Popup Menu

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=6bb2e3a8e27c7134b152111ba4ba95a1e5261f07;hb=dfc0fa51c8c3305bb7a50a5dcde8d10e08430462;hp=734cdc56500609fa0b420048d971b5d7f31f910f;hpb=cbee3032010ef9a5b4b2ff43b47747b1e7f0389b;p=jalview.git diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html index 734cdc5..6bb2e3a 100755 --- a/help/html/menus/popupMenu.html +++ b/help/html/menus/popupMenu.html @@ -1,110 +1,208 @@ - -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.
- 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 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
- 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. +
  +
+
Structure + This menu is only visible if you right-click on a sequence name. + +
- 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 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 its "View 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 Structure
  + If the sequence has an associated PDB file added by one + of the methods described above, Jalview will open a 3D interactive + view of the file.
  + 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.
+
+

+ +