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•	apollo.dataadapter.das.simple.* (11)

• apollo.dataadapter.das: Javadoc index of package apollo.dataadapter.das.


Package Samples:

• apollo.dataadapter.das.simple: Defines the interfaces to support the reading of DAS datasources by Apollo.  

Classes:

• SimpleDASServer: I am a lightweight implementation of a DAS Server which doesn't use external code (apart from a general SAX-parser). I perform client-side assembly of all nested features from a das 'features' call, as well as ensuring that the features are presented in the highest-level (entry-point) coordinate system (typically this are chromosome coords). I should be instantiated with the URL of the datasource, for example http://servlet.sanger.ac.uk:8080/das http://genome.cse.ucsc.edu/cgi-bin/das Calls to me after I've been instantiated are stateless - typically you call getDSNs to isolate a single DSN to study, ...
• DASFeatureContentHandler: I am the ContentHandler used when SimpleDASServer parses the result of a 'features' call to a das data source (with a specified dsn and segment). I am DAS 1.0 compliant. During the parse, I create a list, stored on myself, of the returned features. This list is retrieved by calling getFeaturess after the parse is complete If any of the features retrieved during my run contain subparts or are reference features (have children), then I store them away. When I am done with my parse, I re-invoke the SimpleDASServer with another getFeatures call, passing in all the segments that have children. which ...
• SimpleDASAdapterGUI: I implement a AbstractDataAdapterUI , allowing Apollo to get information from DAS datasources, using 'simple' implementions of DASServerI , DASDsn etc. My whole reason-for-being is to have a das-reading adapter which doesn't rely on a big external codebase (e.g. omnigene or biojava): I create implementations of DASServerI, DASSegment etc which are 'simple' - SimpleDASServerI etc.
• DASSequenceContentHandler: I am the ContentHandler used when SimpleDASServer parses the result of a 'dna' call to a das data source (passing in dsn and segment). I am DAS 1.0 compliant. During the parse, I create a list, stored on myself, of the returned sequences. This list is retrieved by calling getSequences after the parse is complete
• DASEntryPointContentHandler: I am the ContentHandler used when SimpleDASServer parses the result of a 'entry_points' call to a das data source and dsn. I am DAS 1.0 compliant. During the parse, I create a list, stored on myself, of the returned entry points. This list is retrieved by calling getSegments after the parse is complete
• SimpleDASAdapter: I implement a AbstractDataAdapter , allowing Apollo to get information from DAS datasources, using 'simple' implementions of DASServerI , DASDsn etc. My whole reason-for-being is to have a das-reading adapter which doesn't rely on a big external codebase (e.g. omnigene or biojava).
• DASDsnContentHandler: I am the ContentHandler used when SimpleDASServer parses the result of a 'dsn' call to a das data source. I am DAS 1.0 compliant. During the parse, I create a list, stored on myself, of the returned DSN's. This list is retrieved by calling getDsns after the parse is complete
• DASServerI: I represent the capability of a general DASServer, as required by Apollo to make das-data requests. I have a simple (no-frills) implementation in the simple subpackage. NOTE - my name is DASServerI because I wish to avoid conflict with an existing DASServer module historically in the same package.
• DASClient: This will open a DAS server and provide access the DSN element data provided by the server It will: Connect to a datasource Get XML from the data source Parse the XML and provide methods for reading that data
• DASSegment: I represent the contained in a Segment (as defined by the DAS-spec) needed by Apollo to request features for the segment, and display the features of the segment. I have a reference implementation in the simple sub-package
• DASSequence: I represent the data contained in a dna sequence (as defined by the DAS-spec) needed by Apollo to display a sequence. I have a reference implementation in the simple sub-package
• SimpleDASSequence: I am a lightweight implementation of the DASSequence interface. I am a simple bag of attributes with no further internal functionality.
• SimpleDASSegment: I am a lightweight implementation of the DASSegment interface. I am a simple bag of attributes with no further internal functionality.
• SimpleDASFeature: I am a lightweight implementation of the DASFeature interface. I am a simple bag of attributes with no further internal functionality.
• DASLazySequence: I am a Sequence class for implementing lazy load using a DASServer
• DASDsn
• DASFeature
• DASAdapter
• DASAdapterGUI

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