From ab3055b2ebd93e8265cb193e7b6a79f326732316 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 17 Sep 2024 21:39:49 +0100 Subject: [PATCH] JAL-4418 fix link case for linkcheck and window menu documentation update --- help/help/html/menus/alignmentMenu.html | 14 ++++++++++++-- help/help/html/menus/alwannotation.html | 7 ++++++- 2 files changed, 18 insertions(+), 3 deletions(-) diff --git a/help/help/html/menus/alignmentMenu.html b/help/help/html/menus/alignmentMenu.html index 33534b5..351a8c5 100755 --- a/help/help/html/menus/alignmentMenu.html +++ b/help/help/html/menus/alignmentMenu.html @@ -376,7 +376,7 @@ of the annotations.
  • Show Secondary Structure (since 2.11.4.0)
    All and None control display of secondary structure annotations on the alignment. - Additional options allow just a specific source of protein secondary structure to be shown.
    • + Additional options allow just a specific source of Protein secondary structure to be shown.
  • Autocalculated Annotation
    Settings for the display of autocalculated annotation.
      @@ -399,7 +399,14 @@ Enable or disable the display of the Consensus Logo above the consensus sequence.
    • Show SS Consensus Histogram
      -       Enable or disable the display of histogram for Secondary Structure Consensus.
      • + Enable or disable the display of histogram for + Secondary Structure Consensus.

      Note: + consensus secondary structure rows are not shown when no secondary + structure annotations are present for sequences in the alignment. + Use Add Reference Annotation + from the sequence or selection popup menu to add annotations from + structures or secondary structure predictions associated with + the sequences in the alignment.
    • Normalise Consensus Logo
      When enabled, scales all logo stacks to the same height, making it easier to compare symbol diversity in @@ -410,6 +417,9 @@
    • Group Consensus
       When ticked, display a consensus row for all groups.
      • +
    • Group Secondary Structure Consensus
      +       When ticked, display a consensus secondary + structure row for all groups.
  • Alignment Window Format Menu diff --git a/help/help/html/menus/alwannotation.html b/help/help/html/menus/alwannotation.html index 9f014ea..d6a7eb9 100755 --- a/help/help/html/menus/alwannotation.html +++ b/help/help/html/menus/alwannotation.html @@ -29,6 +29,11 @@ Jalview 2.8.2

      +
    • Show Annotations
      +       If this is selected the "Annotation Panel" + will be displayed below the alignment. The default setting + is to display the conservation calculation, quality + calculation and consensus values as bar charts.
    • Show Alignment Related
      Show all annotations that are for the alignment as a whole (for example, Consensus, or secondary structure prediction from @@ -82,7 +87,7 @@ Secondary Structure Consensus.

      Note: consensus secondary structure rows are not shown when no secondary structure annotations are present for sequences in the alignment. - Use Add Reference Annotation + Use Add Reference Annotation from the sequence or selection popup menu to add annotations from structures or secondary structure predictions associated with the sequences in the alignment.
      • -- 1.7.10.2