X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=8eab2d0defc6c04162259c1063fc08e0223e09c9;hb=682b4b598105a0024231bcf5f53206530425fd64;hp=2c50c02ce9582c346f31ef7f726576dd5e7670a3;hpb=bb105fcca41253815982584f4c8f6fae1f8e10a3;p=jalview.git
diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 2c50c02..8eab2d0 100755
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -1,4 +1,21 @@
+
Popup Menu
@@ -9,110 +26,154 @@
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.
-
-
+ - 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.
+
+
+
+ - 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 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.
+
+