X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwannotation.html;h=8ac116b846b45721faf2b97054b7d7e6349130b3;hb=cc83249392010c58e60c1b6d727115c08d5b7a65;hp=02820b95d04d7f24f10b9552dc637e20730bbe38;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git
diff --git a/help/html/menus/alwannotation.html b/help/html/menus/alwannotation.html
index 02820b9..8ac116b 100755
--- a/help/html/menus/alwannotation.html
+++ b/help/html/menus/alwannotation.html
@@ -24,56 +24,67 @@
-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.
+
+
+