Need some assistance coding this Fragment file. I have included the test file for the code. Thank you very much.

package sequencer;

public class Fragment {

/**

* Creates a new Fragment based upon a String representing a sequence of nucleotides,

* containing only the uppercase characters G, C, A and T.

* @param nucleotides

* @throws IllegalArgumentException if invalid characters are in the sequence of nucleotides

*/

public Fragment(String nucleotides) throws IllegalArgumentException {

}

/**

* Returns the length of this fragment.

*

* @return the length of this fragment

*/

public int length() {

return 0;

}

/**

* Returns a String representation of this fragment, exactly as was passed to the constructor.

*

* @return a String representation of this fragment

*/

@Override

public String toString() {

return null;

}

/**

* Return true if and only if this fragment contains the same sequence of nucleotides

* as another sequence.

*/

@Override

public boolean equals(Object o) {

return false;

}

/**

* Returns the number of nucleotides of overlap between the end of this fragment and

* the start of another fragment, f.

*

* The largest overlap is found, for example, CAA and AAG have an overlap of 2, not 1.

*

* @param f the other fragment

* @return the number of nucleotides of overlap

*/

public int calculateOverlap(Fragment f) {

return 0;

}

/**

* Returns a new fragment based upon merging this fragment with another fragment f.

*

* This fragment will be on the left, the other fragment will be on the right; the

* fragments will be overlapped as much as possible during the merge.

*

* @param f the other fragment

* @return a new fragment based upon merging this fragment with another fragment

*/

public Fragment mergedWith(Fragment f) {

return null;

}

}

FragmentTest.java

package sequencer;

import static org.junit.Assert.*;

import org.junit.Rule; import org.junit.Test; import org.junit.rules.Timeout;

public class FragmentTest {

// @Rule // public Timeout globalTimeout = Timeout.seconds(10); // 10 seconds

@Test public void testValidConstructor() { Fragment f = new Fragment("GCAT"); } @Test(expected = IllegalArgumentException.class) public void testInvalidConstructor1() { Fragment f = new Fragment("MARC"); } @Test(expected = IllegalArgumentException.class) public void testInvalidConstructor2() { Fragment f = new Fragment("G C A T"); } @Test public void testLength1() { Fragment f = new Fragment("G"); assertEquals(1, f.length()); } @Test public void testLength5() { Fragment f = new Fragment("GGCAT"); assertEquals(5, f.length()); }

@Test public void testToString() { Fragment f = new Fragment("GCAT"); assertEquals("GCAT", f.toString()); } @Test public void testEqualsTrue1() { Fragment f = new Fragment("GCAT"); assertTrue(f.equals(f)); } @Test public void testEqualsTrue2() { Fragment f = new Fragment(new String("GCAT")); Fragment g = new Fragment(new String("GCAT")); assertTrue(f.equals(g)); assertTrue(g.equals(f)); }

@Test public void testNotEqualsNull() { Fragment f = new Fragment("GCAT"); assertFalse(f.equals(null)); }

@Test public void testNotEqualsObject() { Fragment f = new Fragment("GCAT"); assertFalse(f.equals(new Object())); }

@Test public void testNotEqual() { Fragment f = new Fragment("GCAT"); Fragment g = new Fragment("TACG"); assertFalse(f.equals(g)); }

@Test public void testNoOverlap() { Fragment f = new Fragment("GCAT"); Fragment g = new Fragment("CGTA"); assertEquals(0, f.calculateOverlap(g)); }

@Test public void testOneOverlap() { Fragment f = new Fragment("GGGA"); Fragment g = new Fragment("AGGG"); assertEquals(1, f.calculateOverlap(g)); }

@Test public void testTwoOverlap() { Fragment f = new Fragment("GGAC"); Fragment g = new Fragment("ACGG"); assertEquals(2, f.calculateOverlap(g)); }

@Test public void testTwoOverlapBounds() { Fragment f = new Fragment("TAC"); Fragment g = new Fragment("ACAGAT"); assertEquals(2, f.calculateOverlap(g)); }

@Test public void testThreeOverlap() { Fragment f = new Fragment("GGAAC"); Fragment g = new Fragment("AACGG"); assertEquals(3, f.calculateOverlap(g)); }

@Test public void testOverlapPastBounds() { Fragment f = new Fragment("GGAA"); Fragment g = new Fragment("AAGGAA"); assertEquals(2, f.calculateOverlap(g)); } @Test public void testMultipleOverlap() { Fragment f = new Fragment("GGAACA"); Fragment g = new Fragment("AACAGG"); assertEquals(4, f.calculateOverlap(g)); }

@Test public void testNoMerge() { Fragment f = new Fragment("GCAT"); Fragment g = new Fragment("CGTA"); assertEquals(new Fragment("GCATCGTA"), f.mergedWith(g)); }

@Test public void testOneMerge() { Fragment f = new Fragment("GGGA"); Fragment g = new Fragment("AGGG"); assertEquals(new Fragment("GGGAGGG"), f.mergedWith(g)); }

@Test public void testTwoMerge() { Fragment f = new Fragment("GGAC"); Fragment g = new Fragment("ACGG"); assertEquals(new Fragment("GGACGG"), f.mergedWith(g)); }

@Test public void testSameMergeLength() { Fragment f = new Fragment("GCAT"); Fragment g = new Fragment("GCAT"); assertEquals(4, f.calculateOverlap(g)); }

@Test public void testSameMerge() { Fragment f = new Fragment("GCAT"); Fragment g = new Fragment("GCAT"); assertEquals(new Fragment("GCAT"), f.mergedWith(g)); }

@Test public void testThreeMerge() { Fragment f = new Fragment("GGAAC"); Fragment g = new Fragment("AACGG"); assertEquals(new Fragment("GGAACGG"), f.mergedWith(g)); }

@Test public void testMultipleMerge() { Fragment f = new Fragment("GGAACA"); Fragment g = new Fragment("AACAGG"); assertEquals(new Fragment("GGAACAGG"), f.mergedWith(g)); } }