Popup Menu

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=f84922e6c3c07b70f855c5eb8900af4bf0e4a46a;hb=0943de76f6a7435894e72479671642c05f2f3687;hp=e8c5101bbc896959291ccac7842e7809ff235015;hpb=02a01a05117bb0dc0f09222aba2e63b012b3dbee;p=jalview.git diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html index e8c5101..f84922e 100755 --- a/help/html/menus/popupMenu.html +++ b/help/html/menus/popupMenu.html @@ -1,145 +1,190 @@ + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> 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.
  - 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.
- 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.
  - 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.
  - 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
  - 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.
- 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. -
  -
-
Structure - This menu is only visible if you right-click on a sequence name. - -
- Associate Structure with Sequence +
  + 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)
    - 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.
    - 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. +
  - 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.
    +