X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Fmenus%2Falwannotations.html;h=b604c892b2a030a4002a06dd192cef1fd84fa89e;hb=cb4b4b590add93fb0fb5c5ecd1d0532f1456ecc2;hp=f7b62ca6e51f6f95b77556d9d35891ffc7abd7a9;hpb=effd8d76f34bc7fd4e069603d80565b7ea9d3ff0;p=jalview.git
diff --git a/help/html/menus/alwannotations.html b/help/html/menus/alwannotations.html
index f7b62ca..b604c89 100755
--- a/help/html/menus/alwannotations.html
+++ b/help/html/menus/alwannotations.html
@@ -1,58 +1,87 @@
+
Annotation Panel Menus
Annotation Panel Menus
--
-Annotation Label Popup Menu
-This menu is opened by clicking anywhere on the annotation row labels
-area (below the sequence ID area).
-
--
-Add New Row
-Adds a new, named annotation row (a dialog box will pop up for you
-to enter the label for the new row).
- - Hide Row
-Hides the annotation row whose label was clicked in order to bring
-up the menu.
- - Delete Row
-Deletes the annotation row whose label was clicked in order to bring
-up the menu.
- - Show All Hidden Rows
-Shows all hidden annotation rows.
- - Show Values in Text Box
-Opens a text box with a list of comma-separated values
-corresponding to the annotation (numerical or otherwise) at each
-position in the row. This is useful to export alignment quality
-measurements for further analysis.
-
-
-
-- Annotation Popup Menu
This menu is opened when
-right-clicking on the selected positions of an annotation.
-
-- Helix
Mark selected positions with a helix glyph (a red
-oval), and optional text label (see below). Consecutive ovals
-will be rendered as an unbroken red line.
-
-- Sheet
Mark selected positions with a sheet glyph (a green
-arrow oriented from left to right), and optional text label (see
-below). Consecutive arrows will be joined together to form a single
-green arrow.
-
-- Label
Sets the text label at the selected positions. If
-more that one consecutive position is marked with the same label, only
-the first position's label will be rendered.
-
-- Colour
Changes the colour of the annotation text label.
-
-- Remove Annotation
Blanks any annotation at the selected positions on
-the row. Note: This cannot be undone
-
-
-
+ - Annotation Label Popup Menu
+ This menu is opened by clicking anywhere on the annotation row labels
+ area (below the sequence ID area).
+
+ - Add New Row
+ Adds a new, named annotation row (a dialog box will pop up for you
+ to enter the label for the new row).
+ - Hide Row
+ Hides the annotation row whose label was clicked in order to bring
+ up the menu.
+ - Delete Row
+ Deletes the annotation row whose label was clicked in order to bring
+ up the menu.
+ - Show All Hidden Rows
+ Shows all hidden annotation rows.
+ - Export Annotation (Application only)
+ Annotations can be saved to file or output to a text window in either the
+ Jalview annotations format or as a spreadsheet style set of comma separated values (CSV).
+ - Show Values in Text Box (applet only)
+ Opens a text box with a list of comma-separated values corresponding
+ to the annotation (numerical or otherwise) at each position in the row.
+ This is useful to export alignment quality measurements for further analysis.
+
+
+ The following additional entries are avalable when the popup menu is opened on a consensus sequence annotation row:
+
+ - Ignore Gaps in Consensus
+ If this checkbox is selected, all consensus calculations performed in
+ the current Alignment window will be done without counting gaps as a consensus
+ character.
+ - Copy Consensus Sequence
+ Copies the consensus sequence to the clipboard in Fasta format, to allow
+ the consensus sequence to be added to an alignment. Note the copied sequence
+ is not accessible to other programs if Jalview is running as an applet
+ in a web page.
+
+
+ - Annotation Popup Menu
+ This menu is opened when right-clicking on the selected positions
+ of an annotation.
+
+ - Helix
+ Mark selected positions with a helix glyph (a red oval), and optional
+ text label (see below). Consecutive ovals will be rendered as an unbroken
+ red line.
+ - Sheet
+ Mark selected positions with a sheet glyph (a green arrow oriented
+ from left to right), and optional text label (see below). Consecutive
+ arrows will be joined together to form a single green arrow.
+ - Label
+ Sets the text label at the selected positions. If more that one consecutive
+ position is marked with the same label, only the first position's label
+ will be rendered.
+ - Colour
+ Changes the colour of the annotation text label.
+ - Remove Annotation
+ Blanks any annotation at the selected positions on the row. Note:
+ This cannot be undone
+
+