X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=511b85f2e2b163e6687ad9c3ee46a850dbece35c;hb=bb49a7496f16118471764acae958b416e08c152c;hp=d4b8b5fa5f214a64012b4bdf4832a71e81f63538;hpb=8c0737632c158907098990b81ac702710721e9f2;p=jalview.git
diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index d4b8b5f..511b85f 100755
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -1,71 +1,208 @@
-
-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.
-
- - Define
-
- - Group
- This will display a window asking for the name of the currently
- selected group. Click OK to set the name, cancel to use the default group
- name.
-
- - 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
- 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.
-
- - View PDB Structure
-
- If the sequence has a PDB file associated with it Jalview will display
- a 3D interactive viewer of the file.
-This entry is only present if the sequence has an
- associated PDB structure.
- If you can't see this entry for your sequence, and the sequence name
- is a uniprot identifier, then try enabling the "View
- -> Sequence Features" and opening the popup menu again.
-
-
-
- - Link
- This menu item lists all links which have been set up in the Preferences
- Connections tab. It is only displayed when you right click (Apple click) on
- a sequence id.
-
-
-
-
-
+
+
+
+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
+
+ - 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.
+
+
+
+ - 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.
+
+
+
+
+