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23 <title>Alignment Annotation</title>
27 <strong>Alignment Annotation</strong>
31 In addition to the definition of groups and sequence features,
32 Jalview can display symbols and graphs under the columns of an
33 alignment. These annotation tracks are displayed in the annotation
34 area below the alignment. The annotation area's visibility is
35 controlled with the <strong>View→Show Annotation</strong>
39 <strong>Types of annotation</strong>
41 <li><a name="seqannots"><strong>Sequence
42 associated annotation.</strong></a><br/>Data displayed on sequence annotation
43 rows are associated with the positions of a sequence. Often this
44 is 'Reference annotation' such as secondary structure information
45 derived from 3D structure data, or from the results of sequence
46 based prediction of <a href="../webServices/jnet.html">secondary
47 structure</a> and <a href="../webServices/proteinDisorder.html">disorder</a>.
48 If reference annotation is available for a the currently selected
49 sequences, it can be shown by selecting the <strong>Add
50 Reference Annotation</strong> option in the sequence or selection popup
52 <li><strong>Group associated annotation.</strong><br/>Data can be associated with
53 groups defined on the alignment. If sequence groups are defined, <a
54 href="../calculations/conservation.html">Conservation</a> and <a
55 href="../calculations/consensus.html">Consensus</a> annotation can
56 be enabled for each group from the <a
57 href="../menus/alwannotation.html">Annotations menu</a>, or can be
58 imported from a Jalview <a href="annotationsFormat.html">Annotations
60 <li><strong>Alignment associated annotation.</strong><br />Annotation rows
61 associated with columns on the alignment are simply 'alignment
62 annotation'. Controls allow you to <a href="#iaannot">interactively create
63 alignment annotation</a> to add labels and symbols to alignment columns.
64 Jalview's consensus, conservation and quality calculations also
65 create histogram and sequence logo annotations on the alignment.
69 <strong>Importing and exporting annotation</strong><br />
70 Annotations on an alignment view are saved in Jalview project files.
71 You can also load <a href="annotationsFormat.html">Annotations
72 Files</a> in order to add any kind of quantitative and symbolic
73 annotations to an alignment. To see an example, use the <strong>Export
74 Features/Annotation</strong> option from an alignment window's File menu.
77 <strong>Layout and display controls</strong><br /> Individual and
78 groups of annotation rows can be shown or hidden using the pop-up
79 menu obtained by right-clicking the label. You can also reorder them
80 by dragging the label to a new position with the left mouse button.
82 <strong>Annotations</strong> menu provides settings controlling the
83 ordering and display of sequence, group and alignment associated
85 <strong>Colour by annotation</strong> option in the colour menu
86 allows annotation to be used to
87 <a href="../colourSchemes/annotationColouring.html">shade the
88 alignment</a>. Annotations can also be used to
89 <a href="../features/columnFilterByAnnotation.html">select or
90 hide columns</a> via the dialog opened from the
91 <strong>Selection</strong> menu.
94 <strong>Sequence Highlighting and Selection from Annotation</strong>
97 A <strong>single click</strong> on the label of an annotation row
98 associated with sequences and sequence groups will cause the
99 associated sequences to be highlighted in the alignment view. <strong>Double
100 clicking</strong> the label will select the associated sequences, replacing
101 any existing selection. Like with other kinds of selection, <strong>shift
102 double-click</strong> will add associated sequences, and <strong>Ctrl
103 (Mac CMD) double-click</strong> will toggle inclusion of associated
104 sequences in the selection.
106 <strong>Interactive Alignment Annotation</strong>
109 <a name="iaannot"> Annotation rows</a> are added using the <strong>Annotation
110 Label</strong> menu, which is obtained by clicking anywhere on the
111 annotation row labels area (below the sequence ID area).
114 <li><strong>Add New Row</strong><br> <em>Adds a new,
115 named annotation row (a dialog box will pop up for you to enter
116 the label for the new row). </em></li>
117 <li><strong>Edit Label/Description</strong><br> <em>This
118 opens a dialog where you can change the name (displayed label),
119 or the description (as shown on the label tooltip) of the
120 clicked annotation. </em></li>
121 <li><strong>Hide This Row</strong><br> <em>Hides the
122 annotation row whose label was clicked in order to bring up the
124 <li><strong>Hide All <em><label></em></strong><br> <em>Hides
125 all annotation rows whose label matches the one clicked. (This
126 option is only shown for annotations that relate to individual
127 sequences, not for whole alignment annotations. Since Jalview
129 <li><strong>Delete This Row</strong><br> <em>Deletes
130 the annotation row whose label was clicked in order to bring up
132 <li><strong>Show All Hidden Rows</strong><br> <em>Shows
133 all hidden annotation rows.</em></li>
134 <li><strong>Export Annotation</strong> <em>(Application
135 only)</em><br> <em>Annotations can be saved to file or
136 output to a text window in either the Jalview annotations format
137 or as a spreadsheet style set of comma separated values (CSV). </em>
139 <li><strong>Show Values in Text Box</strong> <em>(applet
140 only)</em><br> <em>Opens a text box with a list of
141 comma-separated values corresponding to the annotation
142 (numerical or otherwise) at each position in the row. This is
143 useful to export alignment quality measurements for further
145 <li><strong>Scale Label To Column</strong><em>(introduced
146 in 2.5)</em><br> <em>Selecting this toggles whether column
147 labels will be shrunk to fit within each column, or displayed
148 using the view's standard font size.</em></li>
151 <strong>Editing labels and secondary structure annotation rows</strong>
154 Use the <strong>left mouse button</strong> to select a position
155 along the row that are to be annotated - these regions will be
156 coloured red. Press <strong>Control</strong> or <strong>shift</strong> in
157 combination with the left-click to either select an additional position,
158 or a range of positions on the alignment.
161 Once positions have been selected, use the <strong>right
162 mouse button</strong> and select one of the following from the <strong>annotation menu</strong>:
166 <em>Marks selected positions with a helix glyph (a red oval),
167 and optional text label (see below). A dialog box will open for
168 you to enter the text. Consecutive ovals will be rendered as an
169 unbroken red line.</em>
172 <em>Marks selected positions with a sheet glyph (a green arrow
173 oriented from left to right), and optional text label (see
174 below). A dialog box will open for you to enter the text.
175 Consecutive arrows will be joined together to form a single
178 <li><a name="rna">RNA Helix</a> (only shown when working with
179 nucleotide sequences)<br> <em>Marks selected positions
180 as participating in a base pair either upstream or downstream.
181 When the dialog box opens, enter a '(' to indicate these bases
182 pair with columns upstream (to right), and ')' to indicate this
183 region pairs with bases to the left of the highlighted columns.
184 Other kinds of base-pair annotation are also supported (e.g. 'A'
185 and 'a', or '<' and '>'), and Jalview will suggest an
186 appropriate symbol based on the closest unmatched
187 parenthesis to the left.<br />If any brackets do not match up, then an
188 orange square will highlight the first position where a bracket
189 was found not to match.
192 <em>Set the text label at the selected positions. A dialog box
193 will open for you to enter the text. If more than one
194 consecutive position is marked with the same label, only the
195 first position's label will be rendered.</em>
198 <em>Changes the colour of the annotation text label.</em>
200 <li>Remove Annotation<br>
201 <em>Blanks any annotation at the selected positions on the row.
202 Note: <strong>This cannot be undone</strong>
207 User defined annotation is stored and retrieved using <a
208 href="../features/jalarchive.html">Jalview Archives</a>.
211 <em>Current Limitations</em>
214 The Jalview user interface does not support interactive
215 creation and editing of quantitative annotation (histograms and line
216 graphs), or to create annotation associated with a specific
217 sequence or group. It is also incapable of annotation grouping or changing
218 the style of existing annotation (e.g. to change between line or bar
219 charts, or to make multiple line graphs). These annotation
220 capabilities are only possible by the import of an <a
221 href="annotationsFormat.html">Annotation file</a>.<br>