obitools4/pkg/obiseq/biosequence_test.go

package obiseq

import (
	"bytes"
	"reflect"
	"sync"
	"testing"
)

// TestNewEmptyBioSequence tests the NewEmptyBioSequence function.
//
// It checks the behavior of the function by creating different BioSequence instances with different preallocate values.
// The function verifies that the sequence is correctly preallocated or not preallocated based on the input value.
// It also checks that the length and capacity of the sequence are set correctly.
// The test fails if the function returns nil or if the sequence length or capacity is not as expected.
func TestNewEmptyBioSequence(t *testing.T) {
	// Test case: preallocate is 0, sequence should not be preallocated
	seq := NewEmptyBioSequence(0)
	if seq == nil {
		t.Errorf("NewEmptyBioSequence(0) returned nil")
	} else if len(seq.sequence) != 0 {
		t.Errorf("Expected sequence length to be 0, got %d", len(seq.sequence))
	}

	// Test case: preallocate is greater than 0, sequence should be preallocated
	seq = NewEmptyBioSequence(100)
	if seq == nil {
		t.Errorf("NewEmptyBioSequence(100) returned nil")
	} else if cap(seq.sequence) < 100 {
		t.Errorf("Expected sequence capacity to be at least 100, got %d", cap(seq.sequence))
	}

	// Test case: preallocate is negative, sequence should not be preallocated
	seq = NewEmptyBioSequence(-100)
	if seq == nil {
		t.Errorf("NewEmptyBioSequence(-100) returned nil")
	} else if len(seq.sequence) != 0 {
		t.Errorf("Expected sequence length to be 0, got %d", len(seq.sequence))
	}
}

// TestNewBioSequence tests the NewBioSequence function.
//
// It checks the correctness of the NewBioSequence function by validating that the BioSequence object
// created has the correct ID, sequence, and definition.
// The function performs two test cases:
//  1. Test case 1 checks if the BioSequence object created using the NewBioSequence function has
//     the expected ID, sequence, and definition when provided with valid inputs.
//  2. Test case 2 checks if the BioSequence object created using the NewBioSequence function has
//     the expected ID, sequence, and definition when provided with different valid inputs.
func TestNewBioSequence(t *testing.T) {
	// Test case 1:
	id := "seq1"
	sequence := []byte("ACGT")
	definition := "DNA sequence"
	expectedID := "seq1"
	expectedSequence := []byte("acgt")
	expectedDefinition := "DNA sequence"

	bs := NewBioSequence(id, sequence, definition)

	if bs.Id() != expectedID {
		t.Errorf("Expected ID to be %s, but got %s", expectedID, bs.Id())
	}

	if !bytes.Equal(bs.Sequence(), expectedSequence) {
		t.Errorf("Expected sequence to be %v, but got %v", expectedSequence, bs.Sequence())
	}

	if bs.Definition() != expectedDefinition {
		t.Errorf("Expected definition to be %s, but got %s", expectedDefinition, bs.Definition())
	}

	// Test case 2:
	id = "seq2"
	sequence = []byte("ATCG")
	definition = "RNA sequence"
	expectedID = "seq2"
	expectedSequence = []byte("atcg")
	expectedDefinition = "RNA sequence"

	bs = NewBioSequence(id, sequence, definition)

	if bs.Id() != expectedID {
		t.Errorf("Expected ID to be %s, but got %s", expectedID, bs.Id())
	}

	if !bytes.Equal(bs.Sequence(), expectedSequence) {
		t.Errorf("Expected sequence to be %v, but got %v", expectedSequence, bs.Sequence())
	}

	if bs.Definition() != expectedDefinition {
		t.Errorf("Expected definition to be %s, but got %s", expectedDefinition, bs.Definition())
	}
}

// TestBioSequence_Recycle tests the Recycle method of the BioSequence struct.
//
// Test case 1: Recycle a BioSequence object with non-nil slices and annotations.
// Test case 2: Recycle a nil BioSequence object.
// Test case 3: Recycle a BioSequence object with nil slices and annotations.
func TestBioSequence_Recycle(t *testing.T) {
	// Test case 1: Recycle a BioSequence object with non-nil slices and annotations
	sequence := &BioSequence{
		sequence:    []byte{'A', 'C', 'G', 'T'},
		feature:     []byte("..."),
		qualities:   []byte{30, 30, 30, 30},
		annotations: Annotation{"description": "Test"},
	}
	sequence.Recycle()

	if len(sequence.sequence) != 0 {
		t.Errorf("Expected sequence to be empty, got %v", sequence.sequence)
	}
	if len(sequence.feature) != 0 {
		t.Errorf("Expected feature to be empty, got %v", sequence.feature)
	}
	if len(sequence.qualities) != 0 {
		t.Errorf("Expected qualities to be empty, got %v", sequence.qualities)
	}
	if sequence.annotations != nil {
		t.Errorf("Expected annotations to be nil, got %v", sequence.annotations)
	}

	// Test case 2: Recycle a nil BioSequence object
	var nilSequence *BioSequence
	nilSequence.Recycle() // No panic expected

	// Test case 3: Recycle a BioSequence object with nil slices and annotations
	emptySequence := &BioSequence{}
	emptySequence.Recycle() // No panic expected
}

// TestCopy tests the Copy function of the BioSequence struct.
//
// It creates a new BioSequence and copies the fields from the original sequence
// to the new one. It then performs various tests to check if the fields were
// copied correctly.
//
// Parameters:
// - t: The testing.T object used for reporting test failures.
//
// Returns: None.
func TestCopy(t *testing.T) {
	seq := &BioSequence{
		id:         "test",
		definition: "test sequence",
		sequence:   []byte("ATCG"),
		qualities:  []byte("1234"),
		feature:    []byte("feature1...feature2"),
		annotations: Annotation{
			"annotation1": "value1",
			"annotation2": "value2",
		},
		annot_lock: sync.Mutex{},
	}

	newSeq := seq.Copy()

	// Test if the id and definition fields are copied correctly
	if newSeq.id != seq.id {
		t.Errorf("Expected id to be %v, got %v", seq.id, newSeq.id)
	}
	if newSeq.definition != seq.definition {
		t.Errorf("Expected definition to be %v, got %v", seq.definition, newSeq.definition)
	}

	// Test if the sequence, qualities, and feature fields are copied correctly
	if !reflect.DeepEqual(newSeq.sequence, seq.sequence) {
		t.Errorf("Expected sequence to be %v, got %v", seq.sequence, newSeq.sequence)
	}
	if !reflect.DeepEqual(newSeq.qualities, seq.qualities) {
		t.Errorf("Expected qualities to be %v, got %v", seq.qualities, newSeq.qualities)
	}
	if !reflect.DeepEqual(newSeq.feature, seq.feature) {
		t.Errorf("Expected feature to be %v, got %v", seq.feature, newSeq.feature)
	}

	// Test if the annotations are copied correctly
	if !reflect.DeepEqual(newSeq.annotations, seq.annotations) {
		t.Errorf("Expected annotations to be %v, got %v", seq.annotations, newSeq.annotations)
	}
}

// TestBioSequence_Id tests the Id method of the BioSequence struct.
//
// It initializes a BioSequence with an ID using the constructor and then
// verifies that the Id method returns the expected ID.
// The expected ID is "ABC123".
// The method takes no parameters and returns a string.
func TestBioSequence_Id(t *testing.T) {
	// Initialize BioSequence with an ID using the constructor
	bioSeq := NewBioSequence("ABC123", []byte(""), "")

	// Test case: ID is returned correctly
	expected := "ABC123"
	result := bioSeq.Id()
	if result != expected {
		t.Errorf("Expected ID to be %s, but got %s", expected, result)
	}
}

// TestBioSequenceDefinition tests the Definition() method of the BioSequence struct.
//
// This function verifies the behavior of the Definition() method in two test cases:
// 1. Empty definition: It creates a BioSequence object with an empty definition and verifies that the Definition() method returns an empty string.
// 2. Non-empty definition: It creates a BioSequence object with a non-empty definition and verifies that the Definition() method returns the expected definition.
func TestBioSequenceDefinition(t *testing.T) {
	// Test case 1: Empty definition
	seq1 := NewBioSequence("", []byte{}, "")
	expected1 := ""
	if got1 := seq1.Definition(); got1 != expected1 {
		t.Errorf("Expected %q, but got %q", expected1, got1)
	}

	// Test case 2: Non-empty definition
	seq2 := NewBioSequence("", []byte{}, "This is a definition")
	expected2 := "This is a definition"
	if got2 := seq2.Definition(); got2 != expected2 {
		t.Errorf("Expected %q, but got %q", expected2, got2)
	}
}

// TestBioSequenceSequence tests the Sequence() method of the BioSequence struct.
//
// It verifies the behavior of the Sequence() method under two scenarios:
// - Test case 1: Empty sequence
// - Test case 2: Non-empty sequence
//
// Parameter(s):
//   - t: The testing object provided by the testing framework.
//     It is used to report errors if the test fails.
//
// Return type(s):
// None.
func TestBioSequenceSequence(t *testing.T) {
	// Test case 1: Empty sequence
	seq := NewBioSequence("", []byte{}, "")
	expected := []byte{}
	actual := seq.Sequence()
	if !bytes.EqualFold(actual, expected) {
		t.Errorf("Expected %v, but got %v", expected, actual)
	}

	// Test case 2: Non-empty sequence
	seq = NewBioSequence("", []byte("atcg"), "")
	expected = []byte("atcg")
	actual = seq.Sequence()
	if !bytes.EqualFold(actual, expected) {
		t.Errorf("Expected %v, but got %v", expected, actual)
	}
}

// TestBioSequence_String tests the String method of the BioSequence struct.
//
// It includes two test cases:
//
//  1. Test case 1: Empty sequence
//     - Creates an empty BioSequence instance.
//     - Expects an empty string as the result of calling the String method on the BioSequence instance.
//
//  2. Test case 2: Non-empty sequence
//     - Creates a BioSequence instance with the sequence "acgt".
//     - Expects the sequence "acgt" as the result of calling the String method on the BioSequence instance.
//
// No parameters are required.
// No return types are specified.
func TestBioSequence_String(t *testing.T) {
	// Test case 1: Empty sequence
	seq1 := &BioSequence{}
	expected1 := ""
	if got1 := seq1.String(); got1 != expected1 {
		t.Errorf("Test case 1 failed: expected %s, got %s", expected1, got1)
	}

	// Test case 2: Non-empty sequence
	seq2 := &BioSequence{sequence: []byte("acgt")}
	expected2 := "acgt"
	if got2 := seq2.String(); got2 != expected2 {
		t.Errorf("Test case 2 failed: expected %s, got %s", expected2, got2)
	}
}

// TestBioSequence_Len tests the Len method of the BioSequence struct.
//
// It verifies the behavior of the method by performing multiple test cases.
// Each test case creates a BioSequence instance with a specific sequence and
// compares the actual length returned by the Len method with the expected
// length.
//
// Test 1: Empty sequence
//   - Create a BioSequence instance with an empty sequence.
//   - The expected length is 0.
//   - Check if the actual length returned by the Len method matches the expected
//     length. If not, report an error.
//
// Test 2: Sequence with 5 characters
//   - Create a BioSequence instance with a sequence of 5 characters.
//   - The expected length is 5.
//   - Check if the actual length returned by the Len method matches the expected
//     length. If not, report an error.
//
// Test 3: Sequence with 10 characters
//   - Create a BioSequence instance with a sequence of 10 characters.
//   - The expected length is 10.
//   - Check if the actual length returned by the Len method matches the expected
//     length. If not, report an error.
func TestBioSequence_Len(t *testing.T) {
	// Test 1: Empty sequence
	s1 := NewBioSequence("", nil, "")
	expected1 := 0
	if len := s1.Len(); len != expected1 {
		t.Errorf("Expected length: %d, but got: %d", expected1, len)
	}

	// Test 2: Sequence with 5 characters
	s2 := NewBioSequence("", []byte("ATCGT"), "")
	expected2 := 5
	if len := s2.Len(); len != expected2 {
		t.Errorf("Expected length: %d, but got: %d", expected2, len)
	}

	// Test 3: Sequence with 10 characters
	s3 := NewBioSequence("", []byte("AGCTAGCTAG"), "")
	expected3 := 10
	if len := s3.Len(); len != expected3 {
		t.Errorf("Expected length: %d, but got: %d", expected3, len)
	}
}

// TestBioSequence_Composition tests the Composition method of the BioSequence struct.
//
// It tests the method with three different test cases:
// 1. Empty sequence: It checks if the Composition method returns the expected composition when the sequence is empty.
// 2. Sequence with valid nucleotides: It checks if the Composition method returns the expected composition when the sequence contains valid nucleotides.
// 3. Sequence with invalid nucleotides: It checks if the Composition method returns the expected composition when the sequence contains invalid nucleotides.
//
// The expected composition for each test case is defined in a map where the keys are the nucleotides and the values are the expected counts.
// The Composition method is expected to return a map with the actual nucleotide counts.
//
// Parameters:
// - t: The testing.T object used for reporting test failures and logging.
//
// Return type: void.
func TestBioSequence_Composition(t *testing.T) {
	// Test case: Empty sequence
	seq1 := NewBioSequence("", []byte(""), "")
	expected1 := map[byte]int{'a': 0, 'c': 0, 'g': 0, 't': 0, 'o': 0}
	if result1 := seq1.Composition(); !reflect.DeepEqual(result1, expected1) {
		t.Errorf("Composition() returned incorrect result for empty sequence. Got %v, expected %v", result1, expected1)
	}

	// Test case: Sequence with valid nucleotides
	seq2 := NewBioSequence("", []byte("acgtACGT"), "")
	expected2 := map[byte]int{'a': 2, 'c': 2, 'g': 2, 't': 2, 'o': 0}
	if result2 := seq2.Composition(); !reflect.DeepEqual(result2, expected2) {
		t.Errorf("Composition() returned incorrect result for sequence with valid nucleotides. Got %v, expected %v", result2, expected2)
	}

	// Test case: Sequence with invalid nucleotides
	seq3 := NewBioSequence("", []byte("acgtACGT1234"), "")
	expected3 := map[byte]int{'a': 2, 'c': 2, 'g': 2, 't': 2, 'o': 4}
	if result3 := seq3.Composition(); !reflect.DeepEqual(result3, expected3) {
		t.Errorf("Composition() returned incorrect result for sequence with invalid nucleotides. Got %v, expected %v", result3, expected3)
	}
}