From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 2 Nov 2016 10:04:18 +0000 (+0000)
Subject: JAL-98 wording "negatively conserved" now "absence conserved"
X-Git-Tag: Release_2_11_0~62^2~81
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=30ac662ca0b66f445e34e90127c05b3e26d90621;p=jalview.git

JAL-98 wording "negatively conserved" now "absence conserved"
---

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 73a9dee..027a096 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -60,7 +60,7 @@ public class Conservation
 
   /*
    * a map per column with {property, conservation} where conservation value is
-   * 1 (property is conserved), 0 (property is negatively conserved) or -1
+   * 1 (property is conserved), 0 (absence of property is conserved) or -1
    * (property is not conserved i.e. column has residues with and without it)
    */
   Map<String, Integer>[] total;
@@ -214,7 +214,7 @@ public class Conservation
 
       /*
        * check observed residues in column and record whether each 
-       * physico-chemical property is conserved (+1), negatively conserved (0),
+       * physico-chemical property is conserved (+1), absence conserved (0),
        * or not conserved (-1)
        * Using TreeMap means properties are displayed in alphabetical order
        */
@@ -442,7 +442,7 @@ public class Conservation
           if (result == -1)
           {
             /*
-             * not conserved either positively or negatively
+             * not conserved (present or absent)
              */
             continue;
           }
@@ -458,7 +458,7 @@ public class Conservation
           if (result == 0 && !positiveOnly)
           {
             /*
-             * negatively conserved property (all residues lack it)
+             * absense of property is conserved (all residues lack it)
              */
             negatives.append(negatives.length() == 0 ? "" : " ");
             negatives.append("!").append(type);
@@ -816,7 +816,8 @@ public class Conservation
   /**
    * Returns the computed tooltip (annotation description) for a given column.
    * The tip is empty if the conservation score is zero, otherwise holds the
-   * positively (and, optionally, negatively) conserved properties.
+   * conserved properties (and, optionally, properties whose absence is
+   * conserved).
    * 
    * @param column
    * @return