<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
<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>Edit Label/Description</strong><br>
- <em>This opens a dialog where you can change the name (displayed label), or the description
- (as shown on the label tooltip) of the clicked annotation. </em> </li>
- <li><strong>Hide This Row</strong><br>
- <em>Hides the annotation row whose label was clicked in order to bring up
- the menu.</em> </li>
- <li><strong>Hide All <em><label></em></strong><br>
- <em>Hides all annotation rows whose label matches the one clicked.
- (This option is only shown for annotations that relate to individual sequences,
- not for whole alignment annotations. Since Jalview 2.8.2.)</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>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>
- <em>The following additional entries are available when the popup menu is opened on a consensus sequence annotation row:</em>
- <ul>
-
- <li><strong>Ignore Gaps in Consensus</strong><br>
- If this checkbox is selected, all consensus calculations performed in
- the current Alignment window will be done without counting gaps as a consensus
- character.</li>
+ <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>Edit Label/Description</strong><br> <em>This
+ opens a dialog where you can change the name (displayed
+ label), or the description (as shown on the label tooltip)
+ of the clicked annotation. </em></li>
+ <li><strong>Hide This Row</strong><br> <em>Hides
+ the annotation row whose label was clicked in order to bring
+ up the menu.</em></li>
+ <li><strong>Hide All <em><label></em></strong><br>
+ <em>Hides all annotation rows whose label matches the one
+ clicked. (This option is only shown for annotations that
+ relate to individual sequences, not for whole alignment
+ annotations. Since Jalview 2.8.2.)</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>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> <em>The following additional entries are available when the
+ popup menu is opened on a consensus sequence annotation row:</em>
+ <ul>
+
+ <li><strong>Ignore Gaps in Consensus</strong><br> If
+ this checkbox is selected, all consensus calculations
+ performed in the current Alignment window will be done without
+ counting gaps as a consensus character.</li>
<li><strong>Show Consensus Histogram<br></strong>
- Enable or disable the display of the histogram above the consensus sequence.
- </li>
- <li>
- <strong>Show Consensus Logo<br></strong>
- Enable or disable the display of the sequence logo above the consensus sequence.
- </li>
+ Enable or disable the display of the histogram above the
+ consensus sequence.</li>
+ <li><strong>Show Consensus Logo<br></strong> Enable or
+ disable the display of the sequence logo above the consensus
+ sequence.</li>
<li><strong>Normalise Consensus Logo<br>
- </strong><em>When enabled, scales all logo stacks to the same height,
- making it easier to compare symbol diversity in highly variable
- regions.</em></li>
+ </strong><em>When enabled, scales all logo stacks to the same
+ height, making it easier to compare symbol diversity in
+ highly variable regions.</em></li>
<li>
- <li><strong>Copy Consensus Sequence</strong><br>
- 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.</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>
+ <li><strong>Copy Consensus Sequence</strong><br>
+ 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.</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>
git://source.jalview.org / jalview.git / blobdiff