From c73e1efb0b980e9faa642cbae090a58f952c33ac Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 21 Sep 2016 12:29:49 +0100 Subject: [PATCH] JAL-2189 reworked annotation docs JAL-2171 autocomplete RNA ss symbol for interactive annotation --- help/html/features/annotation.html | 334 +++++++++++++++++++++--------------- 1 file changed, 199 insertions(+), 135 deletions(-) diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html index 7e52c46..d13afe4 100755 --- a/help/html/features/annotation.html +++ b/help/html/features/annotation.html @@ -19,142 +19,206 @@ * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. --> -Alignment Annotation + +Alignment Annotation + -

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, and allow you to mark particular columns of an alignment and add symbols and text - in the annotation area shown below the alignment (which may be hidden if View→Show - Annotation is not ticked). Any displayed annotation row can be hidden (using the pop-up - menu obtained by right-clicking the label), or re-ordered by dragging the label to a new - position with the left mouse button.

-

-Web services can also add annotation to an alignment (see the JNet and Disorder protein -structure prediction services), and as of Jalview 2.08 quantitative -and symbolic annotations can be added to an alignment via an Annotations File dragged into the -alignment window or loaded from the alignment's file menu. -

-

Sequence Reference Annotation -

-

- Sequence reference annotation is created from 3D structure - data, and from the results of sequence based prediction of - secondary structure and disordered region - prediction methods. -

-

Sequence Group Annotation -

-

- 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. -

-

Sequence Selection from Annotation -

-

- Sequences associated with sequence (or sequence group) annotations can be selected by - double-clicking the annotation label with these key combinations: -

- Note this also works in combination with manual sequence selection in the alignment. -

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). -

- -

-Editing Label and secondary structure Annotation

-

-Use the left mouse button to select a position along the row that are to -be annotated - these regions will be coloured red. Control and shift in combination -with the left-click will select more than one position, or a range of -positions on the alignment. -

-

Once the desired position has been selected, use the right mouse -button to open the annotation menu:

- -

-User defined annotation is stored and retrieved using Jalview Archives. -

-

Current Limitations

-

As of version 2.5, the Jalview user interface does not support the -creation and editing of quantitative annotation (histograms and line graphs), or -to create annotation associated with a specific sequence. It is also incapable of -annotation grouping or changing the style of existing annotation (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.
-

+

+ 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 +

+

+ 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). +

+ +

+ 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: +

+ +

+ 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.
+

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