Popup Menu

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=7625606d972b58cbeb3e2bb9987f99c777920569;hb=a510e9b4726214441e4fdac8a1d6752263c4c73d;hp=2c50c02ce9582c346f31ef7f726576dd5e7670a3;hpb=bb105fcca41253815982584f4c8f6fae1f8e10a3;p=jalview.git diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html index 2c50c02..7625606 100755 --- a/help/html/menus/popupMenu.html +++ b/help/html/menus/popupMenu.html @@ -1,118 +1,201 @@ + 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 -
- 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 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.
- Group
  - Group Operations -
  - GroupThis 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.
  -
-
Sequence Id
- 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.
- Associate Structure with Sequence -
  - 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.
  - 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" menu item.
  - Discover PDB ids
    - This will use the service WSDBFetch, provided by the EBI, to - retrieve all PDB ids associated with the sequences in the alignment - if the sequences have valid Uniprot names or accession ids.
  -
- View PDB 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.
  - This entry is only present if the sequence has an associated PDB structure.
- 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.
  -
-
Hide Sequences
- Hides the currently selected seuqences in this alignment view.
-
-

+ 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.
+