X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Ffeatures%2Fannotation.html;h=7e52c46b822e2320f090d4477bfcf8a8d5bf41be;hb=309af01a4a460b17ef6b924a20057b372d8fbeac;hp=8459e2794d1e74b36ebff83b9168fce6c51e6f66;hpb=e641357d074cf8f3b9ee877f47879d6e22ac1ce1;p=jalview.git diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html index 8459e27..7e52c46 100755 --- a/help/html/features/annotation.html +++ b/help/html/features/annotation.html @@ -1,4 +1,24 @@ +
Alignment Annotation
@@ -10,11 +30,43 @@ 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 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.
++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: +
Interactive Alignment Annotation
Annotation rows are added using the Annotation Label @@ -22,16 +74,23 @@ menu, which is obtained by clicking anywhere on the annotation row labels area (below the sequence ID area).
Current Limitations
-As of version 2.4, the Jalview user interface does not support the -creation and editing quantitative annotation (histograms and line graphs), or +
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.