Added option --algo none

evolbioinfo · Mar 15, 2018 · 07cf645 · 07cf645
1 parent 4939293
commit 07cf645
Show file tree

Hide file tree

Showing 4 changed files with 10 additions and 0 deletions.
diff --git a/acr/parsimony.go b/acr/parsimony.go
@@ -15,6 +15,7 @@ const (
 	ALGO_DELTRAN = iota
 	ALGO_ACCTRAN
 	ALGO_DOWNPASS
+	ALGO_NONE
 )
 
 // Will annotate the tree nodes with ancestral characters
@@ -66,6 +67,8 @@ func ParsimonyAcr(t *tree.Tree, tipCharacters map[string]string, algo int, rando
 		parsimonyDELTRAN(t.Root(), nil, states, stateIndices, randomResolve)
 	case ALGO_ACCTRAN:
 		parsimonyACCTRAN(t.Root(), nil, states, stateIndices, randomResolve)
+	case ALGO_NONE:
+		// No pass after uppass
 	default:
 		return nil, fmt.Errorf("Parsimony algorithm %d unkown", algo)
 	}

diff --git a/asr/parsimony.go b/asr/parsimony.go
@@ -15,6 +15,7 @@ const (
 	ALGO_DELTRAN = iota
 	ALGO_ACCTRAN
 	ALGO_DOWNPASS
+	ALGO_NONE
 )
 
 // Will annotate the tree nodes with ancestral sequences

diff --git a/cmd/acr.go b/cmd/acr.go
@@ -31,6 +31,7 @@ Depending on the chosen algorithm, it will run:
    a) DOWN-PASS or
    b) DOWN-PASS+DELTRAN or
    c) ACCTRAN
+   d) NONE
 
 Should work on multifurcated trees.
 
@@ -52,6 +53,8 @@ randomly before going deeper in the tree.
 			algo = acr.ALGO_DELTRAN
 		case "downpass":
 			algo = acr.ALGO_DOWNPASS
+		case "none":
+			algo = acr.ALGO_NONE
 		default:
 			io.ExitWithMessage(fmt.Errorf("Unkown parsimony algorithm: %s", parsimonyAlgo))
 		}

diff --git a/cmd/asr.go b/cmd/asr.go
@@ -34,6 +34,7 @@ Depending on the chosen algorithm, it will run:
    a) DOWN-PASS or
    b) DOWN-PASS+DELTRAN or
    c) ACCTRAN
+   d) NONE
 
 Should work on multifurcated trees
 
@@ -56,6 +57,8 @@ randomly before going deeper in the tree.
 			algo = asr.ALGO_DELTRAN
 		case "downpass":
 			algo = asr.ALGO_DOWNPASS
+		case "none":
+			algo = asr.ALGO_NONE
 		default:
 			io.ExitWithMessage(fmt.Errorf("Unkown parsimony algorithm: %s", parsimonyAlgo))
 		}