-Select appropriate DAS sources as required then click on {\sl Fetch DAS
-Features}. If you know of additional sources not listed in the configured
-registry, then you may add them with the {\sl Add Local Source} button. Use
-the {\sl Authority},{\sl Type}, and {\sl Label} filters to restrict the list
-of sources to just those that will return features for the sequences in the
-alignment.
-
-Following DAS feature retrieval, the {\sl Feature Settings} panel takes on a
-slightly different appearance (Figure \ref{das} (right)). Each data source is
-listed and groups of features from one data source can be selected/deselected
-by checking the labelled box at the top of the panel.
-
-\exercise{Retrieving Features with DAS}{
-\label{dasfeatretrexcercise}
-\exstep{Load the alignment at
-\textsf{http://www.jalview.org/tutorial/alignment.fa}. Select {\sl View
-$\Rightarrow$ Feature Settings \ldots} from the alignment window menu. Select
-the {\sl DAS Settings} tab. A long list of available DAS sources is listed.
-Select a small number, eg Uniprot, DSSP, signalP and netnglyc. Click.
-A window may prompt whether you wish Jalview to fetch DAS features. Click {\sl
-Yes}.
-Jalview will start retrieving features. As features become available they will be mapped onto the alignment. }
-\exstep{If Jalview is taking too long to retrieve features, the process can be cancelled with the {\sl Cancel Fetch} button.
-Rolling the mouse cursor over the sequences reveals a large number of features annotated in the tool tip.
-Close the Sequence Feature Settings window. }
-\exstep{Move the mouse over the sequence ID panel.
-Non-positional features such as literature references and protein localisation predictions are given in the tooltip, below any database cross references associated with the sequence.}
-\exstep{Search through the alignment to find a feature with a link symbol next to it.
-Right click to bring up the alignment view popup menu, and find a corresponding entry in the {\sl Link } sub menu. }
-% TODO this doesn't work ! \includegraphics[width=.3in]{images/link.pdf}
-
-\exstep{
-Select {\sl View $\Rightarrow$ Feature Settings\ldots} to reopen the Feature Settings window. All the loaded feature types should now be displayed. Those at the top of the list are drawn on top of those below, obscuring them in the alignment view where they overlap. Move the feature settings window so that the alignment is visible and uncheck some of the feature types by clicking the tick box in the display column. Observe how the alignment display changes. Note that unselected feature types do not appear in the tool tip.
-}
-\exstep{Reorder the features by dragging feature types up and down the order in the Feature Settings panel. e.g. Click on {\sl CHAIN} then move the mouse downwards to drag it below {\sl DOMAIN}. Note that {\sl DOMAIN} is now shown on top of {\sl CHAIN} in the alignment window. Drag {\sl METAL} to the top of the list. Observe how the cysteine residues are now highlighted as they have a {\sl METAL} feature associated with them.
-}
-
-\exstep{Press the {\sl Optimise Order} button. The features will be ordered according to increasing length, placing features that annotate shorter regions of sequence higher on the display stack.}
-
-\exstep{Select {\sl File $\Rightarrow$ Export Features\ldots} from the Alignment window. You can choose to export the retrieved features as a GFF file, or Jalview's own Features format.
-% TODO: describe working with features files and GFF
-}
-}
-
-\subsubsection{The Fetch Uniprot IDs Dialog Box}
-\label{discoveruniprotids}
-If any sources are selected which refer to Uniprot coordinates as their reference system,
-then you may be asked if you wish to retrieve Uniprot IDs for your sequence. Pressing OK instructs Jalview to verify the sequences against Uniprot records retrieved using the sequence's ID string. This operates in much the same way as the {\sl Web Service $\Rightarrow$ Fetch Database References } function described in Section \ref{fetchdbrefs}. If a sequence is verified, then the start/end numbering will be adjusted to match the Uniprot record to ensure that features retrieved from the DAS source are rendered at the correct position.
-
-\subsubsection{Rate of Feature Retrieval}
-Feature retrieval can take some time if a large number of sources is selected and if the alignment
-contains a large number of sequences. This is because Jalview only queries a particular DAS source with one sequence at a time, to avoid overloading it. As features are retrieved, they are immediately added to the current alignment view. The retrieved features are shown on the sequence and can be customised as described previously.
+Feature display can be toggled on or off by selecting the {\sl View
+$\Rightarrow$ Show Sequence Features} menu option. When multiple features are
+present it is usually necessary to customise the display. Jalview allows the
+display, colour, rendering order and transparency of features to be modified
+{\sl via} the {\sl View $\Rightarrow$ Feature Settings\ldots} menu option. This
+brings up a dialog window (Figure \ref{custfeat}) which allows the
+visibility of individual feature types to be selected, assigned colours to be changed (by
+clicking on the colour of each sequence feature type) and the rendering order
+modified by dragging feature types to a new position in the list. Dragging the
+slider alters the transparency of the feature rendering. Clicking in the {\sl Configuration} column
+ opens the {\sl Display Settings} dialog which allows more complex shading schemes
+ and also the creation of filters, and right-clicking opens a context sensitive menu
+ that offers options for selecting and hiding columns or sorting the alignment according
+ the the feature's distribution or score attribute.
+These capabilities are described further in sections
+\ref{featureschemes} and \ref{featureordering}.