Popup Menu

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=2c50c02ce9582c346f31ef7f726576dd5e7670a3;hb=df22dee52c85b43767658a079c87172d79c0af06;hp=94ffb3c67e3e967f85377e74a85999a06942926a;hpb=ac5cc638b08386985f91503c81b27263230046e3;p=jalview.git diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html index 94ffb3c..2c50c02 100755 --- a/help/html/menus/popupMenu.html +++ b/help/html/menus/popupMenu.html @@ -1,66 +1,118 @@ - -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 +
- 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.
+
+

+ +