X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwannotation.html;h=6f91d2f75816158b1c288670b0889cd6ed182749;hb=46914f7ccdff5e88bf104f61315d533462c4d056;hp=02820b95d04d7f24f10b9552dc637e20730bbe38;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git diff --git a/help/html/menus/alwannotation.html b/help/html/menus/alwannotation.html index 02820b9..6f91d2f 100755 --- a/help/html/menus/alwannotation.html +++ b/help/html/menus/alwannotation.html @@ -24,56 +24,68 @@ -

Alignment Window Annotations Menu (Since Jalview 2.8.2)

Show Alignment Related
- Show all annotations that are for the alignment as a whole (for example, Consensus, - or secondary structure prediction from alignment)).
Hide Alignment Related
- Hide all annotations that are for the alignment as a whole.
Show Sequence Related
- Show all annotations that are for individual sequences.
Hide Sequence Related
- Hide all annotations that are for individual sequences.
Show Alignment Related
- Show all annotations that are for the alignment as a whole (for example, Consensus).
You can also selectively show or hide annotations from the Popup - or Annotation menus.
Sort by Sequence
Sort sequence-specific annotations by sequence order in the alignment - (and within that, by label).
Sort by Label
Sort sequence-specific annotations by label - (and within that, by sequence order). If neither sort order is selected, no sorting is applied, - allowing you to make a manual ordering of the annotations.
Autocalculated Annotation
Settings - for the display of autocalculated annotation. -
- Show first
  - Show autocalculated annotations above sequence-specific annotations. - Note this also applies to other annotations for the alignment, for example secondary - structure prediction from alignment.
- Show last
  - Show autocalculated / alignment annotations below sequence-specific annotations.
- Apply to all groups
  When - ticked, any modification to the current settings will be applied - to all autocalculated annotation.
- Show Consensus Histogram
  - Enable or disable the display of the histogram above the - consensus sequence.
- Show Consensus Logo
  Enable - or disable the display of the Consensus Logo above the consensus - sequence.
- Normalise Consensus Logo
  - When enabled, scales all logo stacks to the same height, - making it easier to compare symbol diversity in highly variable - regions.
- Group Conservation
  When - ticked, display a conservation row for all groups (only available - for protein alignments).
- Group Consensus
  When - ticked, display a consensus row for all groups.
-

+ Alignment Window Annotations Menu Since Jalview + 2.8.2 +

Show Alignment Related
+ Show all annotations that are for the alignment as a whole (for + example, Consensus, or secondary structure prediction from + alignment)).
Hide Alignment Related
+ Hide all annotations that are for the alignment as a whole.
Show Sequence Related
+ Show all annotations that are for individual sequences.
Hide Sequence Related
+ Hide all annotations that are for individual sequences.
Show Alignment Related
+ Show all annotations that are for the alignment as a whole (for + example, Consensus).
You can also selectively show or hide annotations + from the Popup or Annotation menus. +
Sort by Sequence
Sort + sequence-specific annotations by sequence order in the alignment + (and within that, by label).
Sort by Label
Sort + sequence-specific annotations by label (and within that, by + sequence order). If neither sort order is selected, no sorting + is applied, allowing you to make a manual ordering of the + annotations.
Autocalculated Annotation
+ Settings for the display of autocalculated annotation. +
- Show first
  Show + autocalculated annotations above sequence-specific + annotations. Note this also applies to other annotations for + the alignment, for example secondary structure prediction + from alignment.
- Show last
  Show + autocalculated / alignment annotations below + sequence-specific annotations.
- Apply to all groups
  + When ticked, any modification to the current settings + will be applied to all autocalculated annotation.
- Show Consensus Histogram
  + Enable or disable the display of the histogram above + the consensus sequence.
- Show Consensus Logo
  + Enable or disable the display of the Consensus Logo + above the consensus sequence.
- Normalise Consensus Logo
  + When enabled, scales all logo stacks to the same + height, making it easier to compare symbol diversity in + highly variable regions.
- Group Conservation
  + When ticked, display a conservation row for all groups + (only available for protein alignments).
- Group Consensus
  + When ticked, display a consensus row for all groups.