X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=353fb41e8f6e941434f1021f3856a94389333cde;hb=53e232c25d1956fdcc239b0db8d6b18cecc601a4;hp=f84922e6c3c07b70f855c5eb8900af4bf0e4a46a;hpb=dbb8e925003ee2249a65bed6e6c74b378b673a18;p=jalview.git
diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index f84922e..353fb41 100755
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -24,196 +24,174 @@
-
- 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.
-
+
+ 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.
-
- - View Structure This menu is only
- visible if you right-click on a sequence name. If the
- sequence has an associated PDB file(s), 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.
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.
-
-
-
-
- - Hide Sequences
Hides the
- currently selected sequences in this alignment 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.
+
+
+ - 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.
+
+