Alignment Annotation

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fannotation.html;h=b3e09c86e5d888bcf7604dc62dccf1fc403ba408;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=e2d471eec595c2889f452da1e0507702a4550cf2;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html index e2d471e..b3e09c8 100755 --- a/help/html/features/annotation.html +++ b/help/html/features/annotation.html @@ -1,22 +1,24 @@ + --> Alignment Annotation

Alignment Annotation

@@ -37,6 +39,15 @@ 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 @@ -44,16 +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 @@ -114,7 +132,7 @@ href="../features/jalarchive.html">Jalview Archives.

Current Limitations

As of version 2.5, the Jalview user interface does not support the -creation and editing quantitative annotation (histograms and line graphs), or +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.