better comments on charset

LinguaPhylo · Nov 16, 2023 · d099112 · d099112
1 parent 2422221
commit d099112
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Showing 3 changed files with 5 additions and 2 deletions.
diff --git a/lphy-base/src/main/java/lphy/base/evolution/alignment/CharSetBlock.java b/lphy-base/src/main/java/lphy/base/evolution/alignment/CharSetBlock.java
@@ -7,6 +7,8 @@
 
 /**
  * Parse charset, especially codon position expressions.
+ * It should follow the Nexus Format (Maddison et al. 1997).
+ * <a href="https://doi.org/10.1093/sysbio/46.4.590"/>
  */
 public class CharSetBlock {
 

diff --git a/lphy-base/src/main/java/lphy/base/evolution/alignment/MetaDataAlignment.java b/lphy-base/src/main/java/lphy/base/evolution/alignment/MetaDataAlignment.java
@@ -169,7 +169,7 @@ public void setChronoUnit(ChronoUnit chronoUnit) {
             "If the string doesn't match charset's syntax, then check if the string matches " +
             "a defined name in the nexus file. Otherwise it is an error. " +
             "The string is referred to one partition at a call, but can be multiple blocks, " +
-            "such as d.charset(\"2-457\\3 660-896\\3\").",
+            "such as a dummy example: d.charset([\"2-457\\3\", \"660-896\\3\", \"1-.\\3\"]).",
             narrativeName = "character set",
             category = GeneratorCategory.TAXA_ALIGNMENT,
             examples = {"twoPartitionCoalescentNex.lphy","https://linguaphylo.github.io/tutorials/time-stamped-data/"})

diff --git a/tutorials/RSV2.lphy b/tutorials/RSV2.lphy
@@ -2,7 +2,8 @@ data {
   options = {ageDirection="forward", ageRegex="s(\d+)$"};
   D = readNexus(file="data/RSV2.nex", options=options);
   taxa = D.taxa();
-  codon = D.charset(["3-629\3","1-629\3", "2-629\3"]);
+  // codon positions
+  codon = D.charset(["1-.\3", "2-.\3", "3-.\3"]);
   L = codon.nchar();
   n=length(codon); // 3 partitions
 }