Databases and Systems

258
and updates a model accordingly. When the model is updated the view receives
notification and updates its representation accordingly.
In our case, the model is defined as a set of Java interfaces. An interface is
an abstract specification of functionality in the form of a set of method signatures.
Using interfaces allows us to define a model without detailing how the model will be
implemented. A critical step in defining a widget is defining the model of which it
will be a view. Because a widget is designed for reuse throughout the genomics
community, its model must be generic enough so that it will not be inconsistent with
data models used by would-be consumers. The philosophy therefore in defining
models for bioWidgets is to keep them as simple as possible.
Here is the interface that defines the model of (ungapped) sequence used by
our sequence widget:
public interface SequenceReadOnly {
public int getFirstChar();
public int getLastChar();
public String getSubSeq(int first, int last);
public Interval[] getSelectedIntervals();
}
In this case, sequence is viewed simply as a string that can easily provide substrings
and that also has a set of selected sub-intervals. Because this interface is easy
to satisfy, it allows data to be read into the bioWidgets from flat files, databases
(possibly using the JDBC[11] database access specification), or even directly from
other widgets or applications, using remote communication protocols such as MI or
CORBA[12]. Components called transducers do the job of translating data in
disparate formats into objects satisfying the interface specifications recognized by the
widget. Note that, in terms of performance, the above interface does not require that
the sequence be stored as a string. It could be stored in a compressed format and
decompressed on the fly in response to getSubSeq requests. It is the widget’s
responsibility to ask for only that part of the sequence it needs, so that the entire
sequence need not be duplicated in every view.
In addition, the MVC approach ensures that any updates to the underlying
databases or data sources are immediately propagated to the widgets’ displays.
Another feature of the bioWidget architecture-the use of multiple concurrent
Threads of execution—ensures that the widgets will not freeze while performing
such updates; the user will be able to continue to interact with the widgets while they
incorporate new or updated data into their displays.