From 85c6a9ff7bb1e0711b4c8503f10186bb083fb871 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 9 Sep 2015 12:55:43 +0100 Subject: [PATCH] JAL-1684 clarification of which alignment will be used to guide the reconstruction of the linked alignment --- examples/appletParameters.html | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/examples/appletParameters.html b/examples/appletParameters.html index 6dd26e2..8daa4ee 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). -- 1.7.10.2