edu.mssm.crover.webservices.rbde
Class CopyTMtoSS

java.lang.Object
  |
  +--javax.servlet.GenericServlet
        |
        +--javax.servlet.http.HttpServlet
              |
              +--edu.mssm.crover.webservices.rbde.AnnotationsEditor
                    |
                    +--edu.mssm.crover.webservices.rbde.CopyTMtoSS

All Implemented Interfaces:

java.io.Serializable, javax.servlet.Servlet, javax.servlet.ServletConfig

public class CopyTMtoSS

extends edu.mssm.crover.webservices.rbde.AnnotationsEditor

Servlet that copies transmembrane segment annotations to secondary structure annotations. Implements method editAnnotations() from AnnotationsEditor abstract class. This method provides the servlet with functionality to copy Transmembrane (TM) segment Annotations (TM_Annotation class) (start-s and end-s of TM subunits) to Secondary Structure annotations (SecondaryStructure_Annotation) as helices.

See Also:

TM_Annotation, SecondaryStructure_Annotation, Serialized Form

Constructor Summary

CopyTMtoSS()

Method Summary

void	doGet(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response)
void	doPost(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response)
protected void	editAnnotations(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response, javax.servlet.http.HttpSession session, URLRepository repository, ServletCentral sc, BiologicalAnnotations ba, DS_UserSession us) This method needs to be implemented in all subclasses and provides the functionality.
static void	mapTmtoSecStructure(javax.servlet.http.HttpSession session, AnnotatedBioSequence seq, ServletCentral sc)
static void	mapTmtoSecStructure(javax.servlet.http.HttpSession session, BiologicalAnnotations ba, ServletCentral sc)

Methods inherited from class javax.servlet.http.HttpServlet

doDelete, doHead, doOptions, doPut, doTrace, getLastModified, service, service

Methods inherited from class javax.servlet.GenericServlet

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

Methods inherited from class java.lang.Object

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

Constructor Detail

CopyTMtoSS

public CopyTMtoSS()

Method Detail

editAnnotations

protected void editAnnotations(javax.servlet.http.HttpServletRequest request,
                               javax.servlet.http.HttpServletResponse response,
                               javax.servlet.http.HttpSession session,
                               URLRepository repository,
                               ServletCentral sc,
                               BiologicalAnnotations ba,
                               DS_UserSession us)
                        throws java.io.IOException,
                               javax.servlet.ServletException

Description copied from class: edu.mssm.crover.webservices.rbde.AnnotationsEditor

This method needs to be implemented in all subclasses and provides the functionality. The BiologicalAnnotations, extracted from the AnnotatedBioSequence, can be altered in this method.

Specified by:

editAnnotations in class edu.mssm.crover.webservices.rbde.AnnotationsEditor

java.io.IOException

javax.servlet.ServletException

mapTmtoSecStructure

public static void mapTmtoSecStructure(javax.servlet.http.HttpSession session,
                                       AnnotatedBioSequence seq,
                                       ServletCentral sc)
                                throws SecondaryStructure_Annotation.InvalidTypeException

SecondaryStructure_Annotation.InvalidTypeException

mapTmtoSecStructure

public static void mapTmtoSecStructure(javax.servlet.http.HttpSession session,
                                       BiologicalAnnotations ba,
                                       ServletCentral sc)
                                throws SecondaryStructure_Annotation.InvalidTypeException

SecondaryStructure_Annotation.InvalidTypeException

doPost

public void doPost(javax.servlet.http.HttpServletRequest request,
                   javax.servlet.http.HttpServletResponse response)
            throws java.io.IOException,
                   javax.servlet.ServletException

Overrides:

doPost in class javax.servlet.http.HttpServlet

java.io.IOException

javax.servlet.ServletException

doGet

public void doGet(javax.servlet.http.HttpServletRequest request,
                  javax.servlet.http.HttpServletResponse response)
           throws java.io.IOException,
                  javax.servlet.ServletException

Overrides:

doGet in class javax.servlet.http.HttpServlet

java.io.IOException

javax.servlet.ServletException