X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=0b9839073cebb042298b43ee64b1a609d85bc368;hb=fd102a4945da5c62de156159c98a6a2c51f1ebbc;hp=940e3cf0673f114d8a129b98b2815fa53ce53de4;hpb=caad315933db2600eaca9bf111932d5767ccb78b;p=jalview.git
diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 940e3cf..0b98390 100755
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -1,93 +1,195 @@
-
-
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).
-
- - 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.
-
-
-
- - 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.
-
-
- - To Lower Case
- Changes the case of selected region to upper case.
-
- - To Upper Case
- Changes the case of selected region to lower case.
-
- - Toggle Case
- Switches the case of all residues within the selected region.
-
-
-
-
-
- - 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.
+
+ - 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.
+
+
+
+