edu.mssm.crover.webservices.rbde
Class ShowDiagram

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

All Implemented Interfaces:

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

public class ShowDiagram

extends javax.servlet.http.HttpServlet

Servlet to build a diagram in one GET connection. ShowDiagram is the front-end to call when one needs to render a diagram using only one GET connection. The diagram is returned as an image on this connection. An HTML client file would look like:

   <_img
   SRC="http://transport.physbio.mssm.edu:8080/fabien/show-diagram?TM=10-20,30-40&helices=10-20,30-40&betas=25-27&sequence=ASDFGHKLAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAW">
   

"_img" is to be read "img". ShowDiagram parses its arguments, creates a guest session, configures the CustomizedDiagram in the session according to the arguments, redirects the browser to the SequenceDiagramGif diagram rendering servlet. For the encoding of the parameters, sequence intervals are defined by two integers separated by '-'. The first integer gives the position of the first residue of the sequence interval, the second integer gives the position of the last residue of the interval. Positions start at zero. The following parameters are supported:

• sequence - The residue codes in one letter encoding, Nterm residues first.
• helices - Describes the helix SSE. List of sequence intervals separated by commas for which a helix SSR must be rendered. ex: 10-20,30-40
betas - Describes the beta SSE. List of sequence intervals separated by commas for which a beta SSR must be rendered.
• tm - Describes the TransMembrane segments. List of sequence intervals separated by commas which should be considered part of the transmembrane domain.
• nterm - The direction of the Nterminal domain representation on the page, can be "up" or "down"
• mutationServer - The name of the server to obtain the mutants from.
• ac - The accession code of the sequence for which mutants should be retrieved.
• db - The sequence database that defined the accession code.

See Also:

Serialized Form

Constructor Summary

ShowDiagram()

Method Summary

boolean	cleanup(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response, DS_UserSession us)
void	doGet(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response) Does whatever the parameter request to do, return an image that encodes the success or failure of the operation.
void	doPost(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response)
void	fails(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response, java.io.OutputStream dest)
java.awt.Image	getFailureImage()
java.awt.image.BufferedImage	getImage(java.awt.Color color)
long	getLastModified(javax.servlet.http.HttpServletRequest request)
javax.servlet.http.HttpSession	getSession(javax.servlet.http.HttpServletRequest request) Returns a guest session.
java.awt.Image	getSuccessImage()
void	log(int level, java.lang.String msg)
void	log(int level, java.lang.String msg, java.lang.Exception e)
boolean	parseBetas(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response, DS_UserSession us)
boolean	parseHelices(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response, DS_UserSession us)
boolean	parseMutations(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response, DS_UserSession us) Parses the mutation server out of the parameters, if provided.
boolean	parseSequence(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response, DS_UserSession us) Parses the residue codes out of the parameters.
boolean	parseSSE(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response, DS_UserSession us, int start, int end, int type)
boolean	parseTM(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response, DS_UserSession us, int start, int end)
boolean	parseTMs(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response, DS_UserSession us)
void	succeeds(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response, java.io.OutputStream dest)

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

Constructor Detail

ShowDiagram

public ShowDiagram()

Method Detail

doGet

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

Does whatever the parameter request to do, return an image that encodes the success or failure of the operation.

Overrides:

doGet in class javax.servlet.http.HttpServlet

java.io.IOException

javax.servlet.ServletException

parseMutations

public boolean parseMutations(javax.servlet.http.HttpServletRequest request,
                              javax.servlet.http.HttpServletResponse response,
                              DS_UserSession us)

Parses the mutation server out of the parameters, if provided.

Returns:

True for success, False for failure.

parseSequence

public boolean parseSequence(javax.servlet.http.HttpServletRequest request,
                             javax.servlet.http.HttpServletResponse response,
                             DS_UserSession us)

Parses the residue codes out of the parameters. Updates the session's CustomizedDiagram with the residue codes when appropriate (ie residues specified are different).

Returns:

True for success, False for failure.

parseTMs

public boolean parseTMs(javax.servlet.http.HttpServletRequest request,
                        javax.servlet.http.HttpServletResponse response,
                        DS_UserSession us)

parseHelices

public boolean parseHelices(javax.servlet.http.HttpServletRequest request,
                            javax.servlet.http.HttpServletResponse response,
                            DS_UserSession us)

parseBetas

public boolean parseBetas(javax.servlet.http.HttpServletRequest request,
                          javax.servlet.http.HttpServletResponse response,
                          DS_UserSession us)

parseTM

public boolean parseTM(javax.servlet.http.HttpServletRequest request,
                       javax.servlet.http.HttpServletResponse response,
                       DS_UserSession us,
                       int start,
                       int end)

parseSSE

public boolean parseSSE(javax.servlet.http.HttpServletRequest request,
                        javax.servlet.http.HttpServletResponse response,
                        DS_UserSession us,
                        int start,
                        int end,
                        int type)

cleanup

public boolean cleanup(javax.servlet.http.HttpServletRequest request,
                       javax.servlet.http.HttpServletResponse response,
                       DS_UserSession us)

log

public void log(int level,
                java.lang.String msg,
                java.lang.Exception e)

log

public void log(int level,
                java.lang.String msg)

fails

public void fails(javax.servlet.http.HttpServletRequest request,
                  javax.servlet.http.HttpServletResponse response,
                  java.io.OutputStream dest)
           throws java.io.IOException

java.io.IOException

succeeds

public void succeeds(javax.servlet.http.HttpServletRequest request,
                     javax.servlet.http.HttpServletResponse response,
                     java.io.OutputStream dest)
              throws java.io.IOException

java.io.IOException

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

getLastModified

public long getLastModified(javax.servlet.http.HttpServletRequest request)

Overrides:

getLastModified in class javax.servlet.http.HttpServlet

getSession

public javax.servlet.http.HttpSession getSession(javax.servlet.http.HttpServletRequest request)

Returns a guest session.

getImage

public java.awt.image.BufferedImage getImage(java.awt.Color color)

getSuccessImage

public java.awt.Image getSuccessImage()

getFailureImage

public java.awt.Image getFailureImage()