Popup Menu

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;fp=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=7625606d972b58cbeb3e2bb9987f99c777920569;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html deleted file mode 100755 index 7625606..0000000 --- a/help/html/menus/popupMenu.html +++ /dev/null @@ -1,201 +0,0 @@ - - - -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).
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 -
- 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)
- 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. -
- 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.
- Set as Reference or Unmark - 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 - 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 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 both the current - sequence and selected region, and reveals columns not including - gaps. (before 2.10.2, this option hid or revealed columns - according to gaps in just the current sequence)
Hide Sequences
Hides the - currently selected sequences in this alignment view.
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