Examples with Aminoacid beast.evolution.datatype.Aminoacid used on opensource projects

Example 6 with Aminoacid

use of beast.evolution.datatype.Aminoacid in project beast2 by CompEvol.

the class Blosum62 method getEncodingOrder.

@Override
public int[] getEncodingOrder() {
    Aminoacid dataType = new Aminoacid();
    String codeMap = dataType.getCodeMap();
    int[] codeMapNrs = new int[dataType.getStateCount()];
    String encoding = "ARNDCQEGHILKMFPSTWYV";
    for (int i = 0; i < dataType.getStateCount(); i++) {
        codeMapNrs[i] = encoding.indexOf(codeMap.charAt(i));
    }
    return codeMapNrs;
}

Example 7 with Aminoacid

use of beast.evolution.datatype.Aminoacid in project beast2 by CompEvol.

the class DataTypeDeEncodeTest method typestrings.

@Parameterized.Parameters
public static Collection<Object[]> typestrings() {
    Base dAa = new Aminoacid();
    Base dBi = new Binary();
    Base dIn = new IntegerData();
    Base dNt = new Nucleotide();
    Base d2C = new TwoStateCovarion();
    return Arrays.asList(new Object[][] { { dIn, "1,2,14,23,?", Arrays.asList(new Integer[] { 1, 2, 14, 23, -1 }) }, { dNt, "ACGTURYMWSKBDHVNX", Arrays.asList(new Integer[] { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 }) }, { dBi, "01-?10", Arrays.asList(new Integer[] { 0, 1, 2, 3, 1, 0 }) }, { d2C, "01ABCD-?", Arrays.asList(new Integer[] { 0, 1, 2, 3, 4, 5, 6, 7 }) }, { dAa, "ACDEFGHIKLMNPQRSTVWY", Arrays.asList(new Integer[] { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 }) } });
}