-<html>\r
-<head><title>Alignment Annotation</title></head>\r
-<body>\r
-<p><strong>Alignment Annotation</strong></p>\r
-\r
-<p>In addition to the definition of groups and sequence features,\r
- Jalview can display symbols and graphs under the columns of an\r
- alignment, and allow you to mark particular columns of an alignment and add symbols and text \r
- in the annotation area shown below the alignment (which may be hidden if <strong>View→Show \r
- Annotation</strong> is not ticked). </p>\r
-<p>Web services can also add annotation to an alignment (see the\r
- <a href="../webServices/jnet.html">JNet web service</a>), and as of Jalview 2.08 quantitative and symbolic\r
- annotations can be added to an alignment via an <a href="annotationsFormat.html">Annotations \r
- File</a> dragged into the alignment window or loaded from the\r
- alignment's file menu.</p>\r
-<p><strong>Interactive Alignment Annotation</strong></p>\r
-<p>\r
-Annotation rows are added using the <strong>Annotation Label</strong>\r
-menu, which is obtained by clicking anywhere on the annotation row labels\r
-area (below the sequence ID area).\r
-</p>\r
-<ul>\r
- <li>Add New Row<br>\r
- <em>Adds a new, named annotation row (a dialog box will pop up for you to \r
- enter the label for the new row). </em> </li>\r
- <li>Hide Row<br>\r
- <em>Hides the annotation row whose label was clicked in order to bring up \r
- the menu.</em> </li>\r
- <li>Delete Row<br>\r
- <em>Deletes the annotation row whose label was clicked in order to bring up \r
- the menu.</em> </li>\r
- <li>Show All Hidden Rows<br>\r
- <em>Shows all hidden annotation rows.</em> </li>\r
- <li>Show Values in Text Box<br>\r
- <em>Opens a text box with a list of comma-separated values corresponding to \r
- the annotation (numerical or otherwise) at each position in the row. This \r
- is useful to export alignment quality measurements for further analysis.</em> \r
- </li>\r
-</ul>\r
-<p>\r
-<strong>Editing Label and secondary structure Annotation</strong></p>\r
-<p>\r
-Use the <strong>left mouse button</strong> to select a position along the row that are to\r
-be annotated - these regions will be coloured red. <strong>Control</strong> and <strong>shift</strong> in combination\r
-with the left-click will select more than one position, or a range of\r
-positions on the alignment.\r
-</p>\r
-<p>Once the desired position has been selected, use the <strong>right mouse\r
-button</strong> to open the <strong>annotation menu</strong>:</p>\r
-<ul>\r
-<li>Helix<br><em>Mark selected positions with a helix glyph (a red\r
-oval), and optional text label (see below). A\r
-dialog box will open for you to enter the text. Consecutive ovals\r
-will be rendered as an unbroken red line.</em>\r
-</li>\r
-<li>Sheet<br><em>Mark selected positions with a sheet glyph (a green\r
-arrow oriented from left to right), and optional text label (see\r
-below). A dialog box will open for you to enter the text. Consecutive\r
-arrows will be joined together to form a single green arrow.</em>\r
-</li>\r
-<li>Label<br><em>Set the text label at the selected positions. A\r
-dialog box will open for you to enter the text. If\r
-more that one consecutive position is marked with the same label, only\r
-the first position's label will be rendered.</em>\r
-</li>\r
-<li>Colour<br><em>Changes the colour of the annotation text label.</em>\r
-</li>\r
-<li>Remove Annotation<br><em>Blanks any annotation at the selected positions on\r
-the row. Note: <strong>This cannot be undone</strong></em>\r
-</li>\r
-</ul>\r
-<p>\r
-User defined annotation is stored and retrieved using <a\r
-href="../features/jalarchive.html">Jalview Archives</a>.\r
-</p>\r
-<p><em>Current Limitations</em></p>\r
-\r
-<p>In the current version of Jalview, reordering of the annotation\r
-rows is not possible. If you save \r
-your annotation as a Jalview file, however, it will be reloaded with user \r
-annotations at the top (nearest the alignment), above any of the\r
-automatically generated Conservation, Quality or consensus\r
-annotations. Finally, the Jalview GUI will not, as yet, allow you to output\r
-Jalview annotation files for the current alignment, change the line\r
-colour, display style, or create groups of quantitative annotation rows.</p>\r
-</body>\r
-</html>\r
+<html>
+<head><title>Alignment Annotation</title></head>
+<body>
+<p><strong>Alignment Annotation</strong></p>
+
+<p>In addition to the definition of groups and sequence features,
+ Jalview can display symbols and graphs under the columns of an
+ alignment, and allow you to mark particular columns of an alignment and add symbols and text
+ in the annotation area shown below the alignment (which may be hidden if <strong>View→Show
+ Annotation</strong> is not ticked). </p>
+<p>Web services can also add annotation to an alignment (see the
+ <a href="../webServices/jnet.html">JNet web service</a>), and as of Jalview 2.08 quantitative and symbolic
+ annotations can be added to an alignment via an <a href="annotationsFormat.html">Annotations
+ File</a> dragged into the alignment window or loaded from the
+ alignment's file menu.</p>
+<p><strong>Interactive Alignment Annotation</strong></p>
+<p>
+Annotation rows are added using the <strong>Annotation Label</strong>
+menu, which is obtained by clicking anywhere on the annotation row labels
+area (below the sequence ID area).
+</p>
+<ul>
+ <li>Add New Row<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>Hide Row<br>
+ <em>Hides the annotation row whose label was clicked in order to bring up
+ the menu.</em> </li>
+ <li>Delete Row<br>
+ <em>Deletes the annotation row whose label was clicked in order to bring up
+ the menu.</em> </li>
+ <li>Show All Hidden Rows<br>
+ <em>Shows all hidden annotation rows.</em> </li>
+ <li><strong>Export Annotation</strong> <em>(Application only)</em><br>
+ <em>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). </em> </li>
+ <li><strong>Show Values in Text Box</strong> <em>(applet only)</em><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>
+<p>
+<strong>Editing Label and secondary structure Annotation</strong></p>
+<p>
+Use the <strong>left mouse button</strong> to select a position along the row that are to
+be annotated - these regions will be coloured red. <strong>Control</strong> and <strong>shift</strong> in combination
+with the left-click will select more than one position, or a range of
+positions on the alignment.
+</p>
+<p>Once the desired position has been selected, use the <strong>right mouse
+button</strong> to open the <strong>annotation menu</strong>:</p>
+<ul>
+<li>Helix<br><em>Mark selected positions with a helix glyph (a red
+oval), and optional text label (see below). A
+dialog box will open for you to enter the text. Consecutive ovals
+will be rendered as an unbroken red line.</em>
+</li>
+<li>Sheet<br><em>Mark selected positions with a sheet glyph (a green
+arrow oriented from left to right), and optional text label (see
+below). A dialog box will open for you to enter the text. Consecutive
+arrows will be joined together to form a single green arrow.</em>
+</li>
+<li>Label<br><em>Set the text label at the selected positions. A
+dialog box will open for you to enter the text. If
+more that one consecutive position is marked with the same label, only
+the first position's label will be rendered.</em>
+</li>
+<li>Colour<br><em>Changes the colour of the annotation text label.</em>
+</li>
+<li>Remove Annotation<br><em>Blanks any annotation at the selected positions on
+the row. Note: <strong>This cannot be undone</strong></em>
+</li>
+</ul>
+<p>
+User defined annotation is stored and retrieved using <a
+href="../features/jalarchive.html">Jalview Archives</a>.
+</p>
+<p><em>Current Limitations</em></p>
+
+<p>In the current version of Jalview, reordering of the annotation
+rows is not possible. If you save
+your annotation as a Jalview file, however, it will be reloaded with user
+annotations at the top (nearest the alignment), above any of the
+automatically generated Conservation, Quality or consensus
+annotations. Finally, the Jalview GUI will not, as yet, allow you to output
+Jalview annotation files for the current alignment, change the line
+colour, display style, or create groups of quantitative annotation rows.</p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff