/*
* 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.aaproperties.xml;
import org.biojava.nbio.aaproperties.PeptideProperties;
import org.junit.Test;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
import javax.xml.bind.Marshaller;
import javax.xml.bind.Unmarshaller;
import java.io.*;
import java.util.ArrayList;
import java.util.List;
import static org.junit.Assert.assertEquals;
public class AminoAcidTest {
private static final double delta = 0.00001;
@Test
public void generateSchema() throws JAXBException, IOException{
JAXBContext context = JAXBContext.newInstance(AminoAcidCompositionTable.class);
File outputFile = new File(System.getProperty("java.io.tmpdir"),"AminoAcidComposition.xsd");
outputFile.deleteOnExit();
context.generateSchema(new SchemaGenerator(outputFile.toString()));
}
@Test
public void readAdvancedXml() throws JAXBException, IOException{
ElementTable iTable = new ElementTable();
// Get a JAXB Context for the object we created above
JAXBContext jc = JAXBContext.newInstance(iTable.getClass());
Unmarshaller u = jc.createUnmarshaller();
iTable = (ElementTable)u.unmarshal(new FileInputStream("./src/main/resources/AdvancedElementMass.xml" ) );
iTable.populateMaps();
AminoAcidCompositionTable aTable = new AminoAcidCompositionTable();
// Get a JAXB Context for the object we created above
JAXBContext jc2 = JAXBContext.newInstance(aTable.getClass());
Unmarshaller u2 = jc2.createUnmarshaller();
aTable = (AminoAcidCompositionTable)u2.unmarshal(new FileInputStream("./src/main/resources/AdvancedAminoAcidComposition.xml" ) );
aTable.computeMolecularWeight(iTable);
//Assert the weight of the radioactives
String sequence = "00000";
assertEquals(398.558744445, PeptideProperties.getMolecularWeightBasedOnXML(sequence, aTable), delta);
sequence = "1111";
assertEquals(702.335483556, PeptideProperties.getMolecularWeightBasedOnXML(sequence, aTable), delta);
sequence = "JJJJ";
assertEquals(0.0, PeptideProperties.getMolecularWeightBasedOnXML(sequence, aTable), delta);
}
@Test
public void readWithIDXml() throws JAXBException, IOException{
ElementTable iTable = new ElementTable();
// Get a JAXB Context for the object we created above
JAXBContext jc = JAXBContext.newInstance(iTable.getClass());
Unmarshaller u = jc.createUnmarshaller();
iTable = (ElementTable)u.unmarshal(new FileInputStream("./src/main/resources/MinElementMass.xml" ) );
iTable.populateMaps();
AminoAcidCompositionTable aTable = new AminoAcidCompositionTable();
// Get a JAXB Context for the object we created above
JAXBContext jc2 = JAXBContext.newInstance(aTable.getClass());
Unmarshaller u2 = jc2.createUnmarshaller();
aTable = (AminoAcidCompositionTable)u2.unmarshal(new FileInputStream("./src/main/resources/AminoAcidCompositionWithID.xml" ) );
aTable.computeMolecularWeight(iTable);
}
@Test
public void readMinXml() throws JAXBException, IOException{
ElementTable iTable = new ElementTable();
// Get a JAXB Context for the object we created above
JAXBContext jc = JAXBContext.newInstance(iTable.getClass());
Unmarshaller u = jc.createUnmarshaller();
iTable = (ElementTable)u.unmarshal(new FileInputStream("./src/main/resources/MinElementMass.xml" ) );
iTable.populateMaps();
AminoAcidCompositionTable aTable = new AminoAcidCompositionTable();
// Get a JAXB Context for the object we created above
JAXBContext jc2 = JAXBContext.newInstance(aTable.getClass());
Unmarshaller u2 = jc2.createUnmarshaller();
aTable = (AminoAcidCompositionTable)u2.unmarshal(new FileInputStream("./src/main/resources/MinAminoAcidComposition.xml" ) );
aTable.computeMolecularWeight(iTable);
String sequence = "AAAAA";
assertEquals(373.4047, PeptideProperties.getMolecularWeightBasedOnXML(sequence, aTable), delta);
}
@Test
public void readXml() throws JAXBException, IOException{
ElementTable iTable = new ElementTable();
// Get a JAXB Context for the object we created above
JAXBContext jc = JAXBContext.newInstance(iTable.getClass());
Unmarshaller u = jc.createUnmarshaller();
iTable = (ElementTable)u.unmarshal(new FileInputStream("./src/main/resources/ElementMass.xml" ) );
iTable.populateMaps();
AminoAcidCompositionTable aTable = new AminoAcidCompositionTable();
// Get a JAXB Context for the object we created above
JAXBContext jc2 = JAXBContext.newInstance(aTable.getClass());
Unmarshaller u2 = jc2.createUnmarshaller();
aTable = (AminoAcidCompositionTable)u2.unmarshal(new FileInputStream("./src/main/resources/AminoAcidComposition.xml" ) );
aTable.computeMolecularWeight(iTable);
String sequence = "AAAAA";
assertEquals(373.4047, PeptideProperties.getMolecularWeightBasedOnXML(sequence, aTable), delta);
}
@Test
public void generateXml() throws JAXBException, IOException{
List<Name2Count> elementList = new ArrayList<Name2Count>();
elementList.add(new Name2Count("Carbon", 3));
elementList.add(new Name2Count("Hydrogen", 5));
elementList.add(new Name2Count("Nitrogen", 1));
elementList.add(new Name2Count("Oxygen", 1));
AminoAcidComposition alanine = new AminoAcidComposition("A", "Ala", "Alanine", elementList, null);
elementList = new ArrayList<Name2Count>();
elementList.add(new Name2Count("Carbon", 6));
elementList.add(new Name2Count("Hydrogen", 12));
elementList.add(new Name2Count("Nitrogen", 4));
elementList.add(new Name2Count("Oxygen", 1));
AminoAcidComposition arginine = new AminoAcidComposition("R", "Arg", "Arginine", elementList, null);
elementList = new ArrayList<Name2Count>();
elementList.add(new Name2Count("Carbon", 4));
elementList.add(new Name2Count("Hydrogen", 6));
elementList.add(new Name2Count("Nitrogen", 2));
elementList.add(new Name2Count("Oxygen", 2));
AminoAcidComposition asparagine = new AminoAcidComposition("N", "Asn", "Asparagine", elementList, null);
elementList = new ArrayList<Name2Count>();
elementList.add(new Name2Count("Carbon", 4));
elementList.add(new Name2Count("Hydrogen", 5));
elementList.add(new Name2Count("Nitrogen", 1));
elementList.add(new Name2Count("Oxygen", 3));
AminoAcidComposition asparticAcid = new AminoAcidComposition("D", "Asp", "Aspartic Acid", elementList, null);
elementList = new ArrayList<Name2Count>();
elementList.add(new Name2Count("Carbon", 3));
elementList.add(new Name2Count("Hydrogen", 5));
elementList.add(new Name2Count("Nitrogen", 1));
elementList.add(new Name2Count("Oxygen", 1));
elementList.add(new Name2Count("Sulfur", 1));
AminoAcidComposition cysteine = new AminoAcidComposition("C", "Cys", "Cysteine", elementList, null);
elementList = new ArrayList<Name2Count>();
elementList.add(new Name2Count("Carbon", 5));
elementList.add(new Name2Count("Hydrogen", 7));
elementList.add(new Name2Count("Nitrogen", 1));
elementList.add(new Name2Count("Oxygen", 3));
AminoAcidComposition glutamicAcid = new AminoAcidComposition("E", "Glu", "Glutamic Acid", elementList, null);
elementList = new ArrayList<Name2Count>();
elementList.add(new Name2Count("Carbon", 5));
elementList.add(new Name2Count("Hydrogen", 8));
elementList.add(new Name2Count("Nitrogen", 2));
elementList.add(new Name2Count("Oxygen", 2));
AminoAcidComposition glutamine = new AminoAcidComposition("Q", "Gln", "Glutamine", elementList, null);
elementList = new ArrayList<Name2Count>();
elementList.add(new Name2Count("Carbon", 2));
elementList.add(new Name2Count("Hydrogen", 3));
elementList.add(new Name2Count("Nitrogen", 1));
elementList.add(new Name2Count("Oxygen", 1));
AminoAcidComposition glycine = new AminoAcidComposition("G", "Gly", "Glycine", elementList, null);
elementList = new ArrayList<Name2Count>();
elementList.add(new Name2Count("Carbon", 6));
elementList.add(new Name2Count("Hydrogen", 7));
elementList.add(new Name2Count("Nitrogen", 3));
elementList.add(new Name2Count("Oxygen", 1));
AminoAcidComposition histidine = new AminoAcidComposition("H", "His", "Histidine", elementList, null);
elementList = new ArrayList<Name2Count>();
elementList.add(new Name2Count("Carbon", 6));
elementList.add(new Name2Count("Hydrogen", 11));
elementList.add(new Name2Count("Nitrogen", 1));
elementList.add(new Name2Count("Oxygen", 1));
AminoAcidComposition isoleucine = new AminoAcidComposition("I", "Ile", "Isoleucine", elementList, null);
elementList = new ArrayList<Name2Count>();
elementList.add(new Name2Count("Carbon", 6));
elementList.add(new Name2Count("Hydrogen", 11));
elementList.add(new Name2Count("Nitrogen", 1));
elementList.add(new Name2Count("Oxygen", 1));
AminoAcidComposition leucine = new AminoAcidComposition("L", "Leu", "Leucine", elementList, null);
elementList = new ArrayList<Name2Count>();
elementList.add(new Name2Count("Carbon", 6));
elementList.add(new Name2Count("Hydrogen", 12));
elementList.add(new Name2Count("Nitrogen", 2));
elementList.add(new Name2Count("Oxygen", 1));
AminoAcidComposition lysine = new AminoAcidComposition("K", "Lys", "Lysine", elementList, null);
elementList = new ArrayList<Name2Count>();
elementList.add(new Name2Count("Carbon", 5));
elementList.add(new Name2Count("Hydrogen", 9));
elementList.add(new Name2Count("Nitrogen", 1));
elementList.add(new Name2Count("Oxygen", 1));
elementList.add(new Name2Count("Sulfur", 1));
AminoAcidComposition methionine = new AminoAcidComposition("M", "Met", "Methionine", elementList, null);
elementList = new ArrayList<Name2Count>();
elementList.add(new Name2Count("Carbon", 9));
elementList.add(new Name2Count("Hydrogen", 9));
elementList.add(new Name2Count("Nitrogen", 1));
elementList.add(new Name2Count("Oxygen", 1));
AminoAcidComposition phenylalanine = new AminoAcidComposition("F", "Phe", "Phenylalanine", elementList, null);
elementList = new ArrayList<Name2Count>();
elementList.add(new Name2Count("Carbon", 5));
elementList.add(new Name2Count("Hydrogen", 7));
elementList.add(new Name2Count("Nitrogen", 1));
elementList.add(new Name2Count("Oxygen", 1));
AminoAcidComposition proline = new AminoAcidComposition("P", "Pro", "Proline", elementList, null);
elementList = new ArrayList<Name2Count>();
elementList.add(new Name2Count("Carbon", 3));
elementList.add(new Name2Count("Hydrogen", 5));
elementList.add(new Name2Count("Nitrogen", 1));
elementList.add(new Name2Count("Oxygen", 2));
AminoAcidComposition serine = new AminoAcidComposition("S", "Ser", "Serine", elementList, null);
elementList = new ArrayList<Name2Count>();
elementList.add(new Name2Count("Carbon", 4));
elementList.add(new Name2Count("Hydrogen", 7));
elementList.add(new Name2Count("Nitrogen", 1));
elementList.add(new Name2Count("Oxygen", 2));
AminoAcidComposition threonine = new AminoAcidComposition("T", "Thr", "Threonine", elementList, null);
elementList = new ArrayList<Name2Count>();
elementList.add(new Name2Count("Carbon", 11));
elementList.add(new Name2Count("Hydrogen", 10));
elementList.add(new Name2Count("Nitrogen", 2));
elementList.add(new Name2Count("Oxygen", 1));
AminoAcidComposition tryptophan = new AminoAcidComposition("W", "Trp", "Tryptophan", elementList, null);
elementList = new ArrayList<Name2Count>();
elementList.add(new Name2Count("Carbon", 9));
elementList.add(new Name2Count("Hydrogen", 9));
elementList.add(new Name2Count("Nitrogen", 1));
elementList.add(new Name2Count("Oxygen", 2));
AminoAcidComposition tyrosine = new AminoAcidComposition("Y", "Tyr", "Tyrosine", elementList, null);
elementList = new ArrayList<Name2Count>();
elementList.add(new Name2Count("Carbon", 5));
elementList.add(new Name2Count("Hydrogen", 9));
elementList.add(new Name2Count("Nitrogen", 1));
elementList.add(new Name2Count("Oxygen", 1));
AminoAcidComposition valine = new AminoAcidComposition("V", "Val", "Valine", elementList, null);
List<AminoAcidComposition> aList = new ArrayList<AminoAcidComposition>();
aList.add(alanine);
aList.add(arginine);
aList.add(asparagine);
aList.add(asparticAcid);
aList.add(cysteine);
aList.add(glutamicAcid);
aList.add(glutamine);
aList.add(glycine);
aList.add(histidine);
aList.add(isoleucine);
aList.add(leucine);
aList.add(lysine);
aList.add(methionine);
aList.add(phenylalanine);
aList.add(proline);
aList.add(serine);
aList.add(threonine);
aList.add(tryptophan);
aList.add(tyrosine);
aList.add(valine);
AminoAcidCompositionTable aTable = new AminoAcidCompositionTable(aList);
// Get a JAXB Context for the object we created above
JAXBContext context = JAXBContext.newInstance(aTable.getClass());
// To convert ex to XML, I need a JAXB Marshaller
Marshaller marshaller = context.createMarshaller();
// Make the output pretty
marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
StringWriter sw = new StringWriter();
// marshall the object to XML
marshaller.marshal(aTable, sw);
// print it out for this example
File outputFile = new File(System.getProperty("java.io.tmpdir"),"AminoAcidComposition.xml");
outputFile.deleteOnExit();
BufferedWriter output = new BufferedWriter(new FileWriter(outputFile));
output.write(sw.toString());
output.close();
}
}