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


Copyright @ 2003 Mount Sinai School of Medicine. All Rights Reserved.