edu.mssm.crover.webservices.rbde
Class Mutations

java.lang.Object
  |
  +--javax.servlet.GenericServlet
        |
        +--javax.servlet.http.HttpServlet
              |
              +--edu.mssm.crover.webservices.rbde.Mutations
All Implemented Interfaces:
java.io.Serializable, javax.servlet.Servlet, javax.servlet.ServletConfig

public class Mutations
extends javax.servlet.http.HttpServlet

Allow the user to

  • Query mutation servers
  • Filter the set of mutants
  • Select mutants for further processing

    See Also:
    Serialized Form

    Field Summary
     int SERVE_FRAMESET_DOCUMENT
               
     
    Constructor Summary
    Mutations()
               
     
    Method Summary
    static void applyLinks(DS_UserSession us, MutantSubServiceState state)
              Extract the descriptionURL from the selected mutants and apply it to current diagram as a URL on each position which is being altered by the mutant.
    static void applyTool(DS_UserSession us, MutantSubServiceState state, java.lang.String tool)
               
     void choose_server(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response, ServletCentral sc, org.apache.ecs.html.Body body, URLRepository repository, DS_UserSession us)
               
    static void clearMutationPositions(DS_UserSession us, MutantSubServiceState state)
              Clear the color of the residues of the diagram on each position which is being altered by the selected mutants.
    static void colorMutationPositions(DS_UserSession us, MutantSubServiceState state)
              Colors the residues of the diagram on each position which is being altered by the selected mutants.
    static void defineNewColor(BiologicalAnnotations ba, java.lang.String colorName, java.awt.Color color)
               
     void doGet(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response)
               
     void doPost(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response)
               
     long getLastModified(javax.servlet.http.HttpServletRequest request)
               
     java.lang.String getTextMutationType(short type)
               
     org.apache.ecs.Element mutantToHTML(Mutant m, URLRepository repository, javax.servlet.http.HttpServletResponse response, boolean enable_select, boolean enable_unselect)
               
     void query_display(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response, ServletCentral sc, org.apache.ecs.html.Body body, URLRepository repository, DS_UserSession us)
               
    static void removeElipses(DS_UserSession us, MutantSubServiceState state)
              Makes sure that the selected mutations are not located in elipses.
     org.apache.ecs.Element selectionToHTML(MutantSubServiceState state, URLRepository repository, javax.servlet.http.HttpServletResponse response)
               
     void serve_frameset_document(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response, ServletCentral sc, org.apache.ecs.html.Body body, URLRepository repository, DS_UserSession us)
               
     
    Methods inherited from class javax.servlet.http.HttpServlet
    doDelete, doHead, doOptions, doPut, doTrace, 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
     

    Field Detail

    SERVE_FRAMESET_DOCUMENT

    public final int SERVE_FRAMESET_DOCUMENT
    See Also:
    Constant Field Values
    Constructor Detail

    Mutations

    public Mutations()
    Method Detail

    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

    serve_frameset_document

    public void serve_frameset_document(javax.servlet.http.HttpServletRequest request,
                                        javax.servlet.http.HttpServletResponse response,
                                        ServletCentral sc,
                                        org.apache.ecs.html.Body body,
                                        URLRepository repository,
                                        DS_UserSession us)

    choose_server

    public void choose_server(javax.servlet.http.HttpServletRequest request,
                              javax.servlet.http.HttpServletResponse response,
                              ServletCentral sc,
                              org.apache.ecs.html.Body body,
                              URLRepository repository,
                              DS_UserSession us)

    query_display

    public void query_display(javax.servlet.http.HttpServletRequest request,
                              javax.servlet.http.HttpServletResponse response,
                              ServletCentral sc,
                              org.apache.ecs.html.Body body,
                              URLRepository repository,
                              DS_UserSession us)

    selectionToHTML

    public org.apache.ecs.Element selectionToHTML(MutantSubServiceState state,
                                                  URLRepository repository,
                                                  javax.servlet.http.HttpServletResponse response)

    mutantToHTML

    public org.apache.ecs.Element mutantToHTML(Mutant m,
                                               URLRepository repository,
                                               javax.servlet.http.HttpServletResponse response,
                                               boolean enable_select,
                                               boolean enable_unselect)

    getTextMutationType

    public java.lang.String getTextMutationType(short type)

    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

    getLastModified

    public long getLastModified(javax.servlet.http.HttpServletRequest request)
    Overrides:
    getLastModified in class javax.servlet.http.HttpServlet

    applyTool

    public static void applyTool(DS_UserSession us,
                                 MutantSubServiceState state,
                                 java.lang.String tool)

    removeElipses

    public static void removeElipses(DS_UserSession us,
                                     MutantSubServiceState state)
    Makes sure that the selected mutations are not located in elipses.


    applyLinks

    public static void applyLinks(DS_UserSession us,
                                  MutantSubServiceState state)
    Extract the descriptionURL from the selected mutants and apply it to current diagram as a URL on each position which is being altered by the mutant. NB. The tool links only mutants which are in the state and have been selected.


    colorMutationPositions

    public static void colorMutationPositions(DS_UserSession us,
                                              MutantSubServiceState state)
    Colors the residues of the diagram on each position which is being altered by the selected mutants. The coloring is done with the pre-defined "mutation" color. NB. The tool colors only mutants which are in the state and have been selected.


    clearMutationPositions

    public static void clearMutationPositions(DS_UserSession us,
                                              MutantSubServiceState state)
    Clear the color of the residues of the diagram on each position which is being altered by the selected mutants. NB. The tool clears only mutants which are in the state and have been selected.


    defineNewColor

    public static void defineNewColor(BiologicalAnnotations ba,
                                      java.lang.String colorName,
                                      java.awt.Color color)


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