demo for how to load amino acid substitution matrices

andreasprlic · andreasprlic · commit 652cebb23597 · 2012-07-03T18:49:36.000Z
git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@9747 7c6358e6-4a41-0410-a743-a5b2a554c398
diff --git a/biojava3-alignment/src/main/java/demo/DemoLoadSubstMax.java b/biojava3-alignment/src/main/java/demo/DemoLoadSubstMax.java
@@ -0,0 +1,28 @@
+package demo;
+
+import org.biojava3.alignment.SubstitutionMatrixHelper;
+import org.biojava3.alignment.template.SubstitutionMatrix;
+import org.biojava3.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(substMax2);
+
+		// and here BLOSUM62...
+		String max3="HENS920102";
+		SubstitutionMatrix<AminoAcidCompound> substMax3 = SubstitutionMatrixHelper.getMatrixFromAAINDEX(max3);
+		System.out.println(substMax3);
+		
+		// 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.println(substMax4);
+		
+	}
+}
