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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+
+Alignment Annotation
+
+
+
+ Alignment Annotation
+
+
+
+ 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 View→Show Annotation
+ option.
+
+
+ Types of annotation
+
+ - Sequence
+ associated annotation.
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 secondary
+ structure and disorder.
+ If reference annotation is available for a the currently selected
+ sequences, it can be shown by selecting the Add
+ Reference Annotation option in the sequence or selection popup
+ menu.
+ - Group associated annotation.
Data can
+ be associated with groups defined on the alignment. If sequence
+ groups are defined, Conservation
+ and Consensus
+ annotation can be enabled for each group from the Annotations menu, or can be
+ imported from a Jalview Annotations
+ file.
+ - Alignment associated annotation.
Annotation
+ rows associated with columns on the alignment are simply
+ 'alignment annotation'. Controls allow you to interactively
+ create alignment annotation 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.
+
+
+ Importing and exporting annotation
+ Annotations on an alignment view are saved in Jalview project files.
+ You can also load Annotations
+ Files in order to add any kind of quantitative and symbolic
+ annotations to an alignment. To see an example, use the Export
+ Features/Annotation option from an alignment window's File menu.
+
+
+ Layout and display controls
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 Annotations menu provides settings controlling
+ the ordering and display of sequence, group and alignment associated
+ annotation. The Colour by annotation option in the
+ colour menu allows annotation to be used to shade the
+ alignment. Annotations can also be used to select or
+ hide columns via the dialog opened from the Selection
+ menu.
+
+
+ Sequence Highlighting and Selection from Annotation
+
+
+ A single click 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. Double
+ clicking the label will select the associated sequences, replacing
+ any existing selection. Like with other kinds of selection, shift
+ double-click will add associated sequences, and Ctrl
+ (Mac CMD) double-click will toggle inclusion of associated
+ sequences in the selection.
+
+ Interactive Alignment Annotation
+
+
+ Annotation rows are added using the Annotation
+ Label menu, which is obtained by clicking anywhere on the
+ annotation row labels area (below the sequence ID area).
+
+
+ - Add New Row
Adds a new,
+ named annotation row (a dialog box will pop up for you to enter
+ the label for the new row).
+ - Edit Label/Description
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.
+ - Hide This Row
Hides the
+ annotation row whose label was clicked in order to bring up the
+ menu.
+ - Hide All <label>
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.)
+ - Delete This Row
Deletes
+ the annotation row whose label was clicked in order to bring up
+ the menu.
+ - Show All Hidden Rows
Shows
+ all hidden annotation rows.
+ - Export Annotation (Application
+ only)
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).
+
+ - Show Values in Text Box (applet
+ only)
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.
+ - Scale Label To Column(introduced
+ in 2.5)
Selecting this toggles whether column
+ labels will be shrunk to fit within each column, or displayed
+ using the view's standard font size.
+
+
+ Editing labels and secondary structure annotation
+ rows
+
+
+ Use the left mouse button to select a position
+ along the row that are to be annotated - these regions will be
+ coloured red. Press Control or shift
+ in combination with the left-click to either select an additional
+ position, or a range of positions on the alignment.
+
+
+ Once positions have been selected, use the right
+ mouse button and select one of the following from the annotation
+ menu:
+
+
+ - Helix
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.
+
+ - Sheet
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.
+
+ - RNA Helix (only shown when working with
+ nucleotide sequences)
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.
If any brackets do not match up, then an orange
+ square will highlight the first position where a bracket was
+ found not to match.
+
+ - Label
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.
+
+ - Colour
Changes the colour of the
+ annotation text label.
+
+ - Remove Annotation
Blanks any annotation
+ at the selected positions on the row. Note: This
+ cannot be undone
+
+
+
+
+ User defined annotation is stored and retrieved using Jalview Archives.
+
+
+ Current Limitations
+
+
+ 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 Annotation
+ file.
+
+
+