Popup Menu

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=f84922e6c3c07b70f855c5eb8900af4bf0e4a46a;hb=0943de76f6a7435894e72479671642c05f2f3687;hp=94ffb3c67e3e967f85377e74a85999a06942926a;hpb=ac5cc638b08386985f91503c81b27263230046e3;p=jalview.git diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html index 94ffb3c..f84922e 100755 --- a/help/html/menus/popupMenu.html +++ b/help/html/menus/popupMenu.html @@ -1,66 +1,219 @@ - -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.

Define -
- Group
  - This 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
- This menu is only visible if you right-click on a sequence name. - -
- Edit Name
  - You may edit the name of each sequence. A window will be - displayed asking for a new sequence name to be entered. Press OK to accept - your edit.
  -
- View PDB Structure
  - In the current version you will first need to select "View - -> Sequence Features" before associating a PDB file with a sequence. -
  - If the sequence has a PDB file associated with it Jalview will display - a 3D interactive viewer of the file.
-
Link
- This menu item lists all links which have been set up in the Preferences - Connections tab. It is only displayed when you right click (Apple click) on - a sequence id.
-
-

- - + + + +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 +
- 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.
+

+ +