X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=6bb2e3a8e27c7134b152111ba4ba95a1e5261f07;hb=f27f81a74bbe1be141d23df8aba578515e3179a2;hp=9cf53587bffe76b81ee79c7468345b43d9197d68;hpb=fd6fc6bbcf3cf91b6f218729cc014997782053b1;p=jalview.git
diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 9cf5358..6bb2e3a 100755
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -1,4 +1,24 @@
+
Popup Menu
@@ -11,10 +31,24 @@ 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
- Copys the selected region. In the applet version, the copied sequences
+ 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
@@ -38,18 +72,22 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).
- 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.
+ - 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.
@@ -66,20 +104,37 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).
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.
- - Edit Name/Description
+ - 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.
- 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
@@ -89,7 +144,7 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).
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 2.4.1, links are also shown for non-positional sequence features attached to
+
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.
@@ -105,11 +160,11 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).
- 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.
+ 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 "View PDB Structure"
+ 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
@@ -120,11 +175,28 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).
- 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.
+ 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.
+ href="../features/viewingpdbs.html">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