Stanford Microarray Database: Don Maier
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Stanford Microarray Database: Don Maier

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Stanford Microarray Database: Don Maier Stanford Microarray Database: Don Maier Presentation Transcript

  • MAGE-TAB in SMD-Land Cate Beauheim, Cathy Ball, Don Maier
    • One Validating Parser
    • Graphical Interface to create and load into SMD
    • Avoid the problem of multiple incompatible formats that has plagued MAGE-ML.
    • A single, reference MAGE-TAB parser/validator that can be used in both Java and Perl programming environments.
    • Easily revise the parser along when the MAGE-TAB specification is revised.
    Requirements
    • Formal grammar specification to generate the parser. NO HAND-WAVING ALLOWED
    • Formal UML-specified object model used to generate classes that represent the MAGE information that the parser may discover.
    • Connect the generated parser to the generated MAGE-TAB objects by calls to a hand-coded “apply” method that invokes the generated constructors and setters for MAGE-TAB objects.
    • While all this is in Java, Perl programs get access via Java::Inline.
    Design
  •  
    • Logic specific to MAGE-TAB 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 MAGE-TAB using ANTLR.
    • MAGE-TAB information represented by objects automatically generated from UML by AndroMDA.
    • Either Perl or Java can invoke a parse and access the information generated as MAGE-TAB object attributes.
    • Validation stamping avoids unneeded re-parsing.
    • Java-based implementation runs on any platform that supports Java 1.5.0 or newer.
    Features