X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=353fb41e8f6e941434f1021f3856a94389333cde;hb=eb712aa29e2bc62c57b90df8420052293dd90c6b;hp=6e8eeb2b6ba835a4ea20b1c0232aaaffe8ea9b04;hpb=e641357d074cf8f3b9ee877f47879d6e22ac1ce1;p=jalview.git
diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 6e8eeb2..353fb41 100755
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -1,148 +1,197 @@
+
Popup Menu
-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.
+
+ 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.
- - 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.
- - 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.
-
-
-
- - Group Links
- This menu is only visible if there are group links available for the current selection.
-
-
- - ID links allow you to send IDs associated with the current selection to a web server.
- - Sequence links allow you to send the sequences in the currently selected region to a web server.
- - Sequence and ID links allow you to send sets of IDs and sequences associated with the current selection to a web server.
-
- Group Links were added in Jalview 2.5
-
-
- - Sequence Id
- This menu is only visible if you right-click on a sequence name.
-
-
+ - 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 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.
-
+ - 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.
+
+ - 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.
-
+