org.biomoby.service.test
Class FromFastaToDNASequence

java.lang.Object
  javax.servlet.GenericServlet
      javax.servlet.http.HttpServlet
          org.biomoby.service.MobyServlet
              org.biomoby.service.test.FromFastaToDNASequence

All Implemented Interfaces:

Serializable, Remote, javax.servlet.Servlet, javax.servlet.ServletConfig

@mobyService(name="ConvertFASTAToDNASequence",
             type="FormatConversion",
             provider="moby.ucalgary.ca",
             author="gordonp@ucalgary.ca",
             in="inseq:FASTA",
             out="outseq:DNASequence",
             description={"Converts FastA formatted records into DNASequences, ","primarily to increase inter-service compatibility"})
public class FromFastaToDNASequence
extends MobyServlet

See Also:

Serialized Form

Field Summary

Fields inherited from class org.biomoby.service.MobyServlet

ADMIN_MODE, INIT_OUTPUT_BUFFER_SIZE, MOBY_AUTHORITATIVE_PARAM, MOBY_CENTRAL_URL_PARAM, MOBY_CONTACT_PARAM, MOBY_INPUT_PARAM, MOBY_OUTPUT_PARAM, MOBY_PROVIDER_URI_PARAM, MOBY_SECONDARYINPUT_PARAM, MOBY_SERVICE_DESC_PARAM, MOBY_SERVICENAME_PARAM, MOBY_SERVICETYPE_PARAM, MODE_HTTP_PARAM, RDF_MODE

Constructor Summary

FromFastaToDNASequence()

Method Summary

static boolean	isNucleicAcid(String sequence)
void	processRequest(MobyDataJob request, MobyDataJob result) Parses a FastA string into its header component and sequence, constructing a MOBY DNASequence object (or subclass thereof), which can be used in more services.

Methods inherited from class org.biomoby.service.MobyServlet

createServiceFromConfig, destroy, doGet, doPost, getCentralImpl, getMobyContents, getServiceName, init, log, log, main, processRequests, setCoCInitParameter, setMainTerminationExit, stringToPrimaryDataTemplate, stringToSecondaryDataTemplate, validateArguments

Methods inherited from class javax.servlet.http.HttpServlet

service

Methods inherited from class javax.servlet.GenericServlet

getInitParameter, getInitParameterNames, getServletConfig, getServletContext, getServletInfo, getServletName, init, log

Methods inherited from class java.lang.Object

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

Constructor Detail

FromFastaToDNASequence

public FromFastaToDNASequence()

Method Detail

processRequest

public void processRequest(MobyDataJob request,
                           MobyDataJob result)
                    throws Exception

Parses a FastA string into its header component and sequence, constructing a MOBY DNASequence object (or subclass thereof), which can be used in more services. An exception will be thrown if the data doesn't appear to be FastA, or a warning will be added to the results if the sequence doesn't appear to be DNA.

Overrides:

processRequest in class MobyServlet

Parameters:

request - the request to process, with params guaranteed to be of the type specified in the mobyService annotation, or values overriding the annjotation in a WAR file's WEB-INF/web.xml

Throws:

Exception

isNucleicAcid

public static boolean isNucleicAcid(String sequence)