Fix auto-detection of binary data (#350)

davidcerny · web-flow · commit c741dcb6d7ca · 2024-11-13T22:37:34.000+11:00
diff --git a/alignment/alignment.cpp b/alignment/alignment.cpp
@@ -1335,7 +1335,7 @@ SeqType Alignment::detectSequenceType(StrVector &sequences) {
     }
     if (((double)num_nuc) / num_ungap > 0.9)
         return SEQ_DNA;
-    if (((double)num_bin) / num_ungap > 0.9)
+    if (num_bin == num_ungap) // For binary data, only 0, 1, ?, -, . can occur
         return SEQ_BINARY;
     if (((double)num_alpha + num_nuc) / num_ungap > 0.9)
         return SEQ_PROTEIN;

Original file line number	Diff line number	Diff line change
`@@ -1335,7 +1335,7 @@ SeqType Alignment::detectSequenceType(StrVector &sequences) {`
`1335`	`1335`	`}`
`1336`	`1336`	`if (((double)num_nuc) / num_ungap > 0.9)`
`1337`	`1337`	`return SEQ_DNA;`
`1338`		`- if (((double)num_bin) / num_ungap > 0.9)`
	`1338`	`+ if (num_bin == num_ungap) // For binary data, only 0, 1, ?, -, . can occur`
`1339`	`1339`	`return SEQ_BINARY;`
`1340`	`1340`	`if (((double)num_alpha + num_nuc) / num_ungap > 0.9)`
`1341`	`1341`	`return SEQ_PROTEIN;`