/*
* Copyright (C) Lennart Martens
*
* Contact: lennart.martens AT UGent.be (' AT ' to be replaced with '@')
*/
/*
* Created by IntelliJ IDEA.
* User: Lennart
* Date: 9-okt-02
* Time: 9:17:13
*/
package com.compomics.util.test.protein;
import com.compomics.util.junit.TestCaseLM;
import com.compomics.util.protein.Enzyme;
import com.compomics.util.protein.Protein;
import junit.framework.Assert;
import junit.framework.TestCase;
import org.apache.log4j.Logger;
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
/*
* CVS information:
*
* $Revision: 1.5 $
* $Date: 2008/11/18 11:39:11 $
*/
/**
* This class implements the full test scenario for the enzyme class.
*
* @author Lennart Martens
* @see com.compomics.util.protein.Enzyme
*/
public class TestEnzyme extends TestCase {
// Class specific log4j logger for TestEnzyme instances.
Logger logger = Logger.getLogger(TestEnzyme.class);
public TestEnzyme() {
this("Test scenario for the Enzyme class.");
}
public TestEnzyme(String aName) {
super(aName);
}
/**
* This method test the creation, setters and getters of an Enzyme instance.
*/
public void testCreation() {
// First the two standard constructors with meaningfull data.
// Also test the different setters.
final String title1 = "Title1";
final String cleavage1 = "ARNDCQ";
final String restrict1 = "PG";
final char[] cv1 = cleavage1.toCharArray();
final char[] rs1 = restrict1.toCharArray();
final String pos1 = "Cterm";
final String pos2 = "nteRm";
final int miscleavage = 3;
Enzyme e = new Enzyme(title1, cleavage1, restrict1, pos1);
Assert.assertEquals(title1, e.getTitle());
Assert.assertEquals(new String(cv1), new String(e.getCleavage()));
Assert.assertEquals(new String(rs1), new String(e.getRestrict()));
Assert.assertEquals(Enzyme.CTERM, e.getPosition());
Assert.assertEquals(1, e.getMiscleavages());
final String otherTitle = "other";
final String otherCleavage = "HIK";
final String otherRestrict = "MN";
final char[] otherCv = otherCleavage.toCharArray();
final char[] otherRs = otherRestrict.toCharArray();
e.setTitle(otherTitle);
e.setCleavage(otherCleavage);
e.setRestrict(otherRestrict);
e.setPosition(Enzyme.NTERM);
e.setMiscleavages(miscleavage);
Assert.assertEquals(otherTitle, e.getTitle());
Assert.assertEquals(new String(otherCv), new String(e.getCleavage()));
Assert.assertEquals(new String(otherRs), new String(e.getRestrict()));
Assert.assertEquals(Enzyme.NTERM, e.getPosition());
Assert.assertEquals(miscleavage, e.getMiscleavages());
e.setCleavage(cleavage1);
e.setRestrict(rs1);
Assert.assertEquals(new String(cv1), new String(e.getCleavage()));
Assert.assertEquals(new String(rs1), new String(e.getRestrict()));
e = new Enzyme(null, cleavage1, null, pos2, 5);
Assert.assertTrue(e.getTitle() == null);
Assert.assertEquals(new String(cv1), new String(e.getCleavage()));
Assert.assertTrue(e.getRestrict() == null);
Assert.assertEquals(Enzyme.NTERM, e.getPosition());
Assert.assertEquals(5, e.getMiscleavages());
try {
e = new Enzyme(title1, null, restrict1, null);
fail("No NullPointerException thrown when Enzyme constructor was presented with a 'null' cleavage and position String!");
} catch(NullPointerException npe) {
// Okay, this is what we wanted.
}
try {
e = new Enzyme(title1, cleavage1, restrict1, null);
fail("No NullPointerException thrown when Enzyme constructor was presented with a 'null' position String!");
} catch(NullPointerException npe) {
// Okay, this is what we wanted.
}
}
/**
* This method test the cleaving behaviour of the Enzyme class.
*/
public void testCleave() {
final String inputFile = "testCleave.fas";
final String input = TestCaseLM.getFullFilePath(inputFile).replace("%20", " ");
try {
// We need to obtain a pointer the control file before anything else.
BufferedReader br = new BufferedReader(new FileReader(input));
// First one with zero MC's.
Enzyme e = new Enzyme("TestEnzyme", "KR", "P", "Cterm", 0);
Protein p = new Protein(">sw|Q55645|TEST_HUMAN Test Protein for the cleave() method.", "GHIKLMVSTRPIGASDNPKLHGFVNRTGFDA");
Protein[] result = e.cleave(p);
boolean once = false;
for(int i = 0; i < result.length; i++) {
once = true;
Protein lProtein = result[i];
String header = lProtein.getHeader().getFullHeaderWithAddenda();
String sequence = lProtein.getSequence().getSequence();
Assert.assertEquals(br.readLine(), header);
Assert.assertEquals(br.readLine(), sequence);
}
if(!once) {
fail("NO peptides AT ALL were returned when cleaving '" + p.getSequence().getSequence() + "'!");
}
// Skip to the next part of the controlfile.
br.readLine();
once = false;
// Now with one miscleavage.
e.setMiscleavages(1);
result = e.cleave(p);
for(int i = 0; i < result.length; i++) {
once = true;
Protein lProtein = result[i];
String header = lProtein.getHeader().getFullHeaderWithAddenda();
String sequence = lProtein.getSequence().getSequence();
Assert.assertEquals(br.readLine(), header);
Assert.assertEquals(br.readLine(), sequence);
}
if(!once) {
fail("NO peptides AT ALL were returned when cleaving '" + p.getSequence().getSequence() + "'!");
}
// Skip to the next part of the controlfile.
br.readLine();
once = false;
// Now with three miscleavages.
e.setMiscleavages(3);
result = e.cleave(p);
for(int i = 0; i < result.length; i++) {
once = true;
Protein lProtein = result[i];
String header = lProtein.getHeader().getFullHeaderWithAddenda();
String sequence = lProtein.getSequence().getSequence();
Assert.assertEquals(br.readLine(), header);
Assert.assertEquals(br.readLine(), sequence);
}
if(!once) {
fail("NO peptides AT ALL were returned when cleaving '" + p.getSequence().getSequence() + "'!");
}
// Now check for the edge case where there's only one amino acid after the last cleavage position
// (used to be a bug that this amino acid was never considered).
e.setMiscleavages(1);
result = e.cleave(new Protein(">sw|Q55645|TEST_HUMAN Test Protein for the cleave() method.", "GHIKLMVSTRPIGASDNPKLHGFVNRTGFDRA"));
boolean foundIt = false;
for(int i = 0; i < result.length; i++) {
Protein lProtein = result[i];
if(lProtein.getSequence().getSequence().equals("TGFDRA")){
foundIt = true;
break;
}
}
if(!foundIt) {
fail("The peptide 'TGFDRA' (penultimate amino acid is cleavage site, one missed cleavage allowed) was NOT returned when cleaving '" + p.getSequence().getSequence() + "'!");
}
// Skip to the next part of the controlfile.
br.readLine();
once = false;
// Now Nterm position and 1 miscleavage.
e.setPosition(Enzyme.NTERM);
e.setMiscleavages(1);
result = e.cleave(p);
for(int i = 0; i < result.length; i++) {
once = true;
Protein lProtein = result[i];
String header = lProtein.getHeader().getFullHeaderWithAddenda();
String sequence = lProtein.getSequence().getSequence();
Assert.assertEquals(br.readLine(), header);
Assert.assertEquals(br.readLine(), sequence);
}
if(!once) {
fail("NO peptides AT ALL were returned when cleaving '" + p.getSequence().getSequence() + "'!");
}
// Skip to the next part of the controlfile.
br.readLine();
once = false;
// Next, take an enzyme that does not have restricting residus.
e = new Enzyme("Test", "KR", null, "Cterm", 0);
result = e.cleave(p);
for(int i = 0; i < result.length; i++) {
once = true;
Protein lProtein = result[i];
String header = lProtein.getHeader().getFullHeaderWithAddenda();
String sequence = lProtein.getSequence().getSequence();
Assert.assertEquals(br.readLine(), header);
Assert.assertEquals(br.readLine(), sequence);
}
if(!once) {
fail("NO peptides AT ALL were returned when cleaving '" + p.getSequence().getSequence() + "'!");
}
// Skip to the next part of the controlfile.
br.readLine();
once = false;
// And now take an entry that has a location set and see if the cleavage is adjusted accordingly.
e = new Enzyme("TestEnzyme", "KR", "P", "Cterm", 1);
p = new Protein(">sw|Q55645 (15-45)|TEST_HUMAN Test Protein for the cleave() method.", "GHIKLMVSTRPIGASDNPKLHGFVNRTGFDA");
result = e.cleave(p);
for(int i = 0; i < result.length; i++) {
once = true;
Protein lProtein = result[i];
String header = lProtein.getHeader().getFullHeaderWithAddenda();
String sequence = lProtein.getSequence().getSequence();
Assert.assertEquals(br.readLine(), header);
Assert.assertEquals(br.readLine(), sequence);
}
if(!once) {
fail("NO peptides AT ALL were returned when cleaving '" + p.getSequence().getSequence() + "'!");
}
// Skip to the next part of the controlfile.
br.readLine();
once = false;
// Now take a C-terminally truncated sequence and see if it is cleaved correctly.
e = new Enzyme("TestEnzyme", "KR", "P", "Cterm", 1);
p = new Protein(">sw|Q55645 (15-45)|TEST_HUMAN Test Protein for the cleave() method.", "GHIKLMVSTRPIGASDNPKLHGFVNRTGFDA", true, Protein.CTERMTRUNC);
result = e.cleave(p);
for(int i = 0; i < result.length; i++) {
once = true;
Protein lProtein = result[i];
String header = lProtein.getHeader().getFullHeaderWithAddenda();
String sequence = lProtein.getSequence().getSequence();
Assert.assertEquals(br.readLine(), header);
Assert.assertEquals(br.readLine(), sequence);
}
if(!once) {
fail("NO peptides AT ALL were returned when cleaving '" + p.getSequence().getSequence() + "'!");
}
// Skip to the next part of the controlfile.
br.readLine();
once = false;
// Now take an N-terminally truncated sequence and see if it is cleaved correctly.
e = new Enzyme("TestEnzyme", "KR", "P", "Cterm", 1);
p = new Protein(">sw|Q55645 (15-45)|TEST_HUMAN Test Protein for the cleave() method.", "GHIKLMVSTRPIGASDNPKLHGFVNRTGFDA", true, Protein.NTERMTRUNC);
result = e.cleave(p);
for(int i = 0; i < result.length; i++) {
once = true;
Protein lProtein = result[i];
String header = lProtein.getHeader().getFullHeaderWithAddenda();
String sequence = lProtein.getSequence().getSequence();
Assert.assertEquals(br.readLine(), header);
Assert.assertEquals(br.readLine(), sequence);
}
if(!once) {
fail("NO peptides AT ALL were returned when cleaving '" + p.getSequence().getSequence() + "'!");
}
// Skip to the next part of the controlfile.
br.readLine();
once = false;
// Now take a translated sequence, containing an '_' (stopcodon).
e = new Enzyme("TestEnzyme", "KR", "P", "Cterm", 1);
p = new Protein(">sw|Q55645 (15-45)|TEST_HUMAN Test Protein for the cleave() method.", "GHIKLMVSTRPIGASDNPKLHG_FVNRTGFDA");
result = e.cleave(p);
for(int i = 0; i < result.length; i++) {
once = true;
Protein lProtein = result[i];
String header = lProtein.getHeader().getFullHeaderWithAddenda();
String sequence = lProtein.getSequence().getSequence();
Assert.assertEquals(br.readLine(), header);
Assert.assertEquals(br.readLine(), sequence);
}
if(!once) {
fail("NO peptides AT ALL were returned when cleaving '" + p.getSequence().getSequence() + "'!");
}
// END of file reached.
// Check this!
String line = null;
while((line = br.readLine()) != null) {
if(!line.trim().equals("")) {
fail("More lines in testCleave.fas then were generated by the test cleavage!");
}
}
br.close();
} catch(IOException ioe) {
fail("IOException occurred while testing the cleave() method: '" + ioe.getMessage() + "'.");
}
}
/**
* This method test the cloning of an Enzyme.
*/
public void testClone() {
Enzyme e = new Enzyme("Test", "KR", "P", "Cterm", 5);
Enzyme clone = (Enzyme)e.clone();
Assert.assertEquals(new String(e.getCleavage()), new String(clone.getCleavage()));
Assert.assertEquals(e.getMiscleavages(), clone.getMiscleavages());
Assert.assertEquals(e.getPosition(), clone.getPosition());
Assert.assertEquals(new String(e.getRestrict()), new String(clone.getRestrict()));
Assert.assertEquals(e.getTitle(), clone.getTitle());
// Get a cleaved set of peptides from a sequence.
final Protein p = new Protein(">Test protein.\nLENNARTMARTENS");
Protein[] controlCleave = e.cleave(p);
// Get a cleaved set from the clone.
Protein[] cloneCleave = clone.cleave(p);
// Compare the sets. They should be identical.
for(int i = 0; i < cloneCleave.length; i++) {
Assert.assertEquals(controlCleave[i], cloneCleave[i]);
}
// Now change the clone and see if the original changes.
clone.setCleavage("GH");
clone.setMiscleavages(1);
clone.setPosition(Enzyme.NTERM);
clone.setRestrict("L");
clone.setTitle("Clone");
// Clone should have changed.
Assert.assertEquals("GH", new String(clone.getCleavage()));
Assert.assertEquals(1, clone.getMiscleavages());
Assert.assertEquals(Enzyme.NTERM, clone.getPosition());
Assert.assertEquals("L", new String(clone.getRestrict()));
Assert.assertEquals("Clone", clone.getTitle());
// Original should remain the same.
Assert.assertEquals("KR", new String(e.getCleavage()));
Assert.assertEquals(5, e.getMiscleavages());
Assert.assertEquals(Enzyme.CTERM, e.getPosition());
Assert.assertEquals("P", new String(e.getRestrict()));
Assert.assertEquals("Test", e.getTitle());
}
/**
* This method test whether the isEnzymatic product method functions.
*/
public void testIsProduct() {
// C-terminal cleavage.
Enzyme e = new Enzyme("Test", "KR", "P", "Cterm", 1);
Protein p = new Protein(">Test Protein.\nLENNARTMARTENS");
// A non-enzymatic product by sequence and subsequently by (human readable!) indices.
Assert.assertEquals(Enzyme.ENTIRELY_NOT_ENZYMATIC, e.isEnzymaticProduct(p.getSequence().getSequence(), "ENN"));
Assert.assertEquals(Enzyme.ENTIRELY_NOT_ENZYMATIC, e.isEnzymaticProduct(p.getSequence().getSequence(), 2, 4));
// A half enzymatic sequence (N-terminal), also with the true N-terminus included.
Assert.assertEquals(Enzyme.N_TERM_ENZYMATIC, e.isEnzymaticProduct(p.getSequence().getSequence(), "TMARTE"));
Assert.assertEquals(Enzyme.N_TERM_ENZYMATIC, e.isEnzymaticProduct(p.getSequence().getSequence(), 7, 12));
Assert.assertEquals(Enzyme.N_TERM_ENZYMATIC, e.isEnzymaticProduct(p.getSequence().getSequence(), "LEN"));
Assert.assertEquals(Enzyme.N_TERM_ENZYMATIC, e.isEnzymaticProduct(p.getSequence().getSequence(), 1, 3));
// A half enzymatic sequence (C-terminal), also with the true C-terminus included.
Assert.assertEquals(Enzyme.C_TERM_ENZYMATIC, e.isEnzymaticProduct(p.getSequence().getSequence(), "NNAR"));
Assert.assertEquals(Enzyme.C_TERM_ENZYMATIC, e.isEnzymaticProduct(p.getSequence().getSequence(), 3, 6));
Assert.assertEquals(Enzyme.C_TERM_ENZYMATIC, e.isEnzymaticProduct(p.getSequence().getSequence(), "RTENS"));
Assert.assertEquals(Enzyme.C_TERM_ENZYMATIC, e.isEnzymaticProduct(p.getSequence().getSequence(), 10, 14));
// Check the correct behaviour when multiple occurrences take place.
Assert.assertEquals(Enzyme.ENTIRELY_NOT_ENZYMATIC, e.isEnzymaticProduct("LGHJKLIGHKL", "GH"));
Assert.assertEquals(Enzyme.N_TERM_ENZYMATIC, e.isEnzymaticProduct("GHJKLIGHKL", "GH"));
Assert.assertEquals(Enzyme.N_TERM_ENZYMATIC, e.isEnzymaticProduct("FTTRGHJKLIGHKL", "GH"));
Assert.assertEquals(Enzyme.C_TERM_ENZYMATIC, e.isEnzymaticProduct("FTTGKLIGKPL", "GK"));
Assert.assertEquals(Enzyme.FULLY_ENZYMATIC, e.isEnzymaticProduct("FTTRGKLIGKPL", "GK"));
// Now check the correct handling of restriction locations.
Assert.assertEquals(Enzyme.ENTIRELY_NOT_ENZYMATIC, e.isEnzymaticProduct("LGHRPHVVGRPLMM", "PHVVGR"));
Assert.assertEquals(Enzyme.N_TERM_ENZYMATIC, e.isEnzymaticProduct("LGHRHVVGRPLMM", "HVVGR"));
Assert.assertEquals(Enzyme.N_TERM_ENZYMATIC, e.isEnzymaticProduct("HVVGRPLMM", "HVVGR"));
Assert.assertEquals(Enzyme.C_TERM_ENZYMATIC, e.isEnzymaticProduct("LGHRPHVVGR", "PHVVGR"));
Assert.assertEquals(Enzyme.C_TERM_ENZYMATIC, e.isEnzymaticProduct("LGHRPHVVGRLMM", "PHVVGR"));
Assert.assertEquals(Enzyme.FULLY_ENZYMATIC, e.isEnzymaticProduct("LGHRHVVGRLMM", "HVVGR"));
// N-terminal cleavage.
e = new Enzyme("Test2", "KR", "P", "Nterm", 1);
// A non-enzymatic product.
Assert.assertEquals(Enzyme.ENTIRELY_NOT_ENZYMATIC, e.isEnzymaticProduct("KARVAL", "ARVA"));
Assert.assertEquals(Enzyme.ENTIRELY_NOT_ENZYMATIC, e.isEnzymaticProduct("KARVAL", 2, 5));
// A half enzymatic sequence (N-terminal), also with the true N-terminus included.
Assert.assertEquals(Enzyme.N_TERM_ENZYMATIC, e.isEnzymaticProduct("LLKARVAL", "KARV"));
Assert.assertEquals(Enzyme.N_TERM_ENZYMATIC, e.isEnzymaticProduct("LLKARVAL", 3, 6));
Assert.assertEquals(Enzyme.N_TERM_ENZYMATIC, e.isEnzymaticProduct("ARVAL", "ARV"));
Assert.assertEquals(Enzyme.N_TERM_ENZYMATIC, e.isEnzymaticProduct("ARVAL", 1, 3));
Assert.assertEquals(Enzyme.N_TERM_ENZYMATIC, e.isEnzymaticProduct("KARVAL", "KARV"));
Assert.assertEquals(Enzyme.N_TERM_ENZYMATIC, e.isEnzymaticProduct("KARVAL", 1, 4));
// A half enzymatic sequence (C-terminal), also with the true C-terminus included.
Assert.assertEquals(Enzyme.C_TERM_ENZYMATIC, e.isEnzymaticProduct("LLKARVAL", "LKA"));
Assert.assertEquals(Enzyme.C_TERM_ENZYMATIC, e.isEnzymaticProduct("LLKARVAL", 2, 4));
Assert.assertEquals(Enzyme.C_TERM_ENZYMATIC, e.isEnzymaticProduct("LLKARVAL", "VAL"));
Assert.assertEquals(Enzyme.C_TERM_ENZYMATIC, e.isEnzymaticProduct("LLKARVAL", 6, 8));
// Check the correct behaviour when multiple occurrences take place.
Assert.assertEquals(Enzyme.ENTIRELY_NOT_ENZYMATIC, e.isEnzymaticProduct("LLKARVALGHGHGLKARVRAL", "LKARV"));
Assert.assertEquals(Enzyme.N_TERM_ENZYMATIC, e.isEnzymaticProduct("GHKARVALGHKARVAL", "KARV"));
Assert.assertEquals(Enzyme.C_TERM_ENZYMATIC, e.isEnzymaticProduct("LLKARVALGHGHLKARPAL", "LKA"));
Assert.assertEquals(Enzyme.FULLY_ENZYMATIC, e.isEnzymaticProduct("LLKARVALGHGHLKARPAL", "KA"));
// Now check the correct handling of restriction locations.
Assert.assertEquals(Enzyme.ENTIRELY_NOT_ENZYMATIC, e.isEnzymaticProduct("LGHRPHVVGRPLMM", "RPHVVG"));
Assert.assertEquals(Enzyme.N_TERM_ENZYMATIC, e.isEnzymaticProduct("LGHRHVVGRPLMM", "RHVVG"));
Assert.assertEquals(Enzyme.N_TERM_ENZYMATIC, e.isEnzymaticProduct("HVVGRPLMM", "HVVG"));
Assert.assertEquals(Enzyme.C_TERM_ENZYMATIC, e.isEnzymaticProduct("LGHRPHVVGR", "RPHVVG"));
Assert.assertEquals(Enzyme.C_TERM_ENZYMATIC, e.isEnzymaticProduct("LGHRPHVVGRLMM", "RPHVVG"));
Assert.assertEquals(Enzyme.FULLY_ENZYMATIC, e.isEnzymaticProduct("LGHRHVVGRLMM", "RHVVG"));
// Test exception handling.
try {
e.isEnzymaticProduct("LENNARTMARTENS", "FILIBERKE");
fail("No IllegalArgumentException thrown when confronting an Enzyme with subsequence 'FILIBERKE' in 'LENNARTMARTENS' for 'isEnzymaticProduct(String, String)'!");
} catch(IllegalArgumentException iae) {
// Perfect.
}
try {
e.isEnzymaticProduct("LENNARTMARTENS", "FILIBERKE");
fail("No IllegalArgumentException thrown when confronting an Enzyme with subsequence 'FILIBERKE' in 'LENNARTMARTENS' for 'isEnzymaticProduct(String, String)'!");
} catch(IllegalArgumentException iae) {
// Perfect.
}
try {
e.isEnzymaticProduct("LENNARTMARTENS", -1, 12);
fail("No IllegalArgumentException thrown when confronting an Enzyme with subsequence indices (-1, 12) and 'LENNARTMARTENS' for 'isEnzymaticProduct(String, int, int)'!");
} catch(IllegalArgumentException iae) {
// Perfect.
}
try {
e.isEnzymaticProduct("LENNARTMARTENS", 1, -1);
fail("No IllegalArgumentException thrown when confronting an Enzyme with subsequence indices (1, -1) and 'LENNARTMARTENS' for 'isEnzymaticProduct(String, int, int)'!");
} catch(IllegalArgumentException iae) {
// Perfect.
}
try {
e.isEnzymaticProduct("LENNARTMARTENS", 3, 2);
fail("No IllegalArgumentException thrown when confronting an Enzyme with subsequence indices (3, 2) and 'LENNARTMARTENS' for 'isEnzymaticProduct(String, int, int)'!");
} catch(IllegalArgumentException iae) {
// Perfect.
}
try {
e.isEnzymaticProduct("LENNARTMARTENS", 6, 15);
fail("No IllegalArgumentException thrown when confronting an Enzyme with subsequence indices (6, 15) and 'LENNARTMARTENS' (last char at 14) for 'isEnzymaticProduct(String, int, int)'!");
} catch(IllegalArgumentException iae) {
// Perfect.
}
try {
e.isEnzymaticProduct("LENNARTMARTENS", 6, 129);
fail("No IllegalArgumentException thrown when confronting an Enzyme with subsequence indices (6, 129) and 'LENNARTMARTENS' (last char at 14) for 'isEnzymaticProduct(String, int, int)'!");
} catch(IllegalArgumentException iae) {
// Perfect.
}
}
}