package core;

import edu.umd.cs.findbugs.annotations.SuppressFBWarnings;
import org.junit.Before;
import org.junit.Test;

import java.io.IOException;
import java.io.InputStream;
import java.util.HashMap;

import static org.junit.Assert.*;

/**
 * Created by user on 18-5-2016.
 */
public class ParserTest {
    public Parser p;

    /**
     * Initialize the Parser before testing it.
     */
    @Before
    public void setUp() {
        p = new Parser();
    }

    /**
     * Test the constructor.
     */
    @Test
    public void testConstructor() {
        assertNotNull(p);
    }

    /**
     * Test the readGFA method.
     */
    @SuppressFBWarnings({"DLS_DEAD_LOCAL_STORE",
            "OBL_UNSATISFIED_OBLIGATION_EXCEPTION_EDGE"})
    @Test
    public void readGFA() {
        HashMap<Integer, Node> map = new HashMap<Integer, Node>();
        InputStream is = getClass().getResourceAsStream("/TBTestFile.gfa");

        try {
            map = p.readGFA(is);
            is.close();
        } catch (IOException e) {
            e.printStackTrace();
        }

        assertEquals(4, map.size());

        for (int i = 1; i <= 4; i++) {
            Node n = map.get(i);
            assertEquals(i, n.getId());
            assertEquals(Character.toString((char) ('A' + i - 1)), n.getSequence());
            assertEquals(i, n.getzIndex());
            assertEquals("GENOME_1", n.getGenomes().get(0));
            assertEquals(Integer.valueOf(i + 1), n.getLinks().get(0));
        }
    }

}
package core;

import edu.umd.cs.findbugs.annotations.SuppressFBWarnings;
import org.junit.Before;
import org.junit.Test;

import java.io.IOException;
import java.io.InputStream;
import java.util.HashMap;

import static org.junit.Assert.*;

/**
 * Created by user on 18-5-2016.
 */
public class ParserTest {
    public Parser p;

    /**
     * Initialize the Parser before testing it.
     */
    @Before
    public void setUp() {
        p = new Parser();
    }

    /**
     * Test the constructor.
     */
    @Test
    public void testConstructor() {
        assertNotNull(p);
    }

    /**
     * Test the readGFA method.
     */
    @SuppressFBWarnings({"DLS_DEAD_LOCAL_STORE",
            "OBL_UNSATISFIED_OBLIGATION_EXCEPTION_EDGE"})
    @Test
    public void readGFA() {
        HashMap<Integer, Node> map = new HashMap<Integer, Node>();
        InputStream is = getClass().getResourceAsStream("/TBTestFile.gfa");

        try {
            map = p.readGFAAsResource(is);
            is.close();
        } catch (IOException e) {
            e.printStackTrace();
        }

        assertEquals(4, map.size());

        for (int i = 1; i <= 4; i++) {
            Node n = map.get(i);
            assertEquals(i, n.getId());
            assertEquals(Character.toString((char) ('A' + i - 1)), n.getSequence());
            assertEquals(i, n.getzIndex());
            assertEquals("GENOME_1", n.getGenomes().get(0));
            assertEquals(Integer.valueOf(i + 1), n.getLinks().get(0));
        }
    }

}
test fixed