X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=353fb41e8f6e941434f1021f3856a94389333cde;hb=80fa1ace4f6ce0cea9680fd8a6d683270c8b2944;hp=511b85f2e2b163e6687ad9c3ee46a850dbece35c;hpb=87fa9a883d14416ba0e7f778bad69de813048b9c;p=jalview.git diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html index 511b85f..353fb41 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.
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 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. +

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.

- +