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UnavailableException: Defines an exception that a web service throws to indicate that it is permanently or temporarily unavailable. When a web service is permanently unavailable, something is wrong with it, and it cannot handle requests until action is taken. For example, a web service might be configured incorrectly. A web service is temporarily unavailable if it cannont handle requests momentarily due to some system-wide problem. For example, a database server might be down or insufficient memory to handle request. Web services containers can safely handle both types of unavailable exceptions in the same way. Treating ...
RequestHandler: The base class for all RequestHandler Objects This class is intended to take in a DASRequest object Inspect its contents and then construct a properly formatted URL from that object a typical use for these objects would be to construct a DASRequest: DASDSNRequestHandler handler = new DASRequestHandler(); set its DASRequest with DASRequest 55 get some MetaData about the server MetaData and then execute DASResponse 55
WebService: Defines methods that all Web Services must implement. A Web Service is a program that runs within the OmniGene container. Clients can make RPC calls to Web Service methods by SOAP messages. A SOAP message will contain the method name to call and the parameters the method is expecting. Another SOAP message will be sent back to the client containing the result from the Web Service method. To implement this interface you can write a generic Web Service by extending GenericWebService or one of the known subclasses. This interface defines methods that get the version of the Web Service, the encoding ...
PedFileParser: Title: PedFileParser.java Description: Uses it to parse a pedigree file and store the data in object PedFile. The format of pedigree file is: column 1: familyID column 2: individual ID column 3: dad ID column 4: mom ID column 5: gender ( 1 is male, 2 is female ) column 6: affected status (1 is unaffected, 2 is affected ) column 7: (optional) libility column 8 and 9: marker 1 (seperated by space) column 2n and 2n+1: marker n (seperated by space) Columns are seperated by tab except between one set of marker. Family ID plus individual ID is unique and "0" stands for data missing.
AuthenticateIP: Authenticates an IP address to a specified system or datastore. AuthenticateIP checks the incoming IP address to see if it's allowed to access the specified system or datastore. The access control list is a properties file that has a format of ip-address=system-name1,system-name2. The value is a comma delimited value of system names that the IP address is allowed to access. If a value of "all" is found then the IP address can access all systems and datastores. A value of "none" rejects the incoming request to any systems.
PedFileEntry: Title: PedFileEntry.java Description: Stands for one row in a pedigree file. The columns of pedigree file are: column 1: familyID column 2: individual ID column 3: dad ID column 4: mom ID column 5: gender column 6: affected status column 7: (optional) libility column 8 and 9: marker 1 (seperated by space) column 2n and 2n+1: marker n (seperated by space)
MarkerResult: Title: MarkerResult.java Description: Gets the result for a marker Result includes observed heterozyosity, predicted heterozygosity, Hardy-Weinberg test p-value, genotyped percent, number of families with a fully genotyped trio, number of Mendelian inheritance errors, rating, minor allele, minor allele frequency, major allele and major allele frequency.
DASFeaturesPagingDAO: The methods in this interface are the public face of TraderBean. The signatures of the methods are identical to those of the EJBean, except that these methods throw a java.rmi.RemoteException. Note that the EJBean does not implement this interface. The corresponding code-generated EJBObject, TraderBeanE, implements this interface and delegates to the bean.
View: This class is generated by JAXB using AGAVE XML DTD version 2.3 from DoubleTwist, Inc. Represents the range in a chromosome or contig which contains all available annotations. Since the number of annotations in a chromosome or contig may be large, it allows the annotations to be divided among different documents.
OmniGeneMulticastServer: This class is used to find OmniGene servers on a LAN using a multicast UDP packet protocol we do a single ip --> multiple clients This server sits on a common multicast port and pushes information to clients that join this multicast goup. To get a connection to this class: explanation here
CheckData: Title: CheckData.java Description: Used to check pedigree file and return information about observed heterozyosity, predicted heterozygosity, Hardy-Weinberg test p-value, genotyped percent, number of families with a fully genotyped trio and number of Mendelian inheritance errors.
Sciobj: This class is generated by JAXB using AGAVE XML DTD version 2.3 from DoubleTwist, Inc. Sciobj is the root element for AGAVE, it includes a list of elements BioSequence , Contig , Computation , Chromosome and attributes version, release, date.
DASMetaData: This class represents the DAS headers sent over the wire. It allows the developer to gain access to the 1) Schema that the service is using 2) The schema version 3) The DAS server version 4) All the headers on the wire 5) (optionally) the # of bytes which will be sent over the wire
DBLoader: Title: DBLoader.java Description: This class implements task loading (add and update) and deletion. All task dbloader class will extends this class and implement setup method to setup task name, description, class name and ParameterInfo array
RequestHandlerFactory: This class gives back the proper instance of a RequestHandler given a DASRequest object is a Singleton
DASFeaturesPagingDAOHome: This interface is the home interface for the TraderBean.java, which in WebLogic is implemented by the code-generated container class TraderBeanC. A home interface may support one or more create methods, which must correspond to methods named "ejbCreate" in the EJBean.
AxisServiceDiscovery: This little class is used to generate a SOAP response from Axis telling us exactly what services are deployed in this Axis Engine we'll use this to make SOAP requests to the server after dynamic discovery via the OmniGeneMulticastClient
Transcript: This class is generated by JAXB using AGAVE XML DTD version 2.3 from DoubleTwist, Inc. It represents transcript which is a subset of exons from a gene model along with the possible translation of those exons into cds, mrna, and a predicted_protein
DASTypesRequestImpl: This class is the implementation of the DASTypesRequest interface. Use this class to instantiate new DASTypesRequest objects to be sent to the DAS Service in order to retrieve the available types for a specific segment.
DASStylesheetRequestImpl: This class is the implementation of the DASStylesheetRequest interface. Use this class to instantiate new DASStylesheetRequest objects to be sent to the DAS Service in order to retrieve stylesheet information.
GetSnpClassesHandler: This handles getsnpclasses request, basically this is introduced for HapMap project, to filter snp based on classes. This will be later made generic, to serve getsnpfilter reqest handler. GetSnpClassesHandler.java
GenericWebService: Defines a generic web service. GenericWebService implements the WebService interface. GenericWebService may be directly extended for more specific domain web services.
ObjectBuilder: Object Builder class to parse xml and create object. Client can send DASRequest out directly using this class without going through the omnidas package and generating AGAVE or DAS object from the DASResponse.
ElementId: This class is generated by JAXB using AGAVE XML DTD version 2.3 from DoubleTwist, Inc. Contains an xml IDREF type. Used when need to have an IDREF in an ELEMENT content model. Useful for alternation of DbId.
DASFeaturesRequestImpl: This class is the implementation of the DASFeaturesRequest interface. Use this class to instantiate new DASFeaturesRequest objects to be sent to the DAS Service in order to get features data.