Popup Menu

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=2be60003fd17797e529ba98668f97898768c1d29;hb=6ca7cf3ba5134086da3fae5397e5404c6f7b0a58;hp=b117218746a97f2cb25a7c4b560751c36ccf93c1;hpb=a14da63fa1dabed03c67eadc39c6b4a61c5102f0;p=jalview.git diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html index b117218..2be6000 100755 --- a/help/html/menus/popupMenu.html +++ b/help/html/menus/popupMenu.html @@ -1,125 +1,198 @@ - - -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 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 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.
- 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.
  -
-
Structure -
- 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 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.
  -
-
Hide Sequences
- Hides the currently selected seuqences in this alignment view.
-
-

- - + + + +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.
- 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.
- 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.
- 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 +
  - 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.
+
+

+ +