Annotation Panel Menus

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwannotations.html;h=975b715081595161c5f748d0fd1b8919073cdee2;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=7b9b0d528b18be766c95a7b76543c0657b0d22b5;hpb=a8a3ca19aa9240b9d816ed9e7dc8be45209989ae;p=jalview.git diff --git a/help/html/menus/alwannotations.html b/help/html/menus/alwannotations.html index 7b9b0d5..975b715 100755 --- a/help/html/menus/alwannotations.html +++ b/help/html/menus/alwannotations.html @@ -1,70 +1,102 @@ - - -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
  + + + +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 the - Jalview annotations format.
    - 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 avalable 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.
    - 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
    -
  - - + 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
  +
+ +