JAL-2418 check groovy script one-liners for restoring legacy score model behaviour

diff --git a/help/html/releases.html b/help/html/releases.html
index 89a39a3..23cfb84 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -270,19 +270,22 @@ li:before {
             </li>
             <li>
               <!-- JAL-2397 -->Fixed Jalview's treatment of gaps in PCA
-              and substitution matrix based Tree calculations.<br />In
+              and substitution matrix based Tree calculations.<br /> <br />In
               earlier versions of Jalview, gaps matching gaps were
               penalised, and gaps matching non-gaps penalised even more.
               In the PCA calculation, gaps were actually treated as
               non-gaps - so different costs were applied, which meant
               Jalview's PCAs were different to those produced by
               SeqSpace.<br />Jalview now treats gaps in the same way as
-              SeqSpace (ie it scores them as 0). To restore pre-2.10.2
-              behaviour<br />
-              jalview.viewmodel.PCAModel.scoreGapAsAny=true // for
-              2.10.1 mode<br />
-              jalview.viewmodel.PCAModel.scoreGapAsAny=false // to
-              restore 2.10.2 mode
+              SeqSpace (ie it scores them as 0). <br /> <br />Enter
+              the following in the Groovy console to restore pre-2.10.2
+              behaviour:<br />
+              jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
+              // for 2.10.1 mode <br />
+              jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
+              // to restore 2.10.2 mode <br /> <br /> <em>Note:
+                these settings will affect all subsequent tree and PCA
+                calculations (not recommended)</em>
             </li>
             <li>
               <!-- JAL-2424 -->Fixed off-by-one bug that affected