JAL-2418 JAL-2398 JAL-2397 simpler documentation for reinstating legacy behaviour

diff --git a/examples/legacyblosum62.scm b/examples/legacyblosum62.scm
deleted file mode 100644 (file)
index 57072cf..0000000
--- a/examples/legacyblosum62.scm
+++ /dev/null
@@ -1,33 +0,0 @@
-ScoreMatrix BLOSUM62Legacy
-#
-# The BLOSUM62 substitution matrix, as used in earlier versions of jalview
-#
-# Scores are not symbol case sensitive, unless column(s) are provided for lower case characters
-# The 'guide symbol' at the start of each row of score values is optional
-# Values may be integer or floating point, delimited by tab, space, comma or combinations
-#
-        A       R       N       D       C       Q       E       G       H       I       L       K       M       F       P       S       T       W       Y       V       B       Z       X       * 
-A       4      -1      -2      -2       0      -1      -1       0      -2      -1      -1      -1      -1      -2      -1       1       0      -3      -2       0      -2      -1       0      -4
-R      -1       5       0      -2      -3       1       0      -2       0      -3      -2       2      -1      -3      -2      -1      -1      -3      -2      -3      -1       0      -1      -4
-N      -2       0       6       1      -3       0       0       0       1      -3      -3       0      -2      -3      -2       1       0      -4      -2      -3       3       0      -1      -4
-D      -2      -2       1       6      -3       0       2      -1      -1      -3      -4      -1      -3      -3      -1       0      -1      -4      -3      -3       4       1      -1      -4
-C       0      3       -3      -3       9      -3      -4      -3      -3      -1      -1      -3      -1      -2      -3      -1      -1      -2      -2      -1      -3      -3      -2      -4
-Q      -1       1       0       0      -3       5       2      -2       0      -3      -2       1       0      -3      -1       0      -1      -2      -1      -2       0       3      -1      -4
-E      -1       0       0       2      -4       2       5      -2       0      -3      -3       1      -2      -3      -1       0      -1      -3      -2      -2       1       4      -1      -4
-G       0      -2       0      -1      -3      -2      -2       6      -2      -4      -4      -2      -3      -3      -2       0      -2      -2      -3      -3      -1      -2      -1      -4
-H      -2       0       1      -1      -3       0       0      -2       8      -3      -3      -1      -2      -1      -2      -1      -2      -2       2      -3       0       0      -1      -4
-I      -1      -3      -3      -3      -1      -3      -3      -4      -3       4       2      -3       1       0      -3      -2      -1      -3      -1       3      -3      -3      -1      -4
-L      -1      -2      -3      -4      -1      -2      -3      -4      -3       2       4      -2       2       0      -3      -2      -1      -2      -1       1      -4      -3      -1      -4
-K      -1       2       0      -1      -3       1       1      -2      -1      -3      -2       5      -1      -3      -1       0      -1      -3      -2      -2       0       1      -1      -4
-M      -1      -1      -2      -3      -1       0      -2      -3      -2       1       2      -1       5       0      -2      -1      -1      -1      -1       1      -3      -1      -1      -4
-F      -2      -3      -3      -3      -2      -3      -3      -3      -1       0       0      -3       0       6      -4      -2      -2       1       3      -1      -3      -3      -1      -4
-P      -1      -2      -2      -1      -3      -1      -1      -2      -2      -3      -3      -1      -2      -4       7      -1      -1      -4      -3      -2      -2      -1      -2      -4
-S       1      -1       1       0      -1       0       0       0      -1      -2      -2       0      -1      -2      -1       4       1      -3      -2      -2       0       0       0      -4
-T       0      -1       0      -1      -1      -1      -1      -2      -2      -1      -1      -1      -1      -2      -1       1       5      -2      -2       0      -1      -1       0      -4
-W      -3      -3      -4      -4      -2      -2      -3      -2      -2      -3      -2      -3      -1       1      -4      -3      -2      11       2      -3      -4      -3      -2      -4
-Y      -2      -2      -2      -3      -2      -1      -2      -3       2      -1      -1      -2      -1       3      -3      -2      -2       2       7      -1      -3      -2      -1      -4
-V       0      -3      -3      -3      -1      -2      -2      -3      -3       3       1      -2       1      -1      -2      -2       0      -3      -1       4      -3      -2      -1      -4
-B      -2      -1       3       4      -3       0       1      -1       0      -3      -4       0      -3      -3      -2       0      -1      -4      -3      -3       4       1      -1      -4
-Z      -1       0       0       1      -3       3       4      -2       0      -3      -3       1      -1      -3      -1       0      -1      -3      -2      -2       1       4      -1      -4
-X       0      -1      -1      -1      -2      -1      -1      -1      -1      -1      -1      -1      -1      -1      -2       0       0      -2      -1      -1      -1      -1      -1      -4
-*      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4       1 

diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html
index 14bb9ee..0104078 100755 (executable)
--- a/help/html/calculations/pca.html
+++ b/help/html/calculations/pca.html
@@ -142,16 +142,14 @@ left-clicking and dragging the mouse over the display. -->
     and implemented at the SeqSpace server at the EBI. To reproduce
     calculations performed with earlier Jalview releases it is necessary
     to execute the following Groovy script:
-  
   <pre>
     jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
+    jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
     </pre>
-  Additionally, for PCAs performed with older versions of Jalview and
-  the Blosum62 matrix, it is also necessary to import the legacy
-  BLOSUM62 score matrix (which is asymmetric for mutations between C to
-  R) which can be downloaded at
-  http://www.jalview.org/examples/legacyBlosum62.scm
+  This script enables the legacy PCA mode where gaps were treated as
+  'X', and to modify the BLOSUM62 matrix so it is asymmetric for
+  mutations between C to R (this was a typo in the original Jalview
+  BLOSUM62 matrix which was fixed in 2.10.2).
   </p>
-
 </body>
 </html>