X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=0b9839073cebb042298b43ee64b1a609d85bc368;hb=fd102a4945da5c62de156159c98a6a2c51f1ebbc;hp=63bb815520d0cef043b2b33c22315755c1411292;hpb=2273eba5668e5340354da60fed329c6c716cc439;p=jalview.git diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html index 63bb815..0b98390 100755 --- a/help/html/menus/popupMenu.html +++ b/help/html/menus/popupMenu.html @@ -1,7 +1,7 @@ - -

Sequence Id
- This menu is only visible if you right-click on a sequence name. - -

Sequence Details ...
- (Since Jalview 2.8)
Open an HTML report containing the annotation - and database cross references normally shown in the sequence's - tooltip.
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.
Add Reference Annotations
When enabled, copies any available alignment annotation for this sequence to the current view.

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.
- Since Jalview 2.4, links will also be made for database cross - references (where the database name exactly matches the link name set up in Preferences). -
Since Jalview 2.5, links are also shown for non-positional sequence features attached to - the sequence, and any regular-expression based URL links that - matched the description line. -
+
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.
- - -

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 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 its "View 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 open a 3D interactive - view of the file.
- 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.
-

Other menu entries may also be shown if the current selection includes sequences with associated structure data:
-

"Structure→View all N - structures
- Opens a new window containing all structures associated - with the current selection, superposed according to the currently selected region of the alignment.
(This - capability was added in Jalview 2.7) -
"Structure→View all N - representative structures
- Open a new window containing exactly one structure per - currently selected sequence.
- (The View representative structures option was introduced in - Jalview 2.8.1)

Hide Sequences
- Hides the currently selected sequences in this alignment view.
-
+

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. +
+
Sequence + Details ...
+ (Since Jalview 2.8)
Open an HTML report containing the annotation and database cross + references normally shown in the sequence's tooltip. +
+
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.
+
Add Reference Annotations
+ When enabled, copies any available alignment + annotation for this sequence to the current view.
+
Set as Reference or Unmark + as Reference
Sets or unsets the reference sequence for + the the alignment.
+ +
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.
Since Jalview 2.4, links will + also be made for database cross references (where the + database name exactly matches the link name set up in Preferences).
Since Jalview 2.5, links are also + shown for non-positional sequence features attached to the + sequence, and any regular-expression based URL links that + matched the description line. +

+
+

3D Structure Data... This menu is + visible when you right-click on a sequence name. When this + option is clicked, Jalview will open the 'Structure + Chooser' , which allows you to discover and view 3D structures + for the current selection. For more info, see viewing PDB structures. +

VARNA 2D Structure
+ If the sequence or alignment has RNA structure, then VARNA + 2D Structure entries will also be present enabling you to open + a linked view of the RNA structure in VARNA. +

Hide Insertions
+ Hides columns containing gaps in the current sequence or + selected region, and reveals columns not including gaps. +

Hide Sequences
Hides the + currently selected sequences in this alignment view.

- +