X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fseqfeatures.html;h=b5e644f92b09d0a4fef5a048ea6b94c311b7e8ae;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git
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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see
+ Sequence Features +
++ Jalview can colour parts of a sequence based on the presence of + sequence features - which may be retrieved from database records + (such as Uniprot), the result of sequence + motif searches or simply read from a sequence + features file. You can also create + features from the results of searches or the current selection, + and edit features by double + clicking on them. +
++ Sequence Feature Colouring Styles +
++ By default, Jalview will assign a color to each feature based on its + type. These colours can be changed from the feature settings and amend + features dialog boxes. Since Jalview 2.5, it is also possible to + define feature colourschemes to + shade features based on their associated scores or text labels. +
++ Sequence Feature Groups +
++ Since Jalview 2.08, sequence features assigned to a sequence can be + organised into groups, which may indicate that the features were all + retrieved from the same database (such as Uniprot features), or + generated by the same analysis process (as might be specified in a sequence features file). +
++ Sequence Feature Inheritance +
++ Since Jalview 2.08, sequence features are global to a set + of sequences appearing (independently or together) in many different + alignments. Practically, this means features loaded onto one + alignment can be viewed in any alignments involving the same + sequences. The same sequence appears in different alignments when a + new alignment is generated by submitting an existing set of + sequences to one of the alignment or prediction web services, and + when sequences are copied and pasted into other alignment windows. +
++ View→Show Sequence Features +
+Toggle the display of sequence features in this alignment. If + feature retrieval has not already been carried out, then Jalview + will automatically try to fetch sequence features (as described + below).
++ View→Sequence Feature Settings... +
+
+ Once sequence features have been loaded, their display can be fully
+ controlled using the alignment window's Sequence Feature Settings dialog box. Feature colour schemes and
+ display parameters are unique to a particular alignment, so it is
+ possible to colour the same sequence features differently in
+ different alignment views.
Since Jalview 2.1, it is
+ possible to add DAS features to an
+ alignment via the DAS tabbed pane of the feature settings window.
+
+ View→Sequence ID Tooltip→Show
+ Non-Positional features
Only available in
+ application
+
Toggles the display of non-positional features in the sequence + ID tooltip, and whether they will be included when sequence features + are exported using "File→Export Features".
++ Precalculated Sequence Features may be added to an alignment from + the command line, drag and drop, or from the "File→Load + Features / Annotations" menu item. See the Features File Format for more details. +
+ +