From 9dea135f3eb004158bb67693021f7eb055d0b287 Mon Sep 17 00:00:00 2001
From: Walter <walterxie@users.noreply.github.com>
Date: Mon, 23 Nov 2020 11:28:00 +1300
Subject: [PATCH]  use D.taxa() and deprecate taxa(D) #110

---
 examples/dataModelBlocks.lphy                 |  2 +-
 examples/fullDataExample.lphy                 |  2 +-
 examples/h3n2.lphy                            |  2 +-
 src/lphy/core/functions/TaxaFunction.java     |  2 ++
 .../alignment/AbstractAlignment.java          | 20 ++++++++++++-------
 5 files changed, 18 insertions(+), 10 deletions(-)

diff --git a/examples/dataModelBlocks.lphy b/examples/dataModelBlocks.lphy
index 63dd2ef09..17b4c1376 100644
--- a/examples/dataModelBlocks.lphy
+++ b/examples/dataModelBlocks.lphy
@@ -1,7 +1,7 @@
 data {
   D = readNexus(file="examples/primate.nex");
   L = nchar(D);
-  taxa = D.getTaxa();
+  taxa = D.taxa();
 }
 model {
   theta ~ LogNormal(meanlog=3, sdlog=1);
diff --git a/examples/fullDataExample.lphy b/examples/fullDataExample.lphy
index a8573dd65..03809b409 100644
--- a/examples/fullDataExample.lphy
+++ b/examples/fullDataExample.lphy
@@ -1,7 +1,7 @@
 data {
   D = readNexus(file="examples/primate.nex");
   L = nchar(D);
-  taxa = D.getTaxa();
+  taxa = D.taxa();
 }
 model {
   theta ~ LogNormal(meanlog=3, sdlog=1);
diff --git a/examples/h3n2.lphy b/examples/h3n2.lphy
index f7a156c6b..d832dc9b9 100644
--- a/examples/h3n2.lphy
+++ b/examples/h3n2.lphy
@@ -1,7 +1,7 @@
 data {
   options = {ageDirection="forward", ageRegex="_(\d*\.\d+|\d+\.\d*)$"};
   D = readFasta(file="examples/h3n2_2deme.fna", options=options);
-  taxa = D.getTaxa();
+  taxa = D.taxa();
   L = nchar(D);
   demes = split(str=D.getTaxaNames(), regex="_", i=1);
 }
diff --git a/src/lphy/core/functions/TaxaFunction.java b/src/lphy/core/functions/TaxaFunction.java
index cbe61d32d..b482bc0bb 100644
--- a/src/lphy/core/functions/TaxaFunction.java
+++ b/src/lphy/core/functions/TaxaFunction.java
@@ -9,6 +9,7 @@
 
 import java.util.Arrays;
 
+@Deprecated
 public class TaxaFunction extends DeterministicFunction<Taxa> {
 
     final String paramName;
@@ -18,6 +19,7 @@ public TaxaFunction(@ParameterInfo(name = "taxa", description = "the taxa value
         setParam(paramName, x);
     }
 
+    @Deprecated
     @GeneratorInfo(name="taxa",description = "The taxa of the given taxa-dimensioned object (e.g. alignment, tree et cetera).")
     public Value<Taxa> apply() {
         Value v = getParams().get(paramName);
diff --git a/src/lphy/evolution/alignment/AbstractAlignment.java b/src/lphy/evolution/alignment/AbstractAlignment.java
index 8d89eee5a..3e009cd16 100644
--- a/src/lphy/evolution/alignment/AbstractAlignment.java
+++ b/src/lphy/evolution/alignment/AbstractAlignment.java
@@ -82,12 +82,24 @@ public AbstractAlignment(final AbstractAlignment source) {
     public abstract boolean hasParts();
 
 
-    //****** Sites ******
+    //****** MethodInfo ******
+
     @MethodInfo(description="The number of characters/sites in this alignment.")
     public Integer nchar() {
         return nchar;
     }
 
+    @Override
+    @MethodInfo(description="The names of the taxa.")
+    public String[] getTaxaNames() {
+        return taxa.getTaxaNames();
+    }
+
+    @MethodInfo(description = "the taxa of the alignment.")
+    public Taxa taxa() {
+        return getTaxa();
+    }
+
     //****** Taxa ******
 
     @Override
@@ -109,18 +121,12 @@ public String getTaxonName(int taxonIndex) {
         return getTaxon(taxonIndex).getName();
     }
 
-    @Override
-    @MethodInfo(description="The names of the taxa.")
-    public String[] getTaxaNames() {
-        return taxa.getTaxaNames();
-    }
 
     @Override
     public Taxon[] getTaxonArray() {
         return taxa.getTaxonArray();
     }
 
-    @MethodInfo(description = "the taxa of the alignment.")
     public Taxa getTaxa() {
         return taxa;
     }