X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=4f66696d1fd035dd0e155685915b843141e323e9;hb=0696cffbccbb537be78d9fc2410589adbcd7be35;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git
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index e18e273..4f66696 100755
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@@ -1,6 +1,6 @@
+
+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.
+
+
+
+ - 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 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.
+ These entries will only be present if the sequence has associated PDB structures.
+
+
+
+ - Hide Sequences
+ Hides the currently selected sequences in this alignment view.
+
+
+
+
+