org.biojava.nbio.ronn.ModelLoader Maven / Gradle / Ivy
/*
* @(#)ModelLoader.java 1.0 June 2010
*
* Copyright (c) 2010 Peter Troshin
*
* JRONN version: 3.1
*
* 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.ronn;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
/**
* Class that loads data from the model files into {@link Model} objects
*
* @author Peter Troshin
* @version 1.0
* @since 3.0.2
*/
public final class ModelLoader {
private static final Logger logger = LoggerFactory.getLogger(ModelLoader.class);
/**
* Represents a Threshold
*
*/
public final static class Threshold {
final float mu0;
final float mu1;
final float sigma0;
final float sigma1;
public Threshold(final int modelNum) {
final float[] values = RonnConstraint.Threshold
.getTreshold(modelNum);
mu0 = values[0];
mu1 = values[1];
sigma0 = values[2];
sigma1 = values[3];
}
}
/**
* Represent a RONN model
*
*/
public static class Model {
/**
* Stores encoded sequences from the model similar to seqAA
*
* 190 is a maximum length of the sequence in the model
*/
final short[][] dbAA;// = new short[RonnConstraint.maxD][190];
/**
* This array contains the length of each sequence from the model file
* The length of this array vary with the number of sequences in the
* mode
*/
final short[] Length;// = new int[RonnConstraint.maxD];
/**
* Holds the values from the second column of model file
*/
final float[] W;// = new float[RonnConstraint.maxD];
int numOfDBAAseq;
int modelNum = -1;
public Model(final int modelNum, final int numberofSequence) {
this.modelNum = modelNum;
numOfDBAAseq = numberofSequence;
dbAA = new short[numberofSequence][190];
Length = new short[numberofSequence];
W = new float[numberofSequence];
}
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime * result + Arrays.hashCode(Length);
result = prime * result + Arrays.hashCode(W);
result = prime * result + Arrays.hashCode(dbAA);
result = prime * result + modelNum;
result = prime * result + numOfDBAAseq;
return result;
}
@Override
public boolean equals(final Object obj) {
if (this == obj) {
return true;
}
if (obj == null) {
return false;
}
if (getClass() != obj.getClass()) {
return false;
}
final Model other = (Model) obj;
if (!Arrays.equals(Length, other.Length)) {
return false;
}
if (!Arrays.equals(W, other.W)) {
return false;
}
if (!Arrays.equals(dbAA, other.dbAA)) {
return false;
}
if (modelNum != other.modelNum) {
return false;
}
if (numOfDBAAseq != other.numOfDBAAseq) {
return false;
}
return true;
}
@Override
public String toString() {
return "Model [modelNum=" + modelNum + ", numOfDBAAseq="
+ numOfDBAAseq + "]";
}
}
private static final Map models = new HashMap();
public Model getModel(final int modelNum) {
return ModelLoader.models.get(modelNum);
}
void loadModels() throws NumberFormatException, IOException {
for (int i = 0; i < 10; i++) {
final BufferedReader bfr = new BufferedReader(
new InputStreamReader(ModelLoader.class.getResourceAsStream(
"model" + i + ".rec"),
"ISO-8859-1"));
String line = null;
line = bfr.readLine().trim();
final int numberOfSeqs = Integer.parseInt(line);
final Model model = new Model(i, numberOfSeqs);
// ignore this one, its always 19 defined in RonnConstrain
line = bfr.readLine();
for (int j = 0; j < numberOfSeqs; j++) {
line = bfr.readLine();
final char[] dbseq = line.trim().toCharArray();
assert dbseq.length < Short.MAX_VALUE;
model.Length[j] = (short) dbseq.length;
for (int dResidue = 0; dResidue < dbseq.length; dResidue++) {
model.dbAA[j][dResidue] = RonnConstraint.INDEX[dbseq[dResidue] - 'A'];
assert !((model.dbAA[j][dResidue] < 0) || (model.dbAA[j][dResidue] > 19));
}
line = bfr.readLine().trim();
model.W[j] = Float.parseFloat(line);
}
ModelLoader.models.put(model.modelNum, model);
bfr.close();
}
}
public static void main(final String[] args) throws NumberFormatException,
IOException {
final ModelLoader loader = new ModelLoader();
loader.loadModels();
logger.info("{}", ModelLoader.models.get(0));
logger.info("{}", ModelLoader.models.get(9));
logger.info("{}", ModelLoader.models.size());
}
}