Alignment Annotation

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fannotation.html;h=b3e09c86e5d888bcf7604dc62dccf1fc403ba408;hb=ec669c13867d001e07c9cef157c268afe03be9f3;hp=98599e28b420abd3efa561ac63e7de25c611d4e3;hpb=990fd5f012601024aaeeb09e2901791d242636c4;p=jalview.git diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html index 98599e2..b3e09c8 100755 --- a/help/html/features/annotation.html +++ b/help/html/features/annotation.html @@ -1,4 +1,24 @@ + Alignment Annotation

Alignment Annotation

@@ -7,12 +27,27 @@ 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.

+ 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. +

Interactive Alignment Annotation

Annotation rows are added using the Annotation Label @@ -20,16 +55,23 @@ menu, which is obtained by clicking anywhere on the annotation row labels area (below the sequence ID area).

Add New Row
+
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
+
Edit Label/Description
+ This opens a dialog where you can change the name (displayed label), or the description + (as shown on the label tooltip) of the clicked annotation.
Hide This Row
Hides the annotation row whose label was clicked in order to bring up the menu.
Delete Row
+
Hide All <label>
+ Hides all annotation rows whose label matches the one clicked. + (This option is only shown for annotations that relate to individual sequences, + not for whole alignment annotations. Since Jalview 2.8.2.)
Delete This Row
Deletes the annotation row whose label was clicked in order to bring up the menu.
Show All Hidden Rows
+
Show All Hidden Rows
Shows all hidden annotation rows.
Export Annotation (Application only)
Annotations can be saved to file or output to a text window in either the @@ -39,6 +81,8 @@ 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

@@ -61,6 +105,16 @@ 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 @@ -77,14 +131,11 @@ User defined annotation is stored and retrieved using Jalview Archives.

Current Limitations
- -
In the current version of Jalview, reordering of the annotation -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. 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.
+
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.
+