Package org.intermine.bio.webservice

Class FastaQueryService

    • Field Summary

      • Fields inherited from class org.intermine.webservice.server.WebService

        dataPackageOutput, DEFAULT_CALLBACK, im, out, output, request, response, webProperties

    • Constructor Summary

      Constructors 
      Constructor Description
      FastaQueryService​(org.intermine.api.InterMineAPI im)
      Constructor.

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      protected void checkPathQuery​(org.intermine.pathquery.PathQuery pq)
      No-op stub.
      protected java.lang.String getContentType()  
      protected org.intermine.web.logic.export.Exporter getExporter​(org.intermine.pathquery.PathQuery pq)  
      protected org.intermine.pathquery.PathQuery getQuery()
      Make the path-query to run, and check it has the right number of columns.
      protected java.lang.String getSuffix()  
      protected static int parseExtension​(java.lang.String extension)
      A method for parsing the value of the extension parameter.

      • Methods inherited from class org.intermine.webservice.server.query.AbstractQueryService

        formatIsJsonObj, formatIsNTriples, formatIsRDF, getQueryBuilder, getSchemaLocation, getSchemaUrl

      • Methods inherited from class org.intermine.webservice.server.WebService

        canServe, cleanUp, formatIsFlatFile, formatIsJSON, formatIsJSONP, formatIsXML, getAuthenticatedUser, getCallback, getColumnHeaderStyle, getDefaultOutput, getExtension, getFormat, getIntParameter, getIntParameter, getLineBreak, getListManager, getOptionalParameter, getOptionalParameter, getPermission, getProperty, getRawOutput, getRequestFileName, getRequiredParameter, hasCallback, initState, isAuthenticated, isGzip, isUncompressed, isZip, makeJSONOutput, makeXMLOutput, postInit, service, setFormat, setNameSpace, validateState, wantsColumnHeaders, wantsDataPackage

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • FastaQueryService

        public FastaQueryService​(org.intermine.api.InterMineAPI im)
        Constructor.
        Parameters:
        im - A reference to an InterMine API settings bundle.

    • Method Detail

      • getExporter

        protected org.intermine.web.logic.export.Exporter getExporter​(org.intermine.pathquery.PathQuery pq)
        Specified by:
        getExporter in class BioQueryService
        Parameters:
        pq - pathquery
        Returns:
        exporter

      • getQuery

        protected org.intermine.pathquery.PathQuery getQuery()
        Make the path-query to run, and check it has the right number of columns.
        Overrides:
        getQuery in class BioQueryService
        Returns:
        A suitable pathquery for getting FASTA data from.

      • parseExtension

        protected static int parseExtension​(java.lang.String extension)
                             throws org.intermine.webservice.server.exceptions.BadRequestException
        A method for parsing the value of the extension parameter. Static and protected for testing purposes.
        Parameters:
        extension - The extension as provided by the user.
        Returns:
        An integer representing the number of base pairs.
        Throws:
        org.intermine.webservice.server.exceptions.BadRequestException - If there is a problem interpreting the extension string.

      • checkPathQuery

        protected void checkPathQuery​(org.intermine.pathquery.PathQuery pq)
                       throws java.lang.Exception
        Description copied from class: BioQueryService
        No-op stub. Put query validation here.
        Overrides:
        checkPathQuery in class BioQueryService
        Parameters:
        pq - pathquery
        Throws:
        java.lang.Exception - if something goes wrong