/*
* 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 org.biojava.nbio.alignment.aaindex;
import org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix;
import junit.framework.TestCase;
import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
public class TestAAINDEXLoading extends TestCase{
/**
*
* M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
*
* A R N D C Q E G H I L K M F P S T W Y V
A 2.09
R -0.50 2.87
N -0.57 0.60 3.60
D -0.73 0.13 1.78 4.02
C 0.33 -1.30 -2.08 -2.51 6.99
Q -0.75 0.13 0.33 0.34 -0.83 2.60
E -0.12 0.99 -0.16 1.20 -1.97 1.23 2.97
G 0.27 -0.96 0.79 -1.20 -2.11 -0.12 -0.41 4.36
H -1.42 0.54 0.76 -0.01 -1.50 -0.46 -0.62 -0.40 5.89
I -0.97 -1.40 -2.43 -2.77 0.13 -1.47 -1.81 -2.93 -1.76 2.76
L -0.39 -1.19 -2.10 -2.65 -0.31 -1.49 -2.11 -1.98 -0.93 1.56 2.43
K -0.38 1.42 0.83 0.66 -2.19 0.92 1.11 -0.71 0.31 -1.81 -1.96 2.91
M -0.04 -0.63 -2.01 -2.58 1.04 -0.13 -1.86 -1.86 -1.04 0.99 1.61 -1.62 3.75
F -0.76 -1.40 -2.25 -2.19 1.13 -2.31 -1.61 -2.67 -0.22 0.76 1.23 -2.41 0.80 3.28
P -0.53 0.21 -1.10 0.72 -2.19 0.24 -0.26 -0.04 -1.44 -2.00 -1.56 -0.19 -1.09 -0.91 5.45
S 0.34 -0.06 0.40 0.71 0.31 1.04 0.31 0.29 -0.74 -1.75 -2.30 -0.06 -1.34 -1.11 -0.29 2.36
T 0.13 -0.15 0.30 -0.75 -0.59 0.60 -0.21 -0.81 -0.52 -0.96 -0.86 -0.10 -1.58 -0.69 0.93 1.20 2.04
W -0.66 -0.04 -2.89 -1.91 -0.76 -0.81 -2.70 -1.21 -1.48 0.25 -0.14 -1.94 0.87 2.29 -5.34 -1.18 -0.57 6.96
Y -1.25 -0.75 -0.36 -1.21 0.13 -0.61 -1.64 -1.62 -0.12 0.08 0.70 -1.72 -0.41 1.96 -1.98 -1.56 -0.41 2.15 3.95
V 0.02 -1.52 -2.17 -2.02 0.34 -1.38 -1.84 -1.96 -0.35 1.94 0.81 -1.27 0.61 0.51 -1.11 -1.11 0.05 -1.09 0.21 2.05
*/
public void testSDMmatrix(){
String matrixName = "PRLA000101";
SubstitutionMatrix<AminoAcidCompound> sdm = SubstitutionMatrixHelper.getMatrixFromAAINDEX(matrixName);
int scale = 1;
if ( sdm instanceof ScaledSubstitutionMatrix) {
ScaledSubstitutionMatrix scaledSDM = (ScaledSubstitutionMatrix)sdm;
scale = scaledSDM.getScale();
assertEquals(100,scale);
}
AminoAcidCompoundSet aas = AminoAcidCompoundSet.getAminoAcidCompoundSet();
AminoAcidCompound v = aas.getCompoundForString("V");
AminoAcidCompound w = aas.getCompoundForString("W");
AminoAcidCompound r = aas.getCompoundForString("R");
AminoAcidCompound n = aas.getCompoundForString("N");
short rn = sdm.getValue(r,n);
assertEquals(60,rn);
short nr = sdm.getValue(n,r);
assertEquals(rn,nr);
short vv = sdm.getValue(v,v);
assertEquals(205,vv);
short vw = sdm.getValue(v,w);
assertEquals( -109,vw);
short wv = sdm.getValue(w,v);
assertEquals(vw,wv);
}
/*
*
* M rows = ACDEFGHIKLMNPQRSTVWYJ-, cols = ACDEFGHIKLMNPQRSTVWYJ
*
*
A C D E F G H I K L M N P Q R S T V W Y J
A 0.224 0.013 0.055 0.068 0.031 0.067 0.048 0.053 0.068 0.050 0.087 0.059 0.067 0.073 0.062 0.074 0.059 0.079 0.033 0.035 0.121
C 0.002 0.739 0.001 0.006 0.012 0.000 0.001 0.004 0.003 0.000 0.000 0.001 0.001 0.005 0.008 0.001 0.001 0.000 0.001 0.000 0.008
D 0.044 0.007 0.284 0.091 0.016 0.041 0.056 0.033 0.034 0.012 0.022 0.094 0.047 0.052 0.025 0.054 0.044 0.025 0.014 0.023 0.030
E 0.052 0.029 0.079 0.251 0.016 0.028 0.026 0.026 0.053 0.019 0.031 0.038 0.037 0.071 0.049 0.031 0.044 0.034 0.010 0.027 0.008
F 0.010 0.029 0.006 0.008 0.291 0.004 0.023 0.046 0.011 0.047 0.032 0.012 0.006 0.010 0.009 0.011 0.013 0.018 0.093 0.073 0.000
G 0.079 0.000 0.066 0.047 0.020 0.455 0.042 0.024 0.033 0.028 0.039 0.073 0.054 0.054 0.040 0.064 0.037 0.039 0.041 0.036 0.038
H 0.013 0.003 0.021 0.011 0.024 0.010 0.284 0.008 0.021 0.011 0.020 0.035 0.008 0.020 0.023 0.013 0.012 0.020 0.014 0.025 0.023
I 0.014 0.016 0.017 0.014 0.058 0.006 0.010 0.235 0.015 0.050 0.048 0.018 0.009 0.009 0.015 0.014 0.023 0.075 0.015 0.030 0.008
K 0.062 0.007 0.039 0.072 0.032 0.027 0.068 0.039 0.294 0.050 0.077 0.055 0.045 0.077 0.122 0.043 0.059 0.044 0.037 0.035 0.053
L 0.028 0.000 0.010 0.017 0.097 0.013 0.024 0.094 0.035 0.311 0.141 0.030 0.030 0.028 0.027 0.019 0.029 0.073 0.064 0.033 0.015
M 0.010 0.000 0.003 0.005 0.015 0.005 0.005 0.020 0.011 0.030 0.167 0.004 0.003 0.017 0.005 0.003 0.007 0.013 0.004 0.008 0.015
N 0.041 0.007 0.080 0.041 0.022 0.044 0.087 0.031 0.042 0.035 0.024 0.239 0.019 0.040 0.031 0.050 0.051 0.021 0.008 0.036 0.030
P 0.053 0.000 0.039 0.036 0.036 0.006 0.027 0.018 0.017 0.034 0.014 0.018 0.412 0.021 0.026 0.037 0.031 0.019 0.018 0.008 0.015
Q 0.040 0.013 0.038 0.060 0.018 0.025 0.042 0.017 0.046 0.026 0.075 0.032 0.019 0.231 0.056 0.032 0.042 0.036 0.007 0.015 0.023
R 0.025 0.023 0.015 0.031 0.010 0.017 0.033 0.017 0.062 0.019 0.015 0.022 0.018 0.047 0.248 0.026 0.028 0.022 0.022 0.023 0.000
S 0.100 0.013 0.088 0.059 0.044 0.073 0.057 0.051 0.062 0.043 0.026 0.096 0.070 0.072 0.079 0.290 0.138 0.057 0.025 0.059 0.053
T 0.054 0.010 0.049 0.058 0.042 0.029 0.037 0.059 0.058 0.039 0.049 0.068 0.042 0.066 0.053 0.099 0.266 0.061 0.021 0.041 0.015
V 0.041 0.000 0.021 0.033 0.040 0.020 0.038 0.148 0.031 0.077 0.051 0.018 0.020 0.043 0.033 0.028 0.044 0.269 0.023 0.049 0.091
W 0.005 0.000 0.002 0.002 0.049 0.006 0.006 0.009 0.006 0.017 0.005 0.003 0.004 0.003 0.008 0.003 0.004 0.003 0.421 0.038 0.000
Y 0.014 0.000 0.013 0.018 0.111 0.012 0.034 0.028 0.017 0.023 0.026 0.023 0.005 0.012 0.024 0.018 0.019 0.028 0.109 0.355 0.023
J 0.002 0.000 0.001 0.000 0.001 0.002 0.002 0.001 0.002 0.001 0.003 0.001 0.001 0.001 0.001 0.002 0.001 0.007 0.000 0.001 0.341
- 0.086 0.092 0.072 0.072 0.045 0.089 0.060 0.043 0.061 0.075 0.048 0.061 0.083 0.050 0.056 0.087 0.050 0.057 0.021 0.048 0.091
//
*
*
*/
public void testOVEJ920104(){
String name = "OVEJ920104";
SubstitutionMatrix<AminoAcidCompound> max = SubstitutionMatrixHelper.getMatrixFromAAINDEX(name);
if ( max instanceof ScaledSubstitutionMatrix) {
ScaledSubstitutionMatrix scaledMAX = (ScaledSubstitutionMatrix) max;
int scale = scaledMAX.getScale();
assertEquals(1000,scale);
}
AminoAcidCompoundSet aas = AminoAcidCompoundSet.getAminoAcidCompoundSet();
AminoAcidCompound minus = aas.getCompoundForString("-");
AminoAcidCompound j = aas.getCompoundForString("J");
AminoAcidCompound y = aas.getCompoundForString("Y");
AminoAcidCompound a = aas.getCompoundForString("A");
short ay = max.getValue(a,y);
assertEquals(35,ay);
short ya = max.getValue(y,a);
assertEquals(14,ya);
short minusa = max.getValue(minus, a);
assertEquals(86, minusa);
short minusy = max.getValue(minus, y);
assertEquals( 48,minusy);
short minusj = max.getValue(minus, j);
assertEquals( 91,minusj);
}
}