[Biojava-l] Test failed for Alphabet.getSymbolMatchType method

[pprun]

Hi,
The current implementation uses the same condition equalsIgnoreCase for
EXACT_STRING_MATCH and MIXED_CASE_MATCH


    public SymbolMatchType getSymbolMatchType(Symbol a, Symbol b) {
       ...
        if (a.toString().equalsIgnoreCase(b.toString())) {
            return SymbolMatchType.EXACT_STRING_MATCH;
        }
        if (a.toString().equalsIgnoreCase(b.toString())) {
            return SymbolMatchType.MIXED_CASE_MATCH;
        }
          ...

String.equals should be used for EXACT_STRING_MATCH:

    public SymbolMatchType getSymbolMatchType(Symbol a, Symbol b) {
        ...
        if (a.toString().equals(b.toString())) {
            return SymbolMatchType.EXACT_STRING_MATCH;
        }
        if (a.toString().equalsIgnoreCase(b.toString())) {
            return SymbolMatchType.MIXED_CASE_MATCH;
        }
          ...

The test case used to identify the above bug is:

/*
 *                    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.core.symbol;

import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Test;
import static org.junit.Assert.*;

/**
 *
 * @author pprun
 */
public class AlphabetTest {

    public AlphabetTest() {
    }

    @BeforeClass
    public static void setUpClass() throws Exception {
    }

    @AfterClass
    public static void tearDownClass() throws Exception {
    }

    @Before
    public void setUp() {
    }

    @After
    public void tearDown() {
    }

    /**
     * Test of getSymbolMatchType method, of class Alphabet.
     */
    @Test
    public void testGetSymbolMatchType() {
        System.out.println("getSymbolMatchType");

        Alphabet testAlphabet = new Alphabet("testGetSymbolMatchType");

        // 1. exact match
        Symbol a = Symbol.get("ATGC");
        Symbol b = Symbol.get("ATGC");
        SymbolMatchType expResult = SymbolMatchType.EXACT_MATCH;
        SymbolMatchType result = testAlphabet.getSymbolMatchType(a, b);
        assertEquals(expResult, result);

        // 2. mixed case match
        a = Symbol.get("ATGC");
        b = Symbol.get("aTGC");
        expResult = SymbolMatchType.MIXED_CASE_MATCH;
        result = testAlphabet.getSymbolMatchType(a, b);
        assertEquals(expResult, result);
    }
}


BTW., how can I get the dev/test role?
Then I can contribute to the development or test (as I'm still a
beginner for bio field) for BJ3.

Thanks,
Pprun