mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-03-25 13:30:52 +00:00
Add Jaccard distance and similarity computations for KmerSet and KmerSetGroup
Add Jaccard distance and similarity computations for KmerSet and KmerSetGroup This commit introduces Jaccard distance and similarity methods for KmerSet and KmerSetGroup. For KmerSet: - Added JaccardDistance method to compute the Jaccard distance between two KmerSets - Added JaccardSimilarity method to compute the Jaccard similarity between two KmerSets For KmerSetGroup: - Added JaccardDistanceMatrix method to compute a pairwise Jaccard distance matrix - Added JaccardSimilarityMatrix method to compute a pairwise Jaccard similarity matrix Also includes: - New DistMatrix implementation in pkg/obidist for storing and computing distance/similarity matrices - Updated version handling with bump-version target in Makefile - Added tests for all new methods
This commit is contained in:
Eric Coissac
386
pkg/obidist/dist_matrix_test.go
Normal file
386
pkg/obidist/dist_matrix_test.go
Normal file
@@ -0,0 +1,386 @@
|
||||
package obidist
|
||||
|
||||
import (
|
||||
"math"
|
||||
"testing"
|
||||
)
|
||||
|
||||
func TestNewDistMatrix(t *testing.T) {
|
||||
dm := NewDistMatrix(5)
|
||||
|
||||
if dm.Size() != 5 {
|
||||
t.Errorf("Expected size 5, got %d", dm.Size())
|
||||
}
|
||||
|
||||
// Check that all values are initialized to 0
|
||||
for i := 0; i < 5; i++ {
|
||||
for j := 0; j < 5; j++ {
|
||||
if dm.Get(i, j) != 0.0 {
|
||||
t.Errorf("Expected 0.0 at (%d, %d), got %f", i, j, dm.Get(i, j))
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
func TestDistMatrixDiagonal(t *testing.T) {
|
||||
dm := NewDistMatrix(5)
|
||||
|
||||
// Diagonal should always be 0
|
||||
for i := 0; i < 5; i++ {
|
||||
if dm.Get(i, i) != 0.0 {
|
||||
t.Errorf("Expected diagonal element (%d, %d) to be 0.0, got %f", i, i, dm.Get(i, i))
|
||||
}
|
||||
}
|
||||
|
||||
// Try to set diagonal (should be ignored)
|
||||
dm.Set(2, 2, 5.0)
|
||||
if dm.Get(2, 2) != 0.0 {
|
||||
t.Errorf("Diagonal should remain 0.0 even after Set, got %f", dm.Get(2, 2))
|
||||
}
|
||||
}
|
||||
|
||||
func TestDistMatrixSymmetry(t *testing.T) {
|
||||
dm := NewDistMatrix(4)
|
||||
|
||||
dm.Set(0, 1, 1.5)
|
||||
dm.Set(0, 2, 2.5)
|
||||
dm.Set(1, 3, 3.5)
|
||||
|
||||
// Check symmetry
|
||||
if dm.Get(0, 1) != dm.Get(1, 0) {
|
||||
t.Errorf("Matrix not symmetric: Get(0,1)=%f, Get(1,0)=%f", dm.Get(0, 1), dm.Get(1, 0))
|
||||
}
|
||||
|
||||
if dm.Get(0, 2) != dm.Get(2, 0) {
|
||||
t.Errorf("Matrix not symmetric: Get(0,2)=%f, Get(2,0)=%f", dm.Get(0, 2), dm.Get(2, 0))
|
||||
}
|
||||
|
||||
if dm.Get(1, 3) != dm.Get(3, 1) {
|
||||
t.Errorf("Matrix not symmetric: Get(1,3)=%f, Get(3,1)=%f", dm.Get(1, 3), dm.Get(3, 1))
|
||||
}
|
||||
}
|
||||
|
||||
func TestDistMatrixSetGet(t *testing.T) {
|
||||
dm := NewDistMatrix(4)
|
||||
|
||||
testCases := []struct {
|
||||
i int
|
||||
j int
|
||||
value float64
|
||||
}{
|
||||
{0, 1, 1.5},
|
||||
{0, 2, 2.5},
|
||||
{0, 3, 3.5},
|
||||
{1, 2, 4.5},
|
||||
{1, 3, 5.5},
|
||||
{2, 3, 6.5},
|
||||
}
|
||||
|
||||
for _, tc := range testCases {
|
||||
dm.Set(tc.i, tc.j, tc.value)
|
||||
}
|
||||
|
||||
for _, tc := range testCases {
|
||||
got := dm.Get(tc.i, tc.j)
|
||||
if math.Abs(got-tc.value) > 1e-10 {
|
||||
t.Errorf("Get(%d, %d): expected %f, got %f", tc.i, tc.j, tc.value, got)
|
||||
}
|
||||
|
||||
// Check symmetry
|
||||
got = dm.Get(tc.j, tc.i)
|
||||
if math.Abs(got-tc.value) > 1e-10 {
|
||||
t.Errorf("Get(%d, %d) (symmetric): expected %f, got %f", tc.j, tc.i, tc.value, got)
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
func TestDistMatrixLabels(t *testing.T) {
|
||||
labels := []string{"A", "B", "C", "D"}
|
||||
dm := NewDistMatrixWithLabels(labels)
|
||||
|
||||
if dm.Size() != 4 {
|
||||
t.Errorf("Expected size 4, got %d", dm.Size())
|
||||
}
|
||||
|
||||
for i, label := range labels {
|
||||
if dm.GetLabel(i) != label {
|
||||
t.Errorf("Expected label %s at index %d, got %s", label, i, dm.GetLabel(i))
|
||||
}
|
||||
}
|
||||
|
||||
// Modify a label
|
||||
dm.SetLabel(1, "Modified")
|
||||
if dm.GetLabel(1) != "Modified" {
|
||||
t.Errorf("Expected label 'Modified' at index 1, got %s", dm.GetLabel(1))
|
||||
}
|
||||
|
||||
// Check Labels() returns a copy
|
||||
labelsCopy := dm.Labels()
|
||||
labelsCopy[0] = "ChangedCopy"
|
||||
if dm.GetLabel(0) != "A" {
|
||||
t.Errorf("Modifying Labels() return value should not affect original labels")
|
||||
}
|
||||
}
|
||||
|
||||
func TestDistMatrixMinDistance(t *testing.T) {
|
||||
dm := NewDistMatrix(4)
|
||||
|
||||
dm.Set(0, 1, 2.5)
|
||||
dm.Set(0, 2, 1.5) // minimum
|
||||
dm.Set(0, 3, 3.5)
|
||||
dm.Set(1, 2, 4.5)
|
||||
dm.Set(1, 3, 5.5)
|
||||
dm.Set(2, 3, 6.5)
|
||||
|
||||
minDist, minI, minJ := dm.MinDistance()
|
||||
|
||||
if math.Abs(minDist-1.5) > 1e-10 {
|
||||
t.Errorf("Expected min distance 1.5, got %f", minDist)
|
||||
}
|
||||
|
||||
if (minI != 0 || minJ != 2) && (minI != 2 || minJ != 0) {
|
||||
t.Errorf("Expected min at (0, 2) or (2, 0), got (%d, %d)", minI, minJ)
|
||||
}
|
||||
}
|
||||
|
||||
func TestDistMatrixMaxDistance(t *testing.T) {
|
||||
dm := NewDistMatrix(4)
|
||||
|
||||
dm.Set(0, 1, 2.5)
|
||||
dm.Set(0, 2, 1.5)
|
||||
dm.Set(0, 3, 3.5)
|
||||
dm.Set(1, 2, 4.5)
|
||||
dm.Set(1, 3, 5.5)
|
||||
dm.Set(2, 3, 6.5) // maximum
|
||||
|
||||
maxDist, maxI, maxJ := dm.MaxDistance()
|
||||
|
||||
if math.Abs(maxDist-6.5) > 1e-10 {
|
||||
t.Errorf("Expected max distance 6.5, got %f", maxDist)
|
||||
}
|
||||
|
||||
if (maxI != 2 || maxJ != 3) && (maxI != 3 || maxJ != 2) {
|
||||
t.Errorf("Expected max at (2, 3) or (3, 2), got (%d, %d)", maxI, maxJ)
|
||||
}
|
||||
}
|
||||
|
||||
func TestDistMatrixGetRow(t *testing.T) {
|
||||
dm := NewDistMatrix(3)
|
||||
|
||||
dm.Set(0, 1, 1.0)
|
||||
dm.Set(0, 2, 2.0)
|
||||
dm.Set(1, 2, 3.0)
|
||||
|
||||
row0 := dm.GetRow(0)
|
||||
expected0 := []float64{0.0, 1.0, 2.0}
|
||||
|
||||
for i, val := range expected0 {
|
||||
if math.Abs(row0[i]-val) > 1e-10 {
|
||||
t.Errorf("Row 0[%d]: expected %f, got %f", i, val, row0[i])
|
||||
}
|
||||
}
|
||||
|
||||
row1 := dm.GetRow(1)
|
||||
expected1 := []float64{1.0, 0.0, 3.0}
|
||||
|
||||
for i, val := range expected1 {
|
||||
if math.Abs(row1[i]-val) > 1e-10 {
|
||||
t.Errorf("Row 1[%d]: expected %f, got %f", i, val, row1[i])
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
func TestDistMatrixCopy(t *testing.T) {
|
||||
dm := NewDistMatrixWithLabels([]string{"A", "B", "C"})
|
||||
dm.Set(0, 1, 1.5)
|
||||
dm.Set(0, 2, 2.5)
|
||||
dm.Set(1, 2, 3.5)
|
||||
|
||||
dmCopy := dm.Copy()
|
||||
|
||||
// Check values are copied
|
||||
if dmCopy.Get(0, 1) != dm.Get(0, 1) {
|
||||
t.Errorf("Copy has different value at (0, 1)")
|
||||
}
|
||||
|
||||
// Check labels are copied
|
||||
if dmCopy.GetLabel(0) != dm.GetLabel(0) {
|
||||
t.Errorf("Copy has different label at index 0")
|
||||
}
|
||||
|
||||
// Modify copy and ensure original unchanged
|
||||
dmCopy.Set(0, 1, 99.9)
|
||||
if dm.Get(0, 1) == 99.9 {
|
||||
t.Errorf("Modifying copy affected original matrix")
|
||||
}
|
||||
|
||||
dmCopy.SetLabel(0, "Modified")
|
||||
if dm.GetLabel(0) == "Modified" {
|
||||
t.Errorf("Modifying copy label affected original matrix")
|
||||
}
|
||||
}
|
||||
|
||||
func TestDistMatrixToFullMatrix(t *testing.T) {
|
||||
dm := NewDistMatrix(3)
|
||||
dm.Set(0, 1, 1.0)
|
||||
dm.Set(0, 2, 2.0)
|
||||
dm.Set(1, 2, 3.0)
|
||||
|
||||
full := dm.ToFullMatrix()
|
||||
|
||||
expected := [][]float64{
|
||||
{0.0, 1.0, 2.0},
|
||||
{1.0, 0.0, 3.0},
|
||||
{2.0, 3.0, 0.0},
|
||||
}
|
||||
|
||||
for i := 0; i < 3; i++ {
|
||||
for j := 0; j < 3; j++ {
|
||||
if math.Abs(full[i][j]-expected[i][j]) > 1e-10 {
|
||||
t.Errorf("Full matrix[%d][%d]: expected %f, got %f",
|
||||
i, j, expected[i][j], full[i][j])
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
func TestDistMatrixBoundsChecking(t *testing.T) {
|
||||
dm := NewDistMatrix(3)
|
||||
|
||||
// Test Get out of bounds
|
||||
testPanic := func(f func()) {
|
||||
defer func() {
|
||||
if r := recover(); r == nil {
|
||||
t.Errorf("Expected panic, but didn't get one")
|
||||
}
|
||||
}()
|
||||
f()
|
||||
}
|
||||
|
||||
testPanic(func() { dm.Get(-1, 0) })
|
||||
testPanic(func() { dm.Get(0, 3) })
|
||||
testPanic(func() { dm.Set(3, 0, 1.0) })
|
||||
testPanic(func() { dm.GetLabel(-1) })
|
||||
testPanic(func() { dm.SetLabel(3, "Invalid") })
|
||||
testPanic(func() { dm.GetRow(3) })
|
||||
}
|
||||
|
||||
func TestDistMatrixEmptyMatrix(t *testing.T) {
|
||||
dm := NewDistMatrix(0)
|
||||
|
||||
if dm.Size() != 0 {
|
||||
t.Errorf("Expected size 0, got %d", dm.Size())
|
||||
}
|
||||
|
||||
minDist, minI, minJ := dm.MinDistance()
|
||||
if minDist != 0.0 || minI != -1 || minJ != -1 {
|
||||
t.Errorf("Empty matrix MinDistance should return (0.0, -1, -1), got (%f, %d, %d)",
|
||||
minDist, minI, minJ)
|
||||
}
|
||||
|
||||
maxDist, maxI, maxJ := dm.MaxDistance()
|
||||
if maxDist != 0.0 || maxI != -1 || maxJ != -1 {
|
||||
t.Errorf("Empty matrix MaxDistance should return (0.0, -1, -1), got (%f, %d, %d)",
|
||||
maxDist, maxI, maxJ)
|
||||
}
|
||||
}
|
||||
|
||||
func TestDistMatrixSingleElement(t *testing.T) {
|
||||
dm := NewDistMatrix(1)
|
||||
|
||||
if dm.Size() != 1 {
|
||||
t.Errorf("Expected size 1, got %d", dm.Size())
|
||||
}
|
||||
|
||||
// Only element is diagonal (always 0)
|
||||
if dm.Get(0, 0) != 0.0 {
|
||||
t.Errorf("Expected 0.0 at (0, 0), got %f", dm.Get(0, 0))
|
||||
}
|
||||
|
||||
minDist, minI, minJ := dm.MinDistance()
|
||||
if minDist != 0.0 || minI != -1 || minJ != -1 {
|
||||
t.Errorf("Single element matrix MinDistance should return (0.0, -1, -1), got (%f, %d, %d)",
|
||||
minDist, minI, minJ)
|
||||
}
|
||||
}
|
||||
|
||||
func TestNewSimilarityMatrix(t *testing.T) {
|
||||
sm := NewSimilarityMatrix(4)
|
||||
|
||||
if sm.Size() != 4 {
|
||||
t.Errorf("Expected size 4, got %d", sm.Size())
|
||||
}
|
||||
|
||||
// Check diagonal is 1.0
|
||||
for i := 0; i < 4; i++ {
|
||||
if sm.Get(i, i) != 1.0 {
|
||||
t.Errorf("Expected diagonal element (%d, %d) to be 1.0, got %f", i, i, sm.Get(i, i))
|
||||
}
|
||||
}
|
||||
|
||||
// Check off-diagonal is 0.0
|
||||
if sm.Get(0, 1) != 0.0 {
|
||||
t.Errorf("Expected off-diagonal to be 0.0, got %f", sm.Get(0, 1))
|
||||
}
|
||||
}
|
||||
|
||||
func TestNewSimilarityMatrixWithLabels(t *testing.T) {
|
||||
labels := []string{"A", "B", "C"}
|
||||
sm := NewSimilarityMatrixWithLabels(labels)
|
||||
|
||||
if sm.Size() != 3 {
|
||||
t.Errorf("Expected size 3, got %d", sm.Size())
|
||||
}
|
||||
|
||||
// Check labels
|
||||
for i, label := range labels {
|
||||
if sm.GetLabel(i) != label {
|
||||
t.Errorf("Expected label %s at index %d, got %s", label, i, sm.GetLabel(i))
|
||||
}
|
||||
}
|
||||
|
||||
// Check diagonal is 1.0
|
||||
for i := 0; i < 3; i++ {
|
||||
if sm.Get(i, i) != 1.0 {
|
||||
t.Errorf("Expected diagonal element (%d, %d) to be 1.0, got %f", i, i, sm.Get(i, i))
|
||||
}
|
||||
}
|
||||
|
||||
// Set some similarities
|
||||
sm.Set(0, 1, 0.8)
|
||||
sm.Set(0, 2, 0.6)
|
||||
sm.Set(1, 2, 0.7)
|
||||
|
||||
// Check values
|
||||
if math.Abs(sm.Get(0, 1)-0.8) > 1e-10 {
|
||||
t.Errorf("Expected 0.8 at (0, 1), got %f", sm.Get(0, 1))
|
||||
}
|
||||
|
||||
if math.Abs(sm.Get(1, 0)-0.8) > 1e-10 {
|
||||
t.Errorf("Expected 0.8 at (1, 0) (symmetry), got %f", sm.Get(1, 0))
|
||||
}
|
||||
}
|
||||
|
||||
func TestSimilarityMatrixCopy(t *testing.T) {
|
||||
sm := NewSimilarityMatrix(3)
|
||||
sm.Set(0, 1, 0.9)
|
||||
sm.Set(0, 2, 0.7)
|
||||
|
||||
smCopy := sm.Copy()
|
||||
|
||||
// Check diagonal is preserved
|
||||
if smCopy.Get(0, 0) != 1.0 {
|
||||
t.Errorf("Copied similarity matrix should have diagonal 1.0, got %f", smCopy.Get(0, 0))
|
||||
}
|
||||
|
||||
// Check values are preserved
|
||||
if math.Abs(smCopy.Get(0, 1)-0.9) > 1e-10 {
|
||||
t.Errorf("Copy should preserve values, expected 0.9, got %f", smCopy.Get(0, 1))
|
||||
}
|
||||
|
||||
// Modify copy and ensure original unchanged
|
||||
smCopy.Set(0, 1, 0.5)
|
||||
if math.Abs(sm.Get(0, 1)-0.9) > 1e-10 {
|
||||
t.Errorf("Modifying copy should not affect original, expected 0.9, got %f", sm.Get(0, 1))
|
||||
}
|
||||
}
|
||||
Reference in New Issue
Block a user