X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fannotation.html;h=b63d20bcc86d42cb7642405485ec97d674eba959;hb=b6000a31609b8d7f6b9cca8df5d4878d393e2b24;hp=d13afe452521c229b02ad236ad32a6515baeb543;hpb=c73e1efb0b980e9faa642cbae090a58f952c33ac;p=jalview.git
diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html
index d13afe4..b63d20b 100755
--- a/help/html/features/annotation.html
+++ b/help/html/features/annotation.html
@@ -39,31 +39,31 @@
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
+ 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 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.
-
+ 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
@@ -78,17 +78,15 @@
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.
+ 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
@@ -148,32 +146,32 @@
using the view's standard font size.
- Editing labels and secondary structure annotation rows
+ 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.
+ 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:
+ 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.
+ - 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.
+ - 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
@@ -183,23 +181,22 @@
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.
+ 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.
+ - 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.
+ - 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
+ - Remove Annotation
Blanks any annotation
+ at the selected positions on the row. Note: This
+ cannot be undone
@@ -211,14 +208,14 @@
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.
+ 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.