Annotation Panel Menus

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwannotations.html;h=12acf7e8a2835a67b5bdc63e96ef2a5519149f87;hb=3b94f01f4edf56896ae3b5f0ce6cb4f1996e7bbc;hp=e8a64f6401ea5d306890cced0c3b0278f3a62db2;hpb=8e01fb5c8703be31f7f4f42b8db3d1e99e20cddc;p=jalview.git diff --git a/help/html/menus/alwannotations.html b/help/html/menus/alwannotations.html index e8a64f6..12acf7e 100755 --- a/help/html/menus/alwannotations.html +++ b/help/html/menus/alwannotations.html @@ -1,59 +1,101 @@ - - -Annotation Panel Menus - - -

Annotation Panel Menus

Annotation Label Popup Menu
- This menu is opened by clicking anywhere on the annotation row labels - area (below the sequence ID area). -
- Add New Row
  - Adds a new, named annotation row (a dialog box will pop up for you - to enter the label for the new row).
- Hide Row
  - Hides the annotation row whose label was clicked in order to bring - up the menu.
- Delete Row
  - Deletes the annotation row whose label was clicked in order to bring - up the menu.
- Show All Hidden Rows
  - Shows all hidden annotation rows.
- Show Values in Text Box
  - Opens a text box with a list of comma-separated values corresponding - to the annotation (numerical or otherwise) at each position in the row. - This is useful to export alignment quality measurements for further analysis. -
- Ignore Gaps in Consensus
  - If this checkbox is selected, all consensus calculations performed in the - current Alignment window will be done without counting gaps as - a consensus character.
-
Annotation Popup Menu
- This menu is opened when right-clicking on the selected positions - of an annotation. -
- Helix
  - Mark selected positions with a helix glyph (a red oval), and optional - text label (see below). Consecutive ovals will be rendered as an unbroken - red line.
- Sheet
  - Mark selected positions with a sheet glyph (a green arrow oriented - from left to right), and optional text label (see below). Consecutive - arrows will be joined together to form a single green arrow.
- Label
  - Sets the text label at the selected positions. If more that one consecutive - position is marked with the same label, only the first position's label - will be rendered.
- Colour
  - Changes the colour of the annotation text label.
- Remove Annotation
  - Blanks any annotation at the selected positions on the row. Note: - This cannot be undone
-

- - + + + +Annotation Panel Menus + + +

Annotation Panel Menus

Annotation Label Popup Menu
+ This menu is opened by clicking anywhere on the annotation row labels + area (below the sequence ID area). +
- Add New Row
  + Adds a new, named annotation row (a dialog box will pop up for you + to enter the label for the new row).
- Hide Row
  + Hides the annotation row whose label was clicked in order to bring + up the menu.
- Delete Row
  + Deletes the annotation row whose label was clicked in order to bring + up the menu.
- Show All Hidden Rows
  + Shows all hidden annotation rows.
- Export Annotation (Application only)
  + Annotations can be saved to file or output to a text window in either the + Jalview annotations format or as a spreadsheet style set of comma separated values (CSV).
- Show Values in Text Box (applet only)
  + Opens a text box with a list of comma-separated values corresponding + to the annotation (numerical or otherwise) at each position in the row. + This is useful to export alignment quality measurements for further analysis. +
+ The following additional entries are available when the popup menu is opened on a consensus sequence annotation row: +
- Ignore Gaps in Consensus
  + If this checkbox is selected, all consensus calculations performed in + the current Alignment window will be done without counting gaps as a consensus + character.
- 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 sequence 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.
- +
- Copy Consensus Sequence
  + Copies the consensus sequence to the clipboard in Fasta format, to allow + the consensus sequence to be added to an alignment. Note the copied sequence + is not accessible to other programs if Jalview is running as an applet + in a web page.
+
Annotation Popup Menu
+ This menu is opened when right-clicking on the selected positions + of an annotation. +
- Helix
  + Mark selected positions with a helix glyph (a red oval), and optional + text label (see below). Consecutive ovals will be rendered as an unbroken + red line.
- Sheet
  + Mark selected positions with a sheet glyph (a green arrow oriented + from left to right), and optional text label (see below). Consecutive + arrows will be joined together to form a single green arrow.
- Label
  + Sets the text label at the selected positions. If more that one consecutive + position is marked with the same label, only the first position's label + will be rendered.
- Colour
  + Changes the colour of the annotation text label.
- Remove Annotation
  + Blanks any annotation at the selected positions on the row. Note: + This cannot be undone
+

+ +