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

Example 1 with Aminoacid

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

the class Dayhoff 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 2 with Aminoacid

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

the class WAG 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 3 with Aminoacid

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

the class CPREV 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 4 with Aminoacid

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

the class JTT 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 5 with Aminoacid

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

the class MTREV 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;
}