Importing Data From "Flat" Files
Much data is available
in ASCII files.
These files come
in various formats
from various sources.
The GenoViz SDK includes classes
that recognize several common biological information formats.
These classes are in the package
com.affymetrix.genoviz.parser
and (usually) implement the
ContentParser interface.
The ContentParser interface is simple.
It has an
importContent method
which will parse bytes arriving via an InputStream
and return an object modeling the data.
A new class implementing ContentParser should be defined
for each pair of format and data model.
Here we have a very small applet
that can display the contents of a fasta file
in a NeoSeq.
As you can see,
the source code is quite short.
Exercises
- Use the ExportContent to save the fasta data in another file.
What happened to the comments?
- Create ParseTwo that parses an ABI trace and displays it
in a NeoSeq.
- Modify ParseTwo so that it can also parse a trace from an SCF file.