuPos, genePosRanges);
    assertEquals(null, result.getAminoAcidPosition());
    // trying to find a codon having nucleotide positions out of the gene mapping ranges
    // i.e. at pos 99,100,101
    codonNuPos.clear();
    codonNuPos.addNucleotidePosition(99);
    codonNuPos.addNucleotidePosition(100);
    codonNuPos.addNucleotidePosition(101);
    result = SequencePositionMapper.getCodonNucleotideIndices(codonNuPos, genePosRanges);
    assertEquals(null, result.getAminoAcidPosition());
    // trying to find a codon having nucleotide positions out of the gene mapping ranges
    // i.e. at pos 103,104, 015
    codonNuPos.clear();
    codonNuPos.addNucleotidePosition(103);
    codonNuPos.addNucleotidePosition(104);
    codonNuPos.addNucleotidePosition(105);
    result = SequencePositionMapper.getCodonNucleotideIndices(codonNuPos, genePosRanges);
    assertEquals(null, result.getAminoAcidPosition());
}

Example 4 with NucleotidePositionRange

use of org.nextprot.api.commons.utils.NucleotidePositionRange in project nextprot-api by calipho-sib.

the class IsoformSequencePositionMapperIntegrationTest method getNucleotideCount.

private int getNucleotideCount(List<NucleotidePositionRange> ranges) {
    int nuCount = 0;
    for (NucleotidePositionRange r : ranges) {
        int cnt = r.getUpper() - r.getLower() + 1;
        nuCount += cnt;
    }
    return nuCount;
}

Example 5 with NucleotidePositionRange

use of org.nextprot.api.commons.utils.NucleotidePositionRange in project nextprot-api by calipho-sib.

the class IsoformSequencePositionMapperIntegrationTest method printIsoLengthAndRangesNuCount.

private void printIsoLengthAndRangesNuCount(String isoName, String isoSeq, List<NucleotidePositionRange> ranges) {
    int isoLng = isoSeq.length();
    int nuCount = getNucleotideCount(ranges);
    boolean ok = isoLng * 3 == nuCount;
    for (NucleotidePositionRange r : ranges) if (sout)
        System.out.println(isoName + " has masterMapping range " + r);
    if (sout)
        System.out.println((ok ? "OK - " : "ERROR4 - ") + isoName + " lng in nu:" + isoLng * 3 + " nuCount:" + nuCount);
}