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+
+
+
+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).
+ Mac Users: pressing CTRL whilst clicking
+ the mouse/track pad is the same as a right-click. See your
+ system's settings to configure your track-pad's corners to
+ generate right-clicks.
+
+ - 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).
+ - Edit Label/Description
This
+ opens a dialog where you can change the name (displayed
+ label), or the description (as shown on the label tooltip)
+ of the clicked annotation.
+ - Hide This Row
Hides
+ the annotation row whose label was clicked in order to bring
+ up the menu.
+ - Hide All <label>
+ Hides all annotation rows whose label matches the one
+ clicked. (This option is only shown for annotations that
+ relate to individual sequences, not for whole alignment
+ annotations. Since Jalview 2.8.2.)
+ - 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 than 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
+
+
+
+
+