From: Ben Soares <b.soares@dundee.ac.uk>
Date: Wed, 16 Nov 2022 09:27:49 +0000 (+0000)
Subject: JAL-4019 finalised a boolean option and tidied some comments
X-Git-Tag: Release_2_11_3_0~23^2~8^2~4^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f23edb1da574ceea56f2570996698ab29e61e129;p=jalview.git

JAL-4019 finalised a boolean option and tidied some comments
---

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index 68988c3..9fea705 100644
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -42,6 +42,8 @@ public class Comparison
 
   private static final int NUCLEOTIDE_COUNT_VERY_SHORT_SEQUENCE;
 
+  private static final boolean NUCLEOTIDE_AMBIGUITY_DETECTION;
+
   public static final char GAP_SPACE = ' ';
 
   public static final char GAP_DOT = '.';
@@ -54,6 +56,7 @@ public class Comparison
 
   static
   {
+    // these options read only at start of session
     NUCLEOTIDE_COUNT_PERCENT = Cache.getDefault("NUCLEOTIDE_COUNT_PERCENT",
             55);
     NUCLEOTIDE_COUNT_LONG_SEQUENCE_AMBIGUITY_PERCENT = Cache.getDefault(
@@ -62,6 +65,8 @@ public class Comparison
             .getDefault("NUCLEOTIDE_COUNT_SHORT", 100);
     NUCLEOTIDE_COUNT_VERY_SHORT_SEQUENCE = Cache
             .getDefault("NUCLEOTIDE_COUNT_VERY_SHORT", 4);
+    NUCLEOTIDE_AMBIGUITY_DETECTION = Cache
+            .getDefault("NUCLEOTIDE_AMBIGUITY_DETECTION", true);
   }
 
   /**
@@ -324,7 +329,7 @@ public class Comparison
     }
     long allCount = ntCount + aaCount;
 
-    if (Cache.getDefault("NUCLEOTIDE_AMBIGUITY_DETECTION", true))
+    if (NUCLEOTIDE_AMBIGUITY_DETECTION)
     {
       Console.debug("Performing new nucleotide detection routine");
       if (allCount > NUCLEOTIDE_COUNT_SHORT_SEQUENCE)
@@ -393,18 +398,19 @@ public class Comparison
     // vs := NUCLEOTIDE_COUNT_VERY_SHORT_SEQUENCE
     // s := NUCLEOTIDE_COUNT_SHORT_SEQUENCE
     // lp := NUCLEOTIDE_COUNT_LOWER_PERCENT
-    // vsp := 1 - (1/a) # this is the proportion of required nucleotides in
-    // # a VERY_SHORT Sequence (4 bases).
-    // # should be all but one base is nucleotide.
+    // vsp := 1 - (1/a) # this is the proportion of required definite
+    // nucleotides
+    // # in a VERY_SHORT Sequence (4 bases).
+    // # This should be equivalent to all but one base in the sequence.
     // p := (a - vs)/(s - vs) # proportion of the way between
     // # VERY_SHORT and SHORT thresholds.
-    // tp := vsp + p * (lp/100 - vsp) # the proportion of nucleotides
+    // tp := vsp + p * (lp/100 - vsp) # the proportion of definite nucleotides
     // # required for this length of sequence.
     // minNt := tp * a # the minimum number of definite nucleotide bases
-    // # required for this length of sequences.
+    // # required for this length of sequence.
     //
     // We are then essentially returning:
-    // # ntCount >= 55% of allCount and the rest are all nucleotide ambiguity
+    // # ntCount >= 55% of allCount and the rest are all nucleotide ambiguity:
     // ntCount >= tp * allCount && nCount + ntaCount == aaCount
     // but without going into float/double land
     long LHS = 100 * allCount