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-<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. These annotation tracks are displayed in the annotation
- area below the alignment. The annotation area's visibility is
- controlled with the <strong>View→Show Annotation</strong>
- option.
- </p>
- <p>
- <strong>Types of annotation</strong>
- <ul>
- <li><a name="seqannots"><strong>Sequence
- associated annotation.</strong></a><br />Data displayed on sequence
- annotation rows are associated with the positions of a sequence.
- Often this is 'Reference annotation' such as secondary structure
- information derived from 3D structure data, or from the results of
- sequence based prediction of <a href="../webServices/jnet.html">secondary
- structure</a> and <a href="../webServices/proteinDisorder.html">disorder</a>.
- If reference annotation is available for a the currently selected
- sequences, it can be shown by selecting the <strong>Add
- Reference Annotation</strong> option in the sequence or selection popup
- menu.</li>
- <li><strong>Group associated annotation.</strong><br />Data can
- be associated with groups defined on the alignment. If sequence
- groups are defined, <a href="../calculations/conservation.html">Conservation</a>
- and <a href="../calculations/consensus.html">Consensus</a>
- annotation can be enabled for each group from the <a
- href="../menus/alwannotation.html">Annotations menu</a>, or can be
- imported from a Jalview <a href="annotationsFormat.html">Annotations
- file</a>.</li>
- <li><strong>Alignment associated annotation.</strong><br />Annotation
- rows associated with columns on the alignment are simply
- 'alignment annotation'. Controls allow you to <a href="#iaannot">interactively
- create alignment annotation</a> to add labels and symbols to
- alignment columns. Jalview's consensus, conservation and quality
- calculations also create histogram and sequence logo annotations
- on the alignment.</li>
- </ul>
- <p>
- <strong>Importing and exporting annotation</strong><br />
- Annotations on an alignment view are saved in Jalview project files.
- You can also load <a href="annotationsFormat.html">Annotations
- Files</a> in order to add any kind of quantitative and symbolic
- annotations to an alignment. To see an example, use the <strong>Export
- Features/Annotation</strong> option from an alignment window's File menu.
- </p>
- <p>
- <strong>Layout and display controls</strong><br /> Individual and
- groups of annotation rows can be shown or hidden using the pop-up
- menu obtained by right-clicking the label. You can also reorder them
- by dragging the label to a new position with the left mouse button.
- The <strong>Annotations</strong> menu provides settings controlling
- the ordering and display of sequence, group and alignment associated
- annotation. The <strong>Colour by annotation</strong> option in the
- colour menu allows annotation to be used to <a
- href="../colourSchemes/annotationColouring.html">shade the
- alignment</a>. Annotations can also be used to <a
- href="../features/columnFilterByAnnotation.html">select or
- hide columns</a> via the dialog opened from the <strong>Selection</strong>
- menu.
- </p>
- <p>
- <strong>Sequence Highlighting and Selection from Annotation</strong>
- </p>
- <p>
- A <strong>single click</strong> on the label of an annotation row
- associated with sequences and sequence groups will cause the
- associated sequences to be highlighted in the alignment view. <strong>Double
- clicking</strong> the label will select the associated sequences, replacing
- any existing selection. Like with other kinds of selection, <strong>shift
- double-click</strong> will add associated sequences, and <strong>Ctrl
- (Mac CMD) double-click</strong> will toggle inclusion of associated
- sequences in the selection.
- <p>
- <strong>Interactive Alignment Annotation</strong>
- </p>
- <p>
- <a name="iaannot"> Annotation rows</a> 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><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 This 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>
- <li><strong>Scale Label To Column</strong><em>(introduced
- in 2.5)</em><br> <em>Selecting this toggles whether column
- labels will be shrunk to fit within each column, or displayed
- using the view's standard font size.</em></li>
- </ul>
- <p>
- <strong>Editing labels and secondary structure annotation
- rows</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. Press <strong>Control</strong> or <strong>shift</strong>
- in combination with the left-click to either select an additional
- position, or a range of positions on the alignment.
- </p>
- <p>
- Once positions have been selected, use the <strong>right
- mouse button</strong> and select one of the following from the <strong>annotation
- menu</strong>:
- </p>
- <ul>
- <li>Helix<br> <em>Marks 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>Marks 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><a name="rna">RNA Helix</a> (only shown when working with
- nucleotide sequences)<br> <em>Marks selected positions
- as participating in a base pair either upstream or downstream.
- When the dialog box opens, enter a '(' to indicate these bases
- pair with columns upstream (to right), and ')' to indicate this
- region pairs with bases to the left of the highlighted columns.
- Other kinds of base-pair annotation are also supported (e.g. 'A'
- and 'a', or '<' and '>'), and Jalview will suggest an
- appropriate symbol based on the closest unmatched parenthesis to
- the left.<br />If any brackets do not match up, then an orange
- square will highlight the first position where a bracket was
- found not to match.
- </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 than 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>
- The Jalview user interface does not support interactive creation and
- editing of quantitative annotation (histograms and line graphs), or
- to create annotation associated with a specific sequence or group.
- It is also incapable of annotation grouping or changing the style of
- existing annotation (e.g. to change between line or bar charts, or
- to make multiple line graphs). These annotation capabilities are
- only possible by the import of an <a href="annotationsFormat.html">Annotation
- file</a>.<br>
- </p>
-</body>
-</html>
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