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/*
* IsoelectricPointCalcTest.java
*
* Created on April 2, 2007, 4:01 PM
*
*/
package org.biojava.bio.proteomics;
import junit.framework.TestCase;
import org.biojava.bio.BioException;
import org.biojava.bio.seq.ProteinTools;
import org.biojava.bio.symbol.IllegalSymbolException;
import org.biojava.bio.symbol.SymbolList;
import org.biojava.bio.symbol.SymbolPropertyTable;
/**
*
* @author George Waldon - testGetIsoelectricPointTest
*/
public class IsoelectricPointCalcTest extends TestCase {
/** Test pK tables are loaded in proper order.
*/
public void testPKTables() {
SymbolPropertyTable PK_NtermTable = ProteinTools.getSymbolPropertyTable(SymbolPropertyTable.PK_Nterm);
SymbolPropertyTable pKTable = ProteinTools.getSymbolPropertyTable(SymbolPropertyTable.PK);
SymbolPropertyTable PK_CtermTable = ProteinTools.getSymbolPropertyTable(SymbolPropertyTable.PK_Cterm);
try {
double pK = PK_NtermTable.getDoubleValue(ProteinTools.d());
assertTrue(pK == 7.50);
pK = pKTable.getDoubleValue(ProteinTools.d());
assertTrue(pK == -4.05);
pK = PK_CtermTable.getDoubleValue(ProteinTools.d());
assertTrue(pK == -4.55);
} catch (IllegalSymbolException ex) {
fail(ex.getMessage());
}
}
public void testGetIsoelectricPointTest() {
try {
SymbolList pro = ProteinTools.createProtein("hhhhhher");
double p1 = IsoelectricPointCalc.getIsoelectricPoint(pro);
pro = ProteinTools.createProtein("h-hhhhher");
double p2 = IsoelectricPointCalc.getIsoelectricPoint(pro);
pro = ProteinTools.createProtein("hxhhhhher");
double p3 = IsoelectricPointCalc.getIsoelectricPoint(pro);
assertTrue(p1==p2);
assertTrue(p1==p3);
pro = ProteinTools.createProtein("cdehkry");
double p4 = IsoelectricPointCalc.getIsoelectricPoint(pro);
assertTrue(p4==6.74);
pro = ProteinTools.createProtein("da");
p4 = IsoelectricPointCalc.getIsoelectricPoint(pro);
assertTrue(p4==3.80);
pro = ProteinTools.createProtein("ad");
p4 = IsoelectricPointCalc.getIsoelectricPoint(pro);
assertTrue(p4==4.30);
} catch (IllegalSymbolException ex) {
fail(ex.getMessage());
} catch (BioException ex) {
fail(ex.getMessage());
}
}
}
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