Popup Menu
This menu is visible
when right clicking either within a selected region on the alignment
or on a selected sequence name. It may not be accessible when in
'Cursor Mode' (toggled with the F2 key).
- Selection
- Sequence Details...
(Since Jalview 2.8)
Open an HTML report containing the
annotation and database cross references normally shown in
the sequence's tooltip.
- Show Annotations...
Choose to show (unhide) either All or a selected type of
annotation for the selected sequences. (Since Jalview 2.8.2)
- Hide Annotations...
Choose to hide either All or a selected type of annotation
for the selected sequences. (Since Jalview 2.8.2)
- Add Reference
Annotations
Add to the alignment window any annotations on the
selected sequences which have been read from reference sources or
calculated (for example, secondary structure derived from 3D
structure). (Since Jalview 2.8.2)
- Edit
- Copy
Copies the
selected region. In the applet version, the copied sequences are
not available to the system clipboard.
- Cut
Cuts the selected region from the alignment. In the
applet version, the copied sequences are not available to the
system clipboard.
- Edit Sequence
Edit the
selected sequence(s) directly. Spaces will be converted to the
current gap character.
- To Upper Case
Changes the case of selected region to lower case.
- To Lower Case
Changes the case of selected region to upper case.
- Toggle Case
Switches
the case of all residues within the selected region.
- Output to Textbox
The selection area will be output to a a text window in the
selected alignment format.
- Create
Sequence Feature...
Opens the dialog box for
creating sequence features over the currently selected region on
each selected sequence.
- Create Group
This will define a new group from the current selection.
- Remove Group
This will undefine the selected group.
- Edit (New) Group
Group
Editing Menu
Options in this menu modify the name and
display properties of the currently selected group, or a new group
defined using the current selection.
- Name: <Group> or Edit
name and description
The first entry in the
menu displays the name for the currently selected group, if it
has one. Selecting this option opens a window allowing the name
and description for this group to be edited. Click OK to set the
new name and decription, and cancel to leave the existing name
and description unchanged.
- Group Colour
Sets the colour
of the group.
- Boxes
If selected the background of a residue within the
selected group will be coloured according to the assigned colour
scheme.
- Text
If selected the selected group will display text.
- Colour Text
If selected the selected group will display text in a
colour slightly darker than the background colour of that
residue.
- Border Colour
Selecting this will display a "Colour Chooser"
window. Select a colour than press OK to set the border colour
of a group.
- Show Unconserved
When this is selected, all symbols in the group matching
the consensus sequence at that column will be rendered as a '.',
highlighting mutations in the group area.
- Sequence Id
This menu is only visible if you right-click on a sequence
name.
- View Structure This menu is only
visible if you right-click on a sequence name. If the
sequence has an associated PDB file(s), Jalview will open a 'Structure Chooser'
dialogue with options to select the structure which will eventually be opened in
a 3D interactive view.
These entries will only be present if the sequence
has associated PDB
structures.
If the sequence or alignment has RNA structure,
then 2D RNA entries will also be present enabling
you to open a linked view of the RNA structure in VARNA.
- Hide Sequences
Hides the
currently selected sequences in this alignment view.