-<html>
-<head>
-<title>Annotation Panel Menus</title>
-</head>
-<body>
-<p><strong>Annotation Panel Menus</strong></p>
-<ul>
-<li>
-<strong>Annotation Label Popup Menu</strong><br>
-<em>This menu is opened by clicking anywhere on the annotation row labels
-area (below the sequence ID area).</em>
-<ul>
-<li><strong>
-Add New Row</strong><br>
-<em>Adds a new, named annotation row (a dialog box will pop up for you
-to enter the label for the new row). </em>
-</li><li><strong>Hide Row</strong><br>
-<em>Hides the annotation row whose label was clicked in order to bring
-up the menu.</em>
-</li><li><strong>Delete Row</strong><br>
-<em>Deletes the annotation row whose label was clicked in order to bring
-up the menu.</em>
-</li><li><strong>Show All Hidden Rows</strong><br>
-<em>Shows all hidden annotation rows.</em>
-</li><li><strong>Show Values in Text Box</strong><br>
-<em>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.</em>
-</li>
-</ul>
-</li>
-<li><strong>Annotation Popup Menu<br></strong><em>This menu is opened when
-right-clicking on the selected positions of an annotation.</em>
-<ul>
-<li><strong>Helix</strong><br><em>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.</em>
-</li>
-<li><strong>Sheet</strong><br><em>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.</em>
-</li>
-<li><strong>Label</strong><br><em>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.</em>
-</li>
-<li><strong>Colour</strong><br><em>Changes the colour of the annotation text label.</em>
-</li>
-<li><strong>Remove Annotation</strong><br><em>Blanks any annotation at the selected positions on
-the row. Note: <strong>This cannot be undone</strong></em>
-</li>
-</ul>
-</li>
-</ul>
-</body>
-</html>
+<html>\r
+<head>\r
+<title>Annotation Panel Menus</title>\r
+</head>\r
+<body>\r
+<p><strong>Annotation Panel Menus</strong></p>\r
+<ul>\r
+ <li> <strong>Annotation Label Popup Menu</strong><br>\r
+ <em>This menu is opened by clicking anywhere on the annotation row labels \r
+ area (below the sequence ID area).</em> \r
+ <ul>\r
+ <li><strong> Add New Row</strong><br>\r
+ <em>Adds a new, named annotation row (a dialog box will pop up for you \r
+ to enter the label for the new row). </em> </li>\r
+ <li><strong>Hide Row</strong><br>\r
+ <em>Hides the annotation row whose label was clicked in order to bring \r
+ up the menu.</em> </li>\r
+ <li><strong>Delete Row</strong><br>\r
+ <em>Deletes the annotation row whose label was clicked in order to bring \r
+ up the menu.</em> </li>\r
+ <li><strong>Show All Hidden Rows</strong><br>\r
+ <em>Shows all hidden annotation rows.</em> </li>\r
+ <li><strong>Show Values in Text Box</strong><br>\r
+ <em>Opens a text box with a list of comma-separated values corresponding \r
+ to the annotation (numerical or otherwise) at each position in the row. \r
+ This is useful to export alignment quality measurements for further analysis.</em> \r
+ </li>\r
+ <li><strong>Ignore Gaps in Consensus</strong><br>\r
+ If this checkbox is selected, all conensus calculations performed in the \r
+ current Alignment window will not include gaps in the consensus calculation.</li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Annotation Popup Menu<br>\r
+ </strong><em>This menu is opened when right-clicking on the selected positions \r
+ of an annotation.</em> \r
+ <ul>\r
+ <li><strong>Helix</strong><br>\r
+ <em>Mark selected positions with a helix glyph (a red oval), and optional \r
+ text label (see below). Consecutive ovals will be rendered as an unbroken \r
+ red line.</em> </li>\r
+ <li><strong>Sheet</strong><br>\r
+ <em>Mark selected positions with a sheet glyph (a green arrow oriented \r
+ from left to right), and optional text label (see below). Consecutive \r
+ arrows will be joined together to form a single green arrow.</em> </li>\r
+ <li><strong>Label</strong><br>\r
+ <em>Sets the text label at the selected positions. If more that one consecutive \r
+ position is marked with the same label, only the first position's label \r
+ will be rendered.</em> </li>\r
+ <li><strong>Colour</strong><br>\r
+ <em>Changes the colour of the annotation text label.</em> </li>\r
+ <li><strong>Remove Annotation</strong><br>\r
+ <em>Blanks any annotation at the selected positions on the row. Note: \r
+ <strong>This cannot be undone</strong></em> </li>\r
+ </ul>\r
+ </li>\r
+</ul>\r
+</body>\r
+</html>\r
git://source.jalview.org / jalview.git / blobdiff