<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
+ 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
+ <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>
+ 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 />
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.
+ 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>
using the view's standard font size.</em></li>
</ul>
<p>
- <strong>Editing labels and secondary structure annotation rows</strong>
+ <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.
+ 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>:
+ 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>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>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
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.
+ 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>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>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>
+ <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>
<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>
+ 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>
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</html>
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