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)