controller
Class ProcessusNew

java.lang.Object
  javax.servlet.GenericServlet
      javax.servlet.http.HttpServlet
          controller.ProcessusNew

All Implemented Interfaces:

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

public class ProcessusNew
extends javax.servlet.http.HttpServlet

Attention / take care !
This controller is used on the old code made by Stefan Engelen in 2006 (latest version got) for the web interface...
No garanty are given to the results and good work of algorithms as work has been done on it to fix problems and gett same results !
Seen also tests testsorigin to know exactly some uses and limits.
Main controler ; interaction between modele (algorithms implementation) and viewing with JSP/web pages.
Some uses of new model (2008) for conversion and use of JSP/HTML pages. Conversion are made here for comprehension, control of work and tests.
Some "XXX BLACKBOX warning" in the code due to use of Vector... (java 1.4 => 1.5 and changes).
Compilation could be done with flags [-source 1.4 -target 1.4] (1)
Compilation could be done with flags [-source 1.4 -target 1.4] (2)

Best version we can have now with use of OriginAlgorithmsStefan and OriginAlgoStefanConverter and centralization of algorithms...
Different way of navigation between pages : [-1|0] -> [1|4] -> [-|5] -> [2 ->] 3

Pages are the following :
- (-1) formdefile.jsp : form to upload file alignment
- (0) formdepart.jsp : form to paste alignment
- (1) formselectioncible.jsp : target selection, parameters and applicationsbr> - (2) formselectionhomol.jsp : selection of homologuous sequences (SSCA results and TFold step by step)
- (3) formresults.jsp : pages to visualize results
- (4) formselectioncibleonly.jsp : target selection and palindromes helix could be given
- (5) formselectionparameters.jsp : parameters and applications
- (9) clustalwredirection.jsp

Since:

August 2008

Author:

Gabriel Chandesris (2008)

See Also:

Processus_old, Processus, ADN1cible, ADN1test, Palindrome1cible, Palindrome, PalindromeListe, PalindromeListeListe, Sequence, SequenceListe, Fichier, FichierFasta, Serialized Form

Field Summary

private int	maxPredictions
private boolean	muchpredictions
private boolean	searchPseudoknots
private static long	serialVersionUID Servlet serial Number (42).
private PalindromeListe	userPalindromesTable

Constructor Summary

ProcessusNew()

Method Summary

static java.lang.String	alignmentRecord(java.lang.String alignement) Making the recording of alignment in a file.
private static java.lang.String	decoupeString(java.lang.String chaineDecoupe) This method to cut a String by 80 characters length substring.
void	doGet(javax.servlet.http.HttpServletRequest requete, javax.servlet.http.HttpServletResponse reponse) To prevent from reload pages of accession without any "normal use".
void	doPost(javax.servlet.http.HttpServletRequest requete, javax.servlet.http.HttpServletResponse reponse) To obtain data from POST form.
private static java.lang.String	getScriptDestination(int numInterface) To get the page where to go...

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

Field Detail

serialVersionUID

private static final long serialVersionUID

Servlet serial Number (42).

See Also:

Constant Field Values

muchpredictions

private boolean muchpredictions

maxPredictions

private int maxPredictions

searchPseudoknots

private boolean searchPseudoknots

userPalindromesTable

private PalindromeListe userPalindromesTable

Constructor Detail

ProcessusNew

public ProcessusNew()

Method Detail

doGet

public void doGet(javax.servlet.http.HttpServletRequest requete,
                  javax.servlet.http.HttpServletResponse reponse)

To prevent from reload pages of accession without any "normal use".
Make a redirection to main page of application / servlet.

Overrides:

doGet in class javax.servlet.http.HttpServlet

See Also:

Processus.doPost(HttpServletRequest, HttpServletResponse)

doPost

public void doPost(javax.servlet.http.HttpServletRequest requete,
                   javax.servlet.http.HttpServletResponse reponse)

To obtain data from POST form.

Overrides:

doPost in class javax.servlet.http.HttpServlet

Parameters:

requete - HttpServletRequest

reponse - HttpServletResponse

getScriptDestination

private static java.lang.String getScriptDestination(int numInterface)

To get the page where to go...

Parameters:

numInterface - number of the page

Returns:

(String) Path to the JSP page to go...

alignmentRecord

public static java.lang.String alignmentRecord(java.lang.String alignement)

Making the recording of alignment in a file. Could be done with FichierFasta.

Parameters:

alignement - (String)

Returns:

(String) alignement

Since:

July / August 2008

See Also:

FichierFasta

decoupeString

private static java.lang.String decoupeString(java.lang.String chaineDecoupe)

This method to cut a String by 80 characters length substring.

Parameters:

chaineDecoupe - (String)

Returns:

(String)

See Also:

Processus.doPost(HttpServletRequest, HttpServletResponse)