X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwannotations.html;h=3a1afc304165bc4ab61ad60b85a13a84611f95a1;hb=1b9fc500a75a38d7c4408d4b209384d5236911cc;hp=546a94a943bcaeb086b5c689191479431b28b85c;hpb=21e81f77e2d15005e98574c43b9729f6ca0cb3b9;p=jalview.git
diff --git a/help/html/menus/alwannotations.html b/help/html/menus/alwannotations.html
index 546a94a..3a1afc3 100755
--- a/help/html/menus/alwannotations.html
+++ b/help/html/menus/alwannotations.html
@@ -1,62 +1,102 @@
-
-
-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.
- - Export Annotation
- Annotations can be saved to file or output to a text window in the
- Jalview annotations format.
- - 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
-
-
-
-
-
+
+
+
+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.
+ - 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 available 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.
+ - Show Consensus Histogram
+ Enable or disable the display of the histogram above the consensus sequence.
+
+ -
+ Show Consensus Logo
+ Enable or disable the display of the sequence logo above the consensus sequence.
+
+ - Normalise Consensus Logo
+ When enabled, scales all logo stacks to the same height,
+ making it easier to compare symbol diversity in highly variable
+ regions.
+
+ -
+
- 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
+
+
+
+
+