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).
-
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.
+
+ 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).
+
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.
-
+ 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.
+ 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
-
-
-
+
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
+