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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,396 @@ | ||
| package acr | ||
|
|
||
| import ( | ||
| "fmt" | ||
| "strings" | ||
| "testing" | ||
|
|
||
| "github.com/fredericlemoine/gotree/io/newick" | ||
| "github.com/fredericlemoine/gotree/tree" | ||
| ) | ||
|
|
||
| func TestACRDELTRANParsimony(t *testing.T) { | ||
| // +--- t1 A | ||
| // | | ||
| // t21 +--- t2 A | ||
| // | | | ||
| // | | +---- t3 B | ||
| // +---|t20+---|t7 | ||
| // | | | +--- t4 B | ||
| // | | +----|t6 | ||
| // | | +--- t5 A | ||
| // +---|t19 | ||
| // | +---- t8 B | ||
| // | | | ||
| // +---|t18 +--- t9 B | ||
| // | +---|t11 | ||
| // | | +--- t10 A | ||
| // +----|t17 | ||
| // | +--- t12 A | ||
| // | +---|t14 | ||
| // +---|t16+--- t13 A | ||
| // | | ||
| // +--- t15 A | ||
| treeString := "(t1,(t2,((t3,(t4,t5)t6)t7,(t8,((t9,t10)t11,((t12,t13)t14,t15)t16)t17)t18)t19)t20)t21;" | ||
| tipstates := map[string]string{ | ||
| "t1": "A", "t2": "A", "t3": "B", "t4": "B", "t5": "A", "t8": "B", | ||
| "t9": "B", "t10": "A", "t12": "A", "t13": "A", "t15": "A", | ||
| } | ||
| states := make([]AncestralState, 21) | ||
| alphabet := []string{"A", "B"} | ||
| stateIndices := AncestralStateIndices(alphabet) | ||
| tr, err := newick.NewParser(strings.NewReader(treeString)).Parse() | ||
| if err != nil { | ||
| t.Error(err) | ||
| } | ||
| ni := tree.NewAllNodeIndex(tr) | ||
|
|
||
| for i, n := range tr.Nodes() { | ||
| n.SetId(i) | ||
| states[i] = make(AncestralState, 2) | ||
| } | ||
|
|
||
| // Test UPPASS | ||
| err = parsimonyUPPASS(tr.Root(), nil, tipstates, states, stateIndices) | ||
| if err != nil { | ||
| t.Error(err) | ||
| } | ||
| testCheckStates(t, 2, ni, "t1", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t2", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t3", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t4", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t5", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t6", states, stateIndices, "B", "A") | ||
| testCheckStates(t, 2, ni, "t7", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t8", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t9", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t10", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t11", states, stateIndices, "A", "B") | ||
| testCheckStates(t, 2, ni, "t12", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t13", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t14", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t15", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t16", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t17", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t18", states, stateIndices, "A", "B") | ||
| testCheckStates(t, 2, ni, "t19", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t20", states, stateIndices, "A", "B") | ||
| testCheckStates(t, 2, ni, "t21", states, stateIndices, "A") | ||
|
|
||
| // Test DOWNPASS | ||
| parsimonyDOWNPASS(tr.Root(), nil, states, stateIndices, false) | ||
| testCheckStates(t, 2, ni, "t1", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t2", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t3", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t4", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t5", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t6", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t7", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t8", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t9", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t10", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t11", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t12", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t13", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t14", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t15", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t16", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t17", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t18", states, stateIndices, "A", "B") | ||
| testCheckStates(t, 2, ni, "t19", states, stateIndices, "A", "B") | ||
| testCheckStates(t, 2, ni, "t20", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t21", states, stateIndices, "A") | ||
|
|
||
| // Test DELTRAN | ||
| parsimonyDELTRAN(tr.Root(), nil, states, stateIndices, false) | ||
| testCheckStates(t, 2, ni, "t1", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t2", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t3", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t4", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t5", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t6", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t7", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t8", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t9", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t10", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t11", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t12", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t13", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t14", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t15", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t16", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t17", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t18", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t19", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t20", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t21", states, stateIndices, "A") | ||
|
|
||
| } | ||
|
|
||
| func TestACRACCTRANParsimony(t *testing.T) { | ||
| // +--- t1 A | ||
| // | | ||
| // t21 +--- t2 A | ||
| // | | | ||
| // | | +---- t3 B | ||
| // +---|t20+---|t7 | ||
| // | | | +--- t4 B | ||
| // | | +----|t6 | ||
| // | | +--- t5 A | ||
| // +---|t19 | ||
| // | +---- t8 B | ||
| // | | | ||
| // +---|t18 +--- t9 B | ||
| // | +---|t11 | ||
| // | | +--- t10 A | ||
| // +----|t17 | ||
| // | +--- t12 A | ||
| // | +---|t14 | ||
| // +---|t16+--- t13 A | ||
| // | | ||
| // +--- t15 A | ||
| treeString := "(t1,(t2,((t3,(t4,t5)t6)t7,(t8,((t9,t10)t11,((t12,t13)t14,t15)t16)t17)t18)t19)t20)t21;" | ||
| tipstates := map[string]string{ | ||
| "t1": "A", "t2": "A", "t3": "B", "t4": "B", "t5": "A", "t8": "B", | ||
| "t9": "B", "t10": "A", "t12": "A", "t13": "A", "t15": "A", | ||
| } | ||
| states := make([]AncestralState, 21) | ||
| alphabet := []string{"A", "B"} | ||
| stateIndices := AncestralStateIndices(alphabet) | ||
| tr, err := newick.NewParser(strings.NewReader(treeString)).Parse() | ||
| if err != nil { | ||
| t.Error(err) | ||
| } | ||
| ni := tree.NewAllNodeIndex(tr) | ||
|
|
||
| for i, n := range tr.Nodes() { | ||
| n.SetId(i) | ||
| states[i] = make(AncestralState, 2) | ||
| } | ||
|
|
||
| // Test UPPASS | ||
| err = parsimonyUPPASS(tr.Root(), nil, tipstates, states, stateIndices) | ||
| if err != nil { | ||
| t.Error(err) | ||
| } | ||
| testCheckStates(t, 2, ni, "t1", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t2", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t3", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t4", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t5", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t6", states, stateIndices, "B", "A") | ||
| testCheckStates(t, 2, ni, "t7", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t8", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t9", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t10", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t11", states, stateIndices, "A", "B") | ||
| testCheckStates(t, 2, ni, "t12", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t13", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t14", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t15", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t16", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t17", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t18", states, stateIndices, "A", "B") | ||
| testCheckStates(t, 2, ni, "t19", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t20", states, stateIndices, "A", "B") | ||
| testCheckStates(t, 2, ni, "t21", states, stateIndices, "A") | ||
|
|
||
| // Test ACCTRAN | ||
| parsimonyACCTRAN(tr.Root(), nil, states, stateIndices, false) | ||
| testCheckStates(t, 2, ni, "t1", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t2", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t3", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t4", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t5", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t6", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t7", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t8", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t9", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t10", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t11", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t12", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t13", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t14", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t15", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t16", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t17", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t18", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t19", states, stateIndices, "B") | ||
| testCheckStates(t, 2, ni, "t20", states, stateIndices, "A") | ||
| testCheckStates(t, 2, ni, "t21", states, stateIndices, "A") | ||
| } | ||
|
|
||
| func TestALLDELTRAN(t *testing.T) { | ||
| // +--- t1 A | ||
| // | | ||
| // t21 +--- t2 A | ||
| // | | | ||
| // | | +---- t3 B | ||
| // +---|t20+---|t7 | ||
| // | | | +--- t4 B | ||
| // | | +----|t6 | ||
| // | | +--- t5 A | ||
| // +---|t19 | ||
| // | +---- t8 B | ||
| // | | | ||
| // +---|t18 +--- t9 B | ||
| // | +---|t11 | ||
| // | | +--- t10 A | ||
| // +----|t17 | ||
| // | +--- t12 A | ||
| // | +---|t14 | ||
| // +---|t16+--- t13 A | ||
| // | | ||
| // +--- t15 A | ||
| treeString := "(t1,(t2,((t3,(t4,t5)t6)t7,(t8,((t9,t10)t11,((t12,t13)t14,t15)t16)t17)t18)t19)t20)t21;" | ||
| tipstates := map[string]string{ | ||
| "t1": "A", "t2": "A", "t3": "B", "t4": "B", "t5": "A", "t8": "B", | ||
| "t9": "B", "t10": "A", "t12": "A", "t13": "A", "t15": "A", | ||
| } | ||
| tr, err := newick.NewParser(strings.NewReader(treeString)).Parse() | ||
| if err != nil { | ||
| t.Error(err) | ||
| } | ||
|
|
||
| statemap, err := ParsimonyAcr(tr, tipstates, ALGO_DELTRAN, false) | ||
|
|
||
| if err != nil { | ||
| t.Error(err) | ||
| } | ||
| testCheckMap(t, "t6", statemap, "B") | ||
| testCheckMap(t, "t7", statemap, "B") | ||
| testCheckMap(t, "t11", statemap, "A") | ||
| testCheckMap(t, "t14", statemap, "A") | ||
| testCheckMap(t, "t16", statemap, "A") | ||
| testCheckMap(t, "t17", statemap, "A") | ||
| testCheckMap(t, "t18", statemap, "A") | ||
| testCheckMap(t, "t19", statemap, "A") | ||
| testCheckMap(t, "t20", statemap, "A") | ||
| testCheckMap(t, "t21", statemap, "A") | ||
| } | ||
| func TestALLDOWNPASS(t *testing.T) { | ||
| // +--- t1 A | ||
| // | | ||
| // t21 +--- t2 A | ||
| // | | | ||
| // | | +---- t3 B | ||
| // +---|t20+---|t7 | ||
| // | | | +--- t4 B | ||
| // | | +----|t6 | ||
| // | | +--- t5 A | ||
| // +---|t19 | ||
| // | +---- t8 B | ||
| // | | | ||
| // +---|t18 +--- t9 B | ||
| // | +---|t11 | ||
| // | | +--- t10 A | ||
| // +----|t17 | ||
| // | +--- t12 A | ||
| // | +---|t14 | ||
| // +---|t16+--- t13 A | ||
| // | | ||
| // +--- t15 A | ||
| treeString := "(t1,(t2,((t3,(t4,t5)t6)t7,(t8,((t9,t10)t11,((t12,t13)t14,t15)t16)t17)t18)t19)t20)t21;" | ||
| tipstates := map[string]string{ | ||
| "t1": "A", "t2": "A", "t3": "B", "t4": "B", "t5": "A", "t8": "B", | ||
| "t9": "B", "t10": "A", "t12": "A", "t13": "A", "t15": "A", | ||
| } | ||
| tr, err := newick.NewParser(strings.NewReader(treeString)).Parse() | ||
| if err != nil { | ||
| t.Error(err) | ||
| } | ||
|
|
||
| statemap, err := ParsimonyAcr(tr, tipstates, ALGO_DOWNPASS, false) | ||
| if err != nil { | ||
| t.Error(err) | ||
| } | ||
| testCheckMap(t, "t6", statemap, "B") | ||
| testCheckMap(t, "t7", statemap, "B") | ||
| testCheckMap(t, "t11", statemap, "A") | ||
| testCheckMap(t, "t14", statemap, "A") | ||
| testCheckMap(t, "t16", statemap, "A") | ||
| testCheckMap(t, "t17", statemap, "A") | ||
| testCheckMap(t, "t18", statemap, "A", "B") | ||
| testCheckMap(t, "t19", statemap, "A", "B") | ||
| testCheckMap(t, "t20", statemap, "A") | ||
| testCheckMap(t, "t21", statemap, "A") | ||
| } | ||
|
|
||
| func TestALLACCTRAN(t *testing.T) { | ||
| // +--- t1 A | ||
| // | | ||
| // t21 +--- t2 A | ||
| // | | | ||
| // | | +---- t3 B | ||
| // +---|t20+---|t7 | ||
| // | | | +--- t4 B | ||
| // | | +----|t6 | ||
| // | | +--- t5 A | ||
| // +---|t19 | ||
| // | +---- t8 B | ||
| // | | | ||
| // +---|t18 +--- t9 B | ||
| // | +---|t11 | ||
| // | | +--- t10 A | ||
| // +----|t17 | ||
| // | +--- t12 A | ||
| // | +---|t14 | ||
| // +---|t16+--- t13 A | ||
| // | | ||
| // +--- t15 A | ||
| treeString := "(t1,(t2,((t3,(t4,t5)t6)t7,(t8,((t9,t10)t11,((t12,t13)t14,t15)t16)t17)t18)t19)t20)t21;" | ||
| tipstates := map[string]string{ | ||
| "t1": "A", "t2": "A", "t3": "B", "t4": "B", "t5": "A", "t8": "B", | ||
| "t9": "B", "t10": "A", "t12": "A", "t13": "A", "t15": "A", | ||
| } | ||
| tr, err := newick.NewParser(strings.NewReader(treeString)).Parse() | ||
| if err != nil { | ||
| t.Error(err) | ||
| } | ||
|
|
||
| statemap, err := ParsimonyAcr(tr, tipstates, ALGO_ACCTRAN, false) | ||
| if err != nil { | ||
| t.Error(err) | ||
| } | ||
| testCheckMap(t, "t6", statemap, "B") | ||
| testCheckMap(t, "t7", statemap, "B") | ||
| testCheckMap(t, "t11", statemap, "A") | ||
| testCheckMap(t, "t14", statemap, "A") | ||
| testCheckMap(t, "t16", statemap, "A") | ||
| testCheckMap(t, "t17", statemap, "A") | ||
| testCheckMap(t, "t18", statemap, "B") | ||
| testCheckMap(t, "t19", statemap, "B") | ||
| testCheckMap(t, "t20", statemap, "A") | ||
| testCheckMap(t, "t21", statemap, "A") | ||
| } | ||
|
|
||
| func testCheckStates(t *testing.T, nstates int, ni tree.NodeIndex, nodename string, | ||
| states []AncestralState, stateIndices map[string]int, teststates ...string) { | ||
| n, ok := ni.GetNode(nodename) | ||
| if !ok { | ||
| t.Error(fmt.Errorf("Node %s does not exist in the tree", nodename)) | ||
| } | ||
| a := make(AncestralState, 2) | ||
| for _, s := range teststates { | ||
| idx, ok := stateIndices[s] | ||
| if !ok { | ||
| t.Error(fmt.Errorf("State %s does not exist in the index", s)) | ||
| } | ||
| a[idx] = 1 | ||
| } | ||
| // We compare the two ancestral states now | ||
| for i, v := range a { | ||
| if v != states[n.Id()][i] { | ||
| t.Error(fmt.Errorf("Node %s should have states : %v but has states %v", nodename, a, states[n.Id()])) | ||
| } | ||
| } | ||
| } | ||
| func testCheckMap(t *testing.T, nodename string, statemap map[string]string, states ...string) { | ||
| st, ok := statemap[nodename] | ||
| if !ok { | ||
| t.Error(fmt.Errorf("Node %s does not exist in the output state map", nodename)) | ||
| } | ||
| if strings.Join(states, ",") != st { | ||
| t.Error(fmt.Errorf("Node %s should have states : %s but has states %s", nodename, strings.Join(states, ","), st)) | ||
| } | ||
| } |
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