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/* Data structure */
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_wikis/BioJava3_Proposal.md

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@@ -89,12 +89,12 @@ Data structure
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e.g. Genbank Record to FASTA Record. They allow sensible defaults to
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be provided where one format does not supply enough info to satisfy
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the minimum requirements of another. Some kind of bean conversion
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system based on RDF would be suitable for this.
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system based on RDF would be suitable for this. One possible
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candidate would be [Dozer](http://dozer.sourceforge.net/).
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- A set of tools for converting flat data (e.g. sequence strings,
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taxononmy strings) into BioJava-like objects (e.g. SymbolLists,
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NCBITaxon). These BioJava-like objects could then be used for more
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advanced applications. One possible candidate would be
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[Dozer](http://dozer.sourceforge.net/).
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advanced applications.
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- A set of tools for manipulating the BioJava-like objects.
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Action plan

_wikis/BioJava3_Proposal.mediawiki

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@@ -33,8 +33,8 @@ It is suggested that development stop on the existing BioJava/BioJavaX/BioJava2
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* A RecordFormat is version-specific to the format, as are the Record objects it produces.
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* RecordSearch defines search criteria to be applied to a RecordSource (or group thereof). It provides an iterator which returns all the combined Records from all RecordSources the RecordSearch was applied to. It uses RDF or something similar to map fields between different kinds of Records and the search parameters.
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* Record is a piece of data in any format, as a bean. It should be as lightweight as possible - lazyloading of all non-key data would be ideal. Each different kind of Record has an object structure suitably matched to the RecordFormat that produced it - e.g. Genbank Record objects should be structured internally in almost exactly the same way as the Genbank file. This allows minimal loss of information and maximum flexibility.
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* RecordConverters convert Record objects between different formats, e.g. Genbank Record to FASTA Record. They allow sensible defaults to be provided where one format does not supply enough info to satisfy the minimum requirements of another. Some kind of bean conversion system based on RDF would be suitable for this.
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* A set of tools for converting flat data (e.g. sequence strings, taxononmy strings) into BioJava-like objects (e.g. SymbolLists, NCBITaxon). These BioJava-like objects could then be used for more advanced applications. One possible candidate would be [http://dozer.sourceforge.net/ Dozer].
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* RecordConverters convert Record objects between different formats, e.g. Genbank Record to FASTA Record. They allow sensible defaults to be provided where one format does not supply enough info to satisfy the minimum requirements of another. Some kind of bean conversion system based on RDF would be suitable for this. One possible candidate would be [http://dozer.sourceforge.net/ Dozer].
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* A set of tools for converting flat data (e.g. sequence strings, taxononmy strings) into BioJava-like objects (e.g. SymbolLists, NCBITaxon). These BioJava-like objects could then be used for more advanced applications.
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* A set of tools for manipulating the BioJava-like objects.
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==Action plan==

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