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
- Edit
- Copy
Copys 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.
- Group
Group Operations
- GroupThis is the first entry in the
menu, and will display the currently selected group's
name. Selecting it displays 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.
- Remove Group
This will undefine the selected group.
- 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.
- Sequence Id
This menu is only visible if you right-click on a sequence name.
- Edit Name/Description
You may edit the name and description of each sequence. A
window will be displayed asking for a new sequence name and sequence description
to be entered. Press OK to accept your edit. To save sequence descriptions,
you must save in Fasta, PIR or Jalview File format.
-
- Represent Group With (Sequence Id)
All sequences in the current selection group will be hidden, apart
from (Sequence Id). Any edits performed on the visible representative
sequence will be propagated to the hidden sequences.
- Link
This menu item lists all links which have been set up in the Preferences
Connections tab.
- Structure
This menu is only visible if you right-click on a sequence name.
- Associate Structure with Sequence
- From File
Load a PDB file from local disk which will be associated
with this sequence. This file will be used if the user subsequently
clicks on "View PDB Structure" menu item.
- Enter PDB id
Enter the PDB id from an input window. This PDB id will
be used by the service WSDBFetch, provided by the EBI, to fetch the
PDB file if the user subsequently clicks on "View PDB Structure"
menu item.
- Discover PDB ids
This will use the service WSDBFetch, provided by the
EBI, to retrieve all PDB ids associated with the sequences in the
alignment if the sequences have valid Uniprot names or accession ids.
- View Structure
If the sequence has an associated PDB file added by one
of the methods described above, Jalview will display a 3D interactive
viewer of the file.
These entries will only be present if the sequence has associated PDB structures.
- Hide Sequences
Hides the currently selected sequences in this alignment view.