/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package demo;
import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
public class DemoLoadSubstMax {
public static void main (String[] args){
// that's the PAM250 matrix (named a bit unclear in AAindex...)
String max2="DAYM780301";
SubstitutionMatrix<AminoAcidCompound> substMax2 = SubstitutionMatrixHelper.getMatrixFromAAINDEX(max2);
System.out.println("PAM250 matrix: "+ substMax2);
// and here BLOSUM62...
String max3="HENS920102";
SubstitutionMatrix<AminoAcidCompound> substMax3 = SubstitutionMatrixHelper.getMatrixFromAAINDEX(max3);
System.out.printf("%s matrix: %s", max3, substMax3);
System.out.println();
// This one I developed a while ago to be optimised for the alignment of distantly related sequences
String matrixName4 = "PRLA000101";
SubstitutionMatrix<AminoAcidCompound> substMax4 = SubstitutionMatrixHelper.getMatrixFromAAINDEX(matrixName4);
System.out.printf("%s matrix: %s", matrixName4, substMax4);
System.out.println();
}
}