X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fannotation.html;h=0c0ccfcabf604cb69971b205136182e7adae85ef;hb=6905363d02254a557f93f66a2b69d85aa0b23696;hp=3ad7f3e6cd599e463eaa1a8d470f529cff1c13b7;hpb=effd8d76f34bc7fd4e069603d80565b7ea9d3ff0;p=jalview.git diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html index 3ad7f3e..0c0ccfc 100755 --- a/help/html/features/annotation.html +++ b/help/html/features/annotation.html @@ -3,34 +3,39 @@

Alignment Annotation

In addition to the definition of groups, Jalview also allows 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). -

- +

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).

Web services can also add annotation to an alignment (see the + JNet web service), 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.

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). -
Hide Row
-Hides the annotation row whose label was clicked in order to bring -up the menu. -
Delete 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. -
Show Values in Text Box
-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. -

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).
Hide Row
+ Hides the annotation row whose label was clicked in order to bring up + the menu.
Delete 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.
Show Values in Text Box
+ 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. +

Editing Label and secondary structure Annotation

This cannot be undone

-Annotation is stored and retrieved using Jalview Archives. Quantitative -annnotation is also possible, but currently only possible with the -JNet web service, or by creating your own Jalview Archive (which -contains XML conforming to the Jalview-Vamsas XML schema). +User defined annotation is stored and retrieved using Jalview Archives.

Current Limitations

@@ -78,6 +80,8 @@ rows is not possible. If you save your annotation as a Jalview file, however, it will be reloaded with user annotations at the top (nearest the alignment), above any of the automatically generated Conservation, Quality or consensus -annotations.

+annotations. Finally, the Jalview GUI will not, as yet, allow you to output +Jalview annotation files for the current alignment, change the line +colour, display style, or create groups of quantitative annotation rows.