Stanford Microarray Database: Don Maier
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Transcript of Stanford Microarray Database: Don Maier
MAGE-TAB in SMD-LandMAGE-TAB in SMD-LandCate Beauheim, Cathy Ball, Don MaierCate Beauheim, Cathy Ball, Don Maier
One Validating Parser
Graphical Interface to create and load into SMD
A void the problem of multiple incompatible formats that has plagued MA GE-ML.
A single, reference MA GE-TA B parser/validator that can be used in both Java and Perl programming environments.
Easily revise the parser along when the MA GE-TA B specification is revised.
Requirements
Formal grammar specification to generate the parser.NO HA ND-WA V ING A LLOWED
Formal UML-specified object model used to generate classes that represent the MA GE information that the parser may discover.
Connect the generated parser to the generated MA GE-TA B objects by calls to a hand-coded “ apply” method that invokes the generated constructors and setters for MA GE-TA B objects.
While all this is in Java, Perl programs get access via Java::Inline.
Design
QuickTime and aᆰTIFF (LZW) decompressor
are needed to see this picture.
Logic specific to MA GE-TA B isolated in a formal grammar, a UML-specified object model, and an “ apply” method that links the grammar and objects.
Lexer/parser automatically generated from a formal grammar for MA GE-TA B using A NTLR.
MA GE-TA B information represented by objects automatically generated from UML by A ndroMDA .
Either Perl or Java can invoke a parse and access the information generated as MA GE-TA B object attributes.
V alidation stamping avoids unneeded re-parsing.
Java-based implementation runs on any platform that supports Java 1.5.0 or newer.
Features