X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2FappletParameters.html;h=1e45aae5d5483f661652d5c9a2ea7494bfe9e275;hb=49f0437d385ee4c6dbe701180a4ba704da76b5f8;hp=6dd26e2b03370085d081b43c5473b9fdfd3a6226;hpb=47cbe0d4a22563312b7a841d08cf81b823c4cb39;p=jalview.git
diff --git a/examples/appletParameters.html b/examples/appletParameters.html
index 6dd26e2..1e45aae 100644
--- a/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@ -46,13 +46,20 @@ the applet can be interacted with via its
fileName |
The file to open, must be on same server as the applet. |
-
- file2 |
- fileName |
- A second file to open. If one file is nucleotide and the other peptide, and at least one peptide sequence
- matches the translation of one of the nucleotide sequences, then alignments will be displayed linked in a Split Frame. Parameter is ignored if enableSplitFrame is set to false (since 2.9). |
-
-
+
+ file2 |
+ fileName |
+ A second file to open and show linked in a Split Frame
+ view. If one file is nucleotide and the other peptide, and at
+ least one peptide sequence matches the translation of one of the
+ nucleotide sequences, then gaps will be inserted into the
+ sequences in this file to match the aligned columns for
+ corresponding positions in the primary alignment file. This
+ parameter is ignored if enableSplitFrame is set to false (since
+ 2.9).
+ |
+
+
enableSplitFrame |
true or false (default true) |
Enable or disable the display of linked cDNA and Protein alignments in a split frame (since 2.9). |
@@ -111,6 +118,14 @@ the applet can be interacted with via its
Default is no colour. |
+ defaultColourNuc |
+ A colour scheme (from the list above) to apply to Nucleotide alignments | This overrides defaultColour if it is specified. |
+
+
+ defaultColourProt |
+ A colour scheme (from the list above) to apply to Peptide alignments | This overrides defaultColour if it is specified. |
+
+
userDefinedColour |
Example:
D,E=red; K,R,H=0022FF; c=yellow |