From: gmungoc 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[] 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