X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fannotation.html;h=a6c62df18c93873e451dbb30dda9b2ddb30e4820;hb=59d682209891099d46b960509907c79e3fb276fe;hp=812ed50c1974aac7fb9f0d5e6e635c5929e63b73;hpb=442b6bc246ee877d5e977baf80fd96299e0e05c4;p=jalview.git diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html index 812ed50..a6c62df 100755 --- a/help/html/features/annotation.html +++ b/help/html/features/annotation.html @@ -1,4 +1,21 @@ + Alignment Annotation

Alignment Annotation

@@ -10,11 +27,15 @@ 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. +

Interactive Alignment Annotation

Annotation rows are added using the Annotation Label @@ -41,6 +62,8 @@ area (below the sequence ID area). 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 Label and secondary structure Annotation

    @@ -63,6 +86,16 @@ 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)
    +Mark 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.
    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 that one consecutive position is marked with the same label, only @@ -79,7 +112,7 @@ User defined annotation is stored and retrieved using Jalview Archives.

    Current Limitations

    -

    As of version 2.4, the Jalview user interface does not support the +

    As of version 2.5, the Jalview user interface does not support the creation and editing 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