X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=d42f854c841af1d3fc0af515b32fc0b40ca05673;hb=dde303bc73617ab4eb3e681e67cf899e6a971318;hp=79e7ada6fbdf5a1c2592de70fc73f4d841369a44;hpb=528c0f1815bc67b54618ad5b16c2162946974caf;p=jalview.git
diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 79e7ada..d42f854 100755
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -25,13 +25,13 @@
- 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).
Mac Users: pressing CTRL whilst clicking
- the mouse/track pad is the same as a right-click. See your
- system's settings to configure your track-pad's corners to
- generate right-clicks.
+ 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).
Mac
+ Users: pressing CTRL whilst clicking the mouse/track pad is the
+ same as a right-click. See your system's settings to configure
+ your track-pad's corners to generate right-clicks.
- Selection
@@ -39,9 +39,9 @@
- Sequence
Details...
(Since Jalview 2.8)
Open an HTML report containing the annotation and database cross
- references normally shown in the sequence's tooltip.
+ href="../io/exportseqreport.html">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
@@ -81,10 +81,10 @@
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.
+ href="../features/creatinFeatures.html">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.
@@ -137,9 +137,9 @@
- Sequence
Details ...
(Since Jalview 2.8)
Open an HTML report containing the annotation and database cross
- references normally shown in the sequence's tooltip.
+ href="../io/exportseqreport.html">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.
@@ -147,12 +147,14 @@
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.
+ - Add Reference
+ Annotations
When enabled, copies any
+ available alignment annotation for this sequence to the
+ current view.
- Set as Reference or Unmark
- as Reference
Sets or unsets the reference sequence for
- the the alignment.
+ as Reference
Sets or unsets the reference sequence
+ for the the alignment.
- Represent Group With (Sequence Id)
All sequences in the current selection group will be
@@ -165,27 +167,26 @@
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.
+ href="../features/preferences.html">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 the 'Structure
- Chooser' , which allows you to discover and view 3D structures
- for the current selection. For more info, see '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
+ 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.
+ href="../features/varna.html">VARNA.
Hide Insertions
Hides columns containing gaps in the current sequence or