From 9ceaedcf0e56f41a79bedd1159b1b88e2167439e Mon Sep 17 00:00:00 2001
From: Frederic Lemoine <fredericlemoine@users.noreply.github.com>
Date: Mon, 6 May 2019 10:12:28 +0200
Subject: [PATCH] nexus parser replace match chars #3

---
 align/align.go           | 21 ++++++++++++++++++++-
 io/nexus/nexus_parser.go |  1 +
 2 files changed, 21 insertions(+), 1 deletion(-)

diff --git a/align/align.go b/align/align.go
index f02a381..46333d3 100644
--- a/align/align.go
+++ b/align/align.go
@@ -57,7 +57,9 @@ type Alignment interface {
 	Recombine(rate float64, lenprop float64)
 	RemoveGapSeqs(cutoff float64)             // Removes sequences having >= cutoff gaps
 	RemoveGapSites(cutoff float64, ends bool) // Removes sites having >= cutoff gaps
-	Sample(nb int) (Alignment, error)         // generate a sub sample of the sequences
+	// Replaces match characters (.) by their corresponding characters on the first sequence
+	ReplaceMatchChars()
+	Sample(nb int) (Alignment, error) // generate a sub sample of the sequences
 	ShuffleSites(rate float64, roguerate float64, randroguefirst bool) []string
 	SimulateRogue(prop float64, proplen float64) ([]string, []string) // add "rogue" sequences
 	SiteConservation(position int) (int, error)                       // If the site is conserved:
@@ -322,6 +324,23 @@ func (a *align) Swap(rate float64) {
 	}
 }
 
+// Replaces match characters (.) by their corresponding characters on the first sequence
+//
+// If the correspongind character in the first sequence is also a ".", then leaves it unchanged.
+func (a *align) ReplaceMatchChars() {
+	if a.NbSequences() <= 1 {
+		return
+	}
+	ref := a.seqs[0]
+	for seq := 1; seq < a.NbSequences(); seq++ {
+		for site := 0; site < a.Length(); site++ {
+			if ref.sequence[site] != POINT && a.seqs[seq].sequence[site] == POINT {
+				a.seqs[seq].sequence[site] = ref.sequence[site]
+			}
+		}
+	}
+}
+
 // Translates the alignment, and update the length of
 // the alignment
 func (a *align) Translate(phase int, geneticcode int) (err error) {
diff --git a/io/nexus/nexus_parser.go b/io/nexus/nexus_parser.go
index a07be10..5c96317 100644
--- a/io/nexus/nexus_parser.go
+++ b/io/nexus/nexus_parser.go
@@ -176,6 +176,7 @@ func (p *Parser) Parse() (al align.Alignment, err error) {
 				return
 			}
 		}
+		al.ReplaceMatchChars()
 	}
 	return
 }