Conflit de RequestDispatcher dans ma servlet

Bonjour à tous,

dans ma servlet j'ai une condition avec un requestDispatcher qui redirige ma webapp sur une page d'erreur (erreur.html) si une condition est vérifiée, si la condition n'est pas vérifiée alors le programme s'execute et une page de résultats s'affiche, or depuis que j'ai implémenté la redirection vers une page d'erreur avec mon requestDispatcher la 2 éme partie de mon test ne fonctionne plus, lorsque j'entre un fichier valide en entrée (je suis donc dans le "else") j'ai le message suivant qui apparait sous tomcat :

Citation:

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java.lang.IllegalStateException: Impossible d'utiliser faire-suivre (forward) après que la réponse ait été envoyée
controller.ProcessusNew.doPost(ProcessusNew.java:1644)
javax.servlet.http.HttpServlet.service(HttpServlet.java:637)
javax.servlet.http.HttpServlet.service(HttpServlet.java:717)

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j'ai essayé de contourner ça en codant autrement mais rien n'y fait, j'aimerai savoir si quelqu'un avait une idée, voici le code en question :

Code:

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if (session.getAttribute("status").equals(new Integer(42))) { /** If an error, we go back ... */ //pageDestination = ProcessusNew.getScriptDestination(erreur); RequestDispatcher dispatcher = requete.getRequestDispatcher("erreur.html"); try {dispatcher.forward(requete,reponse); } catch (ServletException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } }   else { /** ... else we continue to the destination ! */ pageDestination = ProcessusNew.getScriptDestination(destinaInterface); } RequestDispatcher rd = this.getServletContext().getRequestDispatcher(pageDestination); try { rd.forward(requete,reponse); } catch (ServletException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } }

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Si je retire le RequestDispatcher du else je n'ai plus de message d'erreur mais je ne suis pu redirigé vers la page des résultats :?


Merci à vous

Salut,

Pourquoi tu ne défini pas un seul RequestDispatcher auquel tu attribue la variable pageDestination ?
La valeur de pageDestination pourra être attribuée en fonction de ton test.
Et enfin tu fais ton forward tout à la fin (après ton if else) ?

quelque chose comme ça ?

Code:

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if (session.getAttribute("status").equals(new Integer(42))) { /** If an error, we go back ... */ destinaInterface = 14; pageDestination = ProcessusNew.getScriptDestination(destinaInterface); RequestDispatcher dispatcher = requete.getRequestDispatcher(pageDestination); try {dispatcher.forward(requete,reponse); } catch (ServletException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } }   else { /** ... else we continue to the destination ! */ pageDestination = ProcessusNew.getScriptDestination(destinaInterface); } RequestDispatcher rd = this.getServletContext().getRequestDispatcher(pageDestination); try { rd.forward(requete,reponse); } catch (ServletException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } }   /** * To get the page where to go... * @param numInterface number of the page * @return (String) Path to the JSP page to go... */   private static String getScriptDestination(int numInterface) { String scriptDestination = "/interblackbox/test.jsp"; switch(numInterface){ /** go to origine or destination */ case(-1):scriptDestination = "/interblackbox/formdefile.jsp";break; case(0):scriptDestination = "/interblackbox/formdepart.jsp";break; case(1):scriptDestination = "/interblackbox/formselectioncible.jsp";break; case(2):scriptDestination = "/interblackbox/formselectionhomol.jsp";break; case(3):scriptDestination = "/interblackbox/formresults.jsp";break; case(4):scriptDestination = "/interblackbox/formselectioncibleonly.jsp";break; case(5):scriptDestination = "/interblackbox/formselectionparameters.jsp";break; case(6):scriptDestination = "/interblackbox/formselectionparameters.jsp";break; case(9):scriptDestination = "/interblackbox/clustalwredirection.jsp";break; case(10):scriptDestination = "/interblackbox/comparaison_performance_submission.jsp";break; case(11):scriptDestination = "/interblackbox/comparaison_performance_results.jsp";break; case(12):scriptDestination = "/interblackbox/gFold/resultat.jsp";break; case(13):scriptDestination = "/interblackbox/gFold/resultat.jsp";break; case(14):scriptDestination = "/interblackbox/erreur.html";break; default:scriptDestination = "/interblackbox/test.jsp"; } return scriptDestination; }

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EDIT: avec ce code j'obtiens le meme message d'erreur.

Citation:

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Et enfin tu fais ton forward tout à la fin (après ton if else) ?

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je débute en java, le forward se fait ici je suppose:

Code:

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public void doGet(HttpServletRequest requete,HttpServletResponse reponse){ String pageDestination = "/"; RequestDispatcher rd = this.getServletContext().getRequestDispatcher(pageDestination); try { rd.forward(requete,reponse); } catch (ServletException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } }

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Cette partie de code est située au début du code (avant le test).


Merci

Il se trouve où ton if exactement ?
Envoi ta classe complète pour y voir plus clair ...

ok, voici le code, les parties intéressantes sont situées en haut et en bas :

Code:

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public class ProcessusNew extends HttpServlet { /** Servlet serial Number (42). */ private static final long serialVersionUID = 42L; private boolean muchpredictions = false; private int maxPredictions = 20; private boolean searchPseudoknots = true; private PalindromeListe userPalindromesTable = new PalindromeListe(); private ListeBean bestSequensOri = new ListeBean(); private Sequence cibleOri = new Sequence(); // private String fileUsed = "Copy/paste was used."; // private boolean isCopyPaste = true;   /** * To prevent from reload pages of accession without any "normal use". * <br>Make a redirection to main page of application / servlet. * @see Processus#doPost(HttpServletRequest, HttpServletResponse) */ public void doGet(HttpServletRequest requete,HttpServletResponse reponse){ String pageDestination = "/"; RequestDispatcher rd = this.getServletContext().getRequestDispatcher(pageDestination); try { rd.forward(requete,reponse); } catch (ServletException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } }   /** * To obtain data from POST form. * @param requete HttpServletRequest * @param reponse HttpServletResponse */ public void doPost(HttpServletRequest requete,HttpServletResponse reponse){ /** TODO SERVLET personnalize user session */ HttpSession session = requete.getSession(true);   /** Numbers of pages of where we went and where we would go... */ int origineInterface = 0;//-1; int destinaInterface = 12;   // session.setAttribute("TinU", false); String alignement = null;   // Boolean isCopyPaste = (Boolean)session.getAttribute("isCopyPaste"); // String fileUsed = (String)session.getAttribute("fileUsed"); if ((Boolean)session.getAttribute("isCopyPaste") == null) { // session.invalidate(); session.setAttribute("fileName", "Copy/paste was used"); session.setAttribute("isCopyPaste", true); } String monOKSubmit = requete.getParameter("OK_submit"); if (monOKSubmit != null) { if (monOKSubmit.replaceAll(" ", "") == "Loadalignment") { session.setAttribute("fileName", "Copy/paste was used"); session.setAttribute("isCopyPaste", true); } }   if (ServletFileUpload.isMultipartContent(requete)) {   String OK_submit = requete.getParameter("OK_submit"); if (OK_submit != null) { if (OK_submit.replaceAll(" ", "") == "Loadalignment") { // session.invalidate(); session.setAttribute("fileName", "Copy/paste was used"); session.setAttribute("isCopyPaste", true); } } /** UPLOAD : The way of uploading files... */ /* if ( (requete.getParameter("fichier_sequence_alignement") != "") && (requete.getParameter("OK_submit") == "Load file") ) { ProcessusNew.fileUsed = "File used : "+requete.getParameter("fichier_sequence_alignement"); } else { ProcessusNew.fileUsed = "Copy/paste was used."; } session.setAttribute("fileName", ProcessusNew.fileUsed);*/ String aln = ""; // session.setAttribute("isCopyPaste", this.isCopyPaste); /* if (requete.getParameter("OK_submit") == "Load file") { System.out.println("OK_submit = Load file"); ProcessusNew.fileUsed = requete.getParameter("fichier_sequence_alignement"); System.out.println(ProcessusNew.fileUsed); session.setAttribute("fileName", ProcessusNew.fileUsed); } else if (requete.getParameter("OK_submit") == "Load alignment") { System.out.println("OK_submit = Load alignment"); ProcessusNew.fileUsed = null; System.out.println(ProcessusNew.fileUsed); session.setAttribute("fileName", null); } else { session.setAttribute("fileName", ProcessusNew.fileUsed); System.out.println("Aucun des OK ..."); }*/ try { /** Create a factory for disk-based file items */ FileItemFactory factory = new DiskFileItemFactory(); /** Create a new file upload handler */ ServletFileUpload upload = new ServletFileUpload(factory); /** Parse the request : FileItem */ List items = upload.parseRequest(requete); System.out.println(items.size()); /** Process the uploaded items */ Iterator iter = items.iterator(); /** Create a temporary file to store informations from the client file */ String FileNameInputGfold = (System.currentTimeMillis()+".fasta"); File fileTempSeq = new File("/usr/share/tomcat/webapps/miRNAFold/interblackbox/gFold/"+FileNameInputGfold); int pos_List = 0; String[] command = new String[6];   while (iter.hasNext()) { pos_List++; FileItem item = (FileItem)iter.next(); if (!item.isFormField()) { boolean writeToFile = true; if (writeToFile) { aln = item.getString(); // session.invalidate(); session.setAttribute("fileName", "File used: "+item.getName()); session.setAttribute("isCopyPaste", false); System.out.println(item.getName()); try{ item.write(fileTempSeq); System.out.println(fileTempSeq.getPath()); System.out.println(fileTempSeq.getName()); } catch (Exception ej) { ej.printStackTrace(); }   if ( (aln != null) && ( (aln.length() > 0) && (!aln.equals("")) ) ) { try { // alignement = this.alignmentRecord(aln); FichierFasta myFastaFile = new FichierFasta(aln); alignement = myFastaFile.getSequencesToString(); /** ICI, rajouter du code pour savoir si on a changer les T en U lors du new FichierFasta **/ session.setAttribute("status", null); } catch (Exception e) { try { FichierClustalW fileTemp = new FichierClustalW(System.currentTimeMillis()+".clustalW", new BufferedReader(new StringReader(aln))); FichierFasta myFile = new FichierFasta(fileTemp.recupererSequences()); alignement = myFile.getSequencesToString(); session.setAttribute("status", null); } catch (Exception ef) { ef.printStackTrace(); session.setAttribute("status",new Integer(42)); session.setAttribute("error","Not a FASTA nor ClustalW Alignment (upload)."); alignement = null; } }     } else { session.setAttribute("status",new Integer(42)); session.setAttribute("error","Alignment empty (upload). "); alignement = null; } } }   command[5]=text; break; } System.out.println(command[4]); } /** Use the else below i want combine upload and / or * [copy / paste|other "normal" form fields] */   } RunMiRNAFold miRNAFold_exec = new RunMiRNAFold("/usr/share/tomcat/webapps/miRNAFold_test/interblackbox/gFold/gFold", fileTempSeq.getPath(), command); miRNAFold_exec.runMiRNAFold(); fileTempSeq.deleteOnExit(); session.setAttribute("result",miRNAFold_exec); /* List list = miRNAFold_exec.getOutput(); System.out.println(list.size()); /** Process the uploaded items */ /* Iterator iterator = list.iterator();   FileItem fitem = (FileItem)iterator.next(); File resultat = new File("/usr/share/tomcat/webapps/GFold_test/interblackbox/gFold/resultat.txt"); fitem.write(resultat); */ /** see end of current method (doPost) */ } catch(FileUploadException e) { // session.invalidate(); session.setAttribute("status",new Integer(42)); session.setAttribute("error","Can't Parse the request. "); alignement = null; } if (alignement == "") { // session.invalidate(); session.setAttribute("status",new Integer(42)); session.setAttribute("error","Not a FASTA Alignment (upload empty). "); alignement = null; }   /** Two (2) major ways in working next from for process : * - target sequence selection and parameters * with application choice (original use : 0 -> 1 -> [2 ->] 3 * - target sequence selection and palindromes indications, * then parameters and application choice : 0 -> 4 -> 5 -> [2 ->] 3 */ /** By the "other way" : sending to the second way of work ! * just comment to return to original way of work... */ origineInterface = 0;//-1; destinaInterface = 13; } else { /** ================================================================ */ /** ================================================================ */ /** content-type == 'application/x-www-form-urlencoded' (POST) */ /** NORMAL USE : usual treament here... */ // System.out.println(ProcessusNew.isCopyPaste); //ProcessusNew.isCopyPaste = requete.getParameter("isCopyPaste");   //Float.parseFloat(requete.getParameter("val_incertitude")) String OK_submit = requete.getParameter("OK_submit"); if (OK_submit != null) { if (OK_submit.replaceAll(" ", "") == "Loadalignment") { // session.invalidate(); session.setAttribute("fileName", "Copy/paste was used"); session.setAttribute("isCopyPaste", true); } } // System.out.println("OK_submit = "+OK_submit); /* if (OK_submit != null) { if ( /*(requete.getParameter("fichier_sequence_alignement") != "") && *///OK_submit.replaceAll(" ", "") == "Loadfile") { // System.out.println("Je suis dans la première condition du if"); /* session.setAttribute("fileName", "File used : "+requete.getParameter("fichier_sequence_alignement")); session.setAttribute("isCopyPaste", false); } else { if (/*ProcessusNew.isCopyPaste/*(requete.getParameter("texte_sequence_alignement") != "") && /*(requete.getParameter("texte_sequence_alignement") != "Put here the alignment in FASTA format... ") && *///OK_submit.replaceAll(" ", "") == "Loadalignment") { // System.out.println("Je suis dans le deuxième if"); /* session.setAttribute("fileName", "Copy/paste was used"); session.setAttribute("isCopyPaste", true); } } }*/ // System.out.println("Et juste apres : "+ProcessusNew.isCopyPaste); origineInterface = Integer.parseInt(requete.getParameter("org_interface")); destinaInterface = Integer.parseInt(requete.getParameter("des_interface")); /** MAIN TREATMENTS HERE */ /** ================================================================ */ /** Submission form of sequence to first step for proceding * (cible selection). */ if ( (origineInterface == 0) && (destinaInterface == 1) ) { /* if (requete.getParameter("OK_submit") == "Load file") { System.out.println("OK_submit = Load file"); ProcessusNew.fileUsed = requete.getParameter("fichier_sequence_alignement"); System.out.println(ProcessusNew.fileUsed); session.setAttribute("fileName", ProcessusNew.fileUsed); } else if (requete.getParameter("OK_submit") == "Load alignment") { System.out.println("OK_submit = Load alignment"); ProcessusNew.fileUsed = null; System.out.println(ProcessusNew.fileUsed); session.setAttribute("fileName", null); } else { session.setAttribute("fileName", ProcessusNew.fileUsed); System.out.println("Aucun des OK ..."); }*/ // if ( (requete.getParameter("fichier_sequence_alignement") != "") && (requete.getParameter("OK_submit") == "Load file") ) { // ProcessusNew.fileUsed = "File used : "+requete.getParameter("fichier_sequence_alignement"); // } else { // } session.setAttribute("fileName", "Copy/paste was used"); session.setAttribute("isCopyPaste", true); alignement = null; session.setAttribute("alignment",""); alignement = requete.getParameter("texte_sequence_alignement");   /** uploading a file is a little bit cmplicated with * servlet see "brouillon" part II */ if ( (alignement != null) && (!alignement.equals("")) ) { /** Getting data from text area. */ // alignement = // requete.getParameter("texte_sequence_alignement");   String aln;     try { // alignement = this.alignmentRecord(aln); FichierFasta myFastaFile = new FichierFasta(alignement); alignement = myFastaFile.getSequencesToString(); /** ICI, rajouter du code pour savoir si on a changer les T en U lors du new FichierFasta **/ session.setAttribute("status", null); } catch (Exception e) { try { FichierClustalW fileTemp = new FichierClustalW(System.currentTimeMillis()+".clustalW", new BufferedReader(new StringReader(alignement))); FichierFasta myFile = new FichierFasta(fileTemp.recupererSequences()); alignement = myFile.getSequencesToString(); session.setAttribute("status", null); } catch (Exception ef) { ef.printStackTrace(); session.setAttribute("status",new Integer(42)); session.setAttribute("error","Not a FASTA nor ClustalW Alignment (upload)."); alignement = null; } }           } else {       /* if (FichierFasta.isFastaAlignment(alignement)) { alignement = ProcessusNew.alignmentRecord(alignement); alignement = FichierFasta.ensureFastaAlignment(alignement); session.setAttribute("status",null); /** see end of current method (doPost) */ /* } else { session.setAttribute("status",new Integer(42)); session.setAttribute("error","Not a FASTA Alignment. "); alignement = null; } } else {*/       /** Error signal : no selection of alignment. */ session.setAttribute("status",new Integer(42)); session.setAttribute("error","No Alignment source. "); alignement = null; } /** for the results at end */ if (requete.getParameter("enregistrer_fasta") != null) { session.setAttribute("output", "FASTA"); } else { session.setAttribute("output", "Rnaviz"); }   /** Two (2) major ways in working next from for process : * - target sequence selection and parameters * with application choice (original use : 0 -> 1 -> [2 ->] 3 * - target sequence selection and palindromes indications, * then parameters and application choice : 0 -> 4 -> 5 -> [2 ->] 3 */ /** By the "other way" : sending to the second way of work ! * just comment to return to original way of work... */ //origineInterface = 0; //destinaInterface = 4; } if ( (origineInterface == 4) && (destinaInterface == 5) ){ /* if (requete.getParameter("OK_submit") == "Load file") { System.out.println("OK_submit = Load file"); ProcessusNew.fileUsed = requete.getParameter("fichier_sequence_alignement"); System.out.println(ProcessusNew.fileUsed); session.setAttribute("fileName", ProcessusNew.fileUsed); } else if (requete.getParameter("OK_submit") == "Load alignment") { System.out.println("OK_submit = Load alignment"); ProcessusNew.fileUsed = null; System.out.println(ProcessusNew.fileUsed); session.setAttribute("fileName", null); } else { session.setAttribute("fileName", ProcessusNew.fileUsed); System.out.println("Aucun des OK ..."); }*/ /** Prise en consideration du retour arriere depuis la fenetre de selection des sequences **/ if (requete.getParameter("OK_submit").equals("Load new alignment")) { // session.invalidate(); origineInterface = 4; destinaInterface = 6; } else { /** Fin de la prise en consideration du retour arriere depuise la fenetre des resultats **/ Sequence cible = new Sequence(); ListeBean bean = (ListeBean)session.getAttribute("generalbean"); // if (bean.getCible() == null) { /** cible selection remembrance. */ int choosenCible = Integer.parseInt(requete.getParameter("choose_cible")); // System.out.println("choosenCible = "+choosenCible); bean = (ListeBean)session.getAttribute("generalbean"); bean.setCible(choosenCible); cible = bean.getSequence(choosenCible); this.cibleOri = cible; session.setAttribute("cible",cible); session.setAttribute("nomcible",cible.getNom()); session.setAttribute("seqaligcible", ProcessusNew.decoupeString(cible.getSequence())); session.setAttribute("seqbasecible", ProcessusNew.decoupeString(cible.getSequenceBaseToString()));   ListeBean bestSequens = new ListeBean(); bestSequens.setCible(this.cibleOri); if (requete.getParameterValues(/* peut etre pb ici */"pdcfold_selection") == null) { /** default selection : all sequences */ for (int i = 0 ; i < bean.length() ; i++) { Sequence seqi = bean.getSequence(i); // System.out.println("Sequence ajoutee au bean : "+seqi.getSequence()); /** if (!seqi.equals(cible)) */ { bestSequens.addSequence(seqi); } } } else { /** selection by user */ String[] values = requete.getParameterValues("pdcfold_selection"); /** tarnsfert to int and check if target is selected */ int[] selection = new int[values.length]; boolean targetselected = false; for (int i = 0 ; i < values.length ; i++) { selection[i] = Integer.parseInt(values[i]); if ( (selection[i] == 0) && (i != 0) ) { targetselected = true; } } if (!targetselected) { bestSequens.addSequence(cible); } /** adding selected sequences */ for (int i = 0 ; i < selection.length ; i++) { Sequence seq_si = bean.getSequence(selection[i]); bestSequens.addSequence(seq_si); } }   this.bestSequensOri = bestSequens;   /** XXX BLACKBOX end selection for P-DCFold... */ session.setAttribute("bestSequens",bestSequens); session.setAttribute("bestSequensOri",this.bestSequensOri); session.setAttribute("length",this.bestSequensOri.length()-1); session.setAttribute("cible",this.cibleOri); session.setAttribute("nomcible",this.cibleOri.getNom()); session.setAttribute("seqaligcible", ProcessusNew.decoupeString(this.cibleOri.getSequence())); session.setAttribute("seqbasecible", ProcessusNew.decoupeString(this.cibleOri.getSequenceBaseToString()));         /** Dectection of user input for helixes. */ PalindromeListe userTabPal = new PalindromeListe(); int l = 1; while (requete.getParameter("helix_"+l) != null) { String begin_text = requete.getParameter("beginhelix_"+l); String endin_text = requete.getParameter("endinhelix_"+l); String lenin_text = requete.getParameter("leninhelix_"+l); if ( (!begin_text.equals("")) && ( (!endin_text.equals("")) && (!lenin_text.equals(""))) ) { int begin = Integer.parseInt(begin_text); int endin = Integer.parseInt(endin_text); int lenin = Integer.parseInt(lenin_text); if ( ( (begin > 0) && (endin < cible.length()) ) && ( (endin > begin) && (lenin < (endin-begin)) ) ){ short niv=1; Palindrome userPal = new Palindrome (begin-1 ,endin-1 ,lenin ,niv); /** setting scores sure to be selected */ userPal.setPertinence(500); /** 5*lenin */ userPal.setLongMut(500); userPal.setTaux(500); userPal.setScore(500); userPal.changer_conservation(100); userPal.setNombreMutationDouble(userPal.length()); userTabPal.addPalindrome(userPal); } } l++; } this.userPalindromesTable = userTabPal; String givenPalindromesHTML = ""; for (int i = 0 ; i < this.userPalindromesTable.length() ; i++) { Palindrome pal = this.userPalindromesTable.getPalindrome(i); givenPalindromesHTML += "<tr><td colspan=\"3\">"+(pal.getPositionDebut()+1)+"</td>\n" +"\t<td colspan=\"3\">"+(pal.getPositionFin()+1)+"</td>\n" +"\t<td colspan=\"3\">"+pal.length()+"</td></tr>\n"; } session.setAttribute("givenPalindromesHTML", givenPalindromesHTML); } } if ( (origineInterface == 0) && (destinaInterface == 4) ) { /* if (requete.getParameter("OK_submit") == "Load file") { System.out.println("OK_submit = Load file"); ProcessusNew.fileUsed = requete.getParameter("fichier_sequence_alignement"); System.out.println(ProcessusNew.fileUsed); session.setAttribute("fileName", ProcessusNew.fileUsed); } else if (requete.getParameter("OK_submit") == "Load alignment") { System.out.println("OK_submit = Load alignment"); ProcessusNew.fileUsed = null; System.out.println(ProcessusNew.fileUsed); session.setAttribute("fileName", null); } else { session.setAttribute("fileName", ProcessusNew.fileUsed); System.out.println("Aucun des OK ..."); }*/ // if ( (requete.getParameter("fichier_sequence_alignement") != "") && (requete.getParameter("OK_submit") == "Load file") ) { // ProcessusNew.fileUsed = "File used : "+requete.getParameter("fichier_sequence_alignement"); // } else { // if ( /*(requete.getParameter("texte_sequence_alignement") != "") && /*(requete.getParameter("texte_sequence_alignement") != "Put here the alignment in FASTA format... ") && */(requete.getParameter("OK_submit") == "Load alignment") ) {ProcessusNew.fileUsed = "Copy/paste was used.";} // } // session.setAttribute("fileName", ProcessusNew.fileUsed); alignement = null; session.setAttribute("alignment",""); alignement = requete.getParameter("texte_sequence_alignement");   /** uploading a file is a little bit cmplicated with * servlet see "brouillon" part II */ if ( (alignement != null) && (!alignement.equals("")) ) { /** Getting data from text area. */ // alignement = // requete.getParameter("texte_sequence_alignement");       try { // alignement = this.alignmentRecord(aln); FichierFasta myFastaFile = new FichierFasta(alignement); alignement = myFastaFile.getSequencesToString(); /** ICI, rajouter du code pour savoir si on a changer les T en U lors du new FichierFasta **/ session.setAttribute("status", null); } catch (Exception e) { try { FichierClustalW fileTemp = new FichierClustalW(System.currentTimeMillis()+".clustalW", new BufferedReader(new StringReader(alignement))); FichierFasta myFile = new FichierFasta(fileTemp.recupererSequences()); alignement = myFile.getSequencesToString(); session.setAttribute("status", null); } catch (Exception ef) { ef.printStackTrace(); session.setAttribute("status",new Integer(42)); session.setAttribute("error","Not a FASTA nor ClustalW Alignment (upload)."); alignement = null; } }                 } else { /** Error signal : no selection of alignment. */ session.setAttribute("status",new Integer(42)); session.setAttribute("error","No Alignment source. "); alignement = null; } /** for the results at end */ if (requete.getParameter("enregistrer_fasta") != null) { session.setAttribute("output", "FASTA"); } else { session.setAttribute("output", "Rnaviz"); }   /** Two (2) major ways in working next from for process : * - target sequence selection and parameters * with application choice (original use : 0 -> 1 -> [2 ->] 3 * - target sequence selection and palindromes indications, * then parameters and application choice : 0 -> 4 -> 5 -> [2 ->] 3 */ /** By the "other way" : sending to the second way of work ! * just comment to return to original way of work... */ //origineInterface = 4; //destinaInterface = 5; } /** ================================================================ */ /** By the "other way" : target selection then parameters and applications */ /** ================================================================ */ /** Cible sequence has been choosen : compute alignment and scores */ if ( ( (origineInterface == 1) || (origineInterface == 5) ) && (destinaInterface == 2) ) {   if (requete.getParameter("OK_submit").equals("Previous")) { origineInterface = 5; destinaInterface = 6; } else { float incertitude = Float.parseFloat(requete.getParameter("val_incertitude")); Sequence cible = new Sequence(); ListeBean bestSequensTemp = new ListeBean(); ListeBean bean = new ListeBean(); if (requete.getParameter("choose_cible") != null) { int choosenCible = Integer.parseInt(requete.getParameter("choose_cible")); bean = (ListeBean)session.getAttribute("generalbean"); bean.setCible(choosenCible); cible = bean.getSequence(choosenCible); session.setAttribute("cible",cible); ListeBean bestSequensOrig = (ListeBean)session.getAttribute("bestSequensOri"); bestSequensOrig.setCible(cible); this.bestSequensOri = bestSequensOrig; session.setAttribute("bestSequens",bestSequensOrig); session.setAttribute("bestSequensOri", bestSequensOrig); bestSequensTemp = this.bestSequensOri; } else { bestSequensTemp = (ListeBean)session.getAttribute("bestSequensOri"); } // bean = (ListeBean)session.getAttribute("generalbean"); session.setAttribute("bestSequens",bestSequensTemp); session.setAttribute("bestSequensOri", bestSequensTemp); ListeBean bestSequens = (ListeBean)session.getAttribute("bestSequens"); cible = bestSequens.getCible(); if (requete.getParameter("OK_submit").equals("P-DCFold")) {   // Sequence[] myList = bestSequens.getListe(); boolean cibleInSequences = false; for (int i=0; i<myList.length; i++) { // System.out.println(myList[i].equals(cible)); if (myList[i].equals(cible)) {cibleInSequences = true;} } if (!cibleInSequences) { bestSequens.addSequence(cible); } /** adding selected sequences */ // for (int i = 0 ; i < selection.length ; i++) { // Sequence seq_si = bean.getSequence(selection[i]); // bestSequens.addSequence(seq_si); // } } if ( ( (requete.getParameter("OK_submit").equals("SSCA")) || (requete.getParameter("OK_submit").equals("Run whole TFold")) ) || (requete.getParameter("OK_submit").equals("Run TFold step by step")) ){ // cible = new Sequence(); bean = (ListeBean)session.getAttribute("generalbean");     SequenceListe listeDesSeq = (ListeBean)session.getAttribute("bestSequensOri"); // SequenceListe listeDesSeq = bestSequensTemp; /** Computing things which needed to compute (SSCA algorithm)... */ /** copy/paste to avoid some changes on bean */ SequenceListe homologuous = new SequenceListe(); /** Prise en considération de toutes les séquences */ /* for (int i = 0 ; i < bean.length() ; i++) { if (listeDesSeq.has(bean.getSequence(i))) { homologuous.addSequence(bean.getSequence(i)); } }*/   // System.out.println("Taille de la liste des séquences : "+listeDesSeq.length());   for (int i=0; i<listeDesSeq.length(); i++) { if (!(cible.equals(listeDesSeq.getSequence(i)))) {homologuous.addSequence(listeDesSeq.getSequence(i));} }   // System.out.println("homologuous = "+homologuous);   homologuous.removeSequence(cible);   // System.out.println("homologuous sans séquence cible = "+homologuous);   /** Prise en considération des séquences sélectionnées */ // for (int i = 0 ; i < listeDesSeq.length() ; i++) // { homologuous.addSequence(listeDesSeq.getSequence(i)); } // homologuous.removeSequence(cible); /** Getting and change some parameters */ double maxHomology = Double.parseDouble(requete.getParameter("maxHomology")); double minHomology = Double.parseDouble(requete.getParameter("minHomology")); int nbMinSequences = Integer.parseInt(requete.getParameter("nbMinSequences")); int nbMaxSequences = Integer.parseInt(requete.getParameter("nbMaxSequences")); int delcrit = Integer.parseInt(requete.getParameter("dele_criteria")); int idecrit = Integer.parseInt(requete.getParameter("homo_criteria")); int homnum = Integer.parseInt(requete.getParameter("homo_numberus")); /** Checking compatibility /* between best identity and homology selection. */ // double ideaverage = (maxHomology+minHomology)/2; /*** REVOIR TEST INUTILE !!! */   // if (idecrit != ideaverage) { if ( (idecrit > maxHomology) && (idecrit < minHomology) ) { minHomology = idecrit-15; maxHomology = idecrit+15; } // } if ( (homnum > nbMaxSequences) && (homnum < nbMinSequences) ) { nbMinSequences = homnum;nbMaxSequences = homnum; } /** Change the value for algorithm (here SSCA then maybe TFold). */ /** XXX BLACKBOX begin SSCA : if P-DCFold only : not here...*/ this.maxPredictions = Integer.parseInt(requete.getParameter("numb_predictions")); if (requete.getParameter("much_predictions") == null) { this.muchpredictions = false; } else { this.muchpredictions = true; } if (requete.getParameter("search_pseudoknots") == null) { this.searchPseudoknots = false; } else { this.searchPseudoknots = true; } /** remembrering parameters given by user and computed... */ session.setAttribute("maxHomology",""+maxHomology); session.setAttribute("minHomology",""+minHomology); session.setAttribute("nbMinSequences",""+nbMinSequences); session.setAttribute("nbMaxSequences",""+nbMaxSequences); session.setAttribute("delcrit",""+delcrit); session.setAttribute("idecrit",""+idecrit); session.setAttribute("homnum",""+homnum); session.setAttribute("incertitude",""+incertitude); session.setAttribute("maxPredictions",""+this.maxPredictions); session.setAttribute("muchpredictions",""+this.muchpredictions); session.setAttribute("searchPseudoknots",""+this.searchPseudoknots);   /** XXX BLACKBOX SSCA use the "SSCA" distances computing... */ /** ListeBean inherits of SequenceListe : * possible conversion and cast... */ /** ==>> Here for selection in SSCA */ bestSequens = new ListeBean(); boolean selection = false; /** to get all sequences : just the line below to "false" * and removing to "some changes" */ if (requete.getParameter("OK_submit").equals("SSCA")) { selection = false; } /** SSCA not only : selection with "true" */ else { selection = true; }   SequenceListe bestSequensTMP = OriginAlgoStefanConverter.algoSSCA(cible,homologuous ,nbMinSequences,nbMaxSequences ,minHomology,maxHomology ,selection ,idecrit ,delcrit); bestSequens = new ListeBean();   // System.out.println("retour de algoSSCA = "+bestSequensTMP);   for (int i = 0 ; i < bestSequensTMP.length() ; i++) { bestSequens.addSequence(bestSequensTMP.getSequence(i)); } /** XXX BLACKBOX end SSCA */ /** some changes... */ bestSequens.removeSequence(cible); bestSequens.setCible(cible); /** for selection : first is old (unused), second is best... */ // bestSequens.computeContenuListe(); bestSequens.computePredictionsListes(homnum); bestSequens.setN(homnum); /** for some results in HTML format*/ bestSequens.computeEffectsInContenuListe(); /** recording selection made by SSCA... */ session.setAttribute("status",new Integer(3)); session.setAttribute("bestSequens",bestSequens); } /** * The special conditions below are to permit different ways of work. * Whole TFold<br> * SSCA only<br> * P-DCFold only<br> * Step by step TFold (default) */ if (requete.getParameter("OK_submit").equals("Run whole TFold")) { origineInterface = 2; /** change origine */ destinaInterface = 3; /** change destination */ session.setAttribute("TFold", "direct"); } else { session.setAttribute("TFold", "stop"); } if (requete.getParameter("OK_submit").equals("SSCA")) { session.setAttribute("SSCA", "only"); } else { session.setAttribute("SSCA", "notonly"); } if (requete.getParameter("OK_submit").equals("P-DCFold")) { origineInterface = 2; /** change origine */ destinaInterface = 3; /** change destination */ session.setAttribute("P-DCFold", "only"); /** normal process : which is the cible ? */ /* J'ai enlever ici la sélection des séquences */ /** Some values of interest... */ this.maxPredictions = Integer.parseInt(requete.getParameter("numb_predictions")); if (requete.getParameter("much_predictions") == null) { this.muchpredictions = false; } else { this.muchpredictions = true; } if (requete.getParameter("search_pseudoknots") == null) { this.searchPseudoknots = false; } else { this.searchPseudoknots = true; } /** end values of interest */ /** remembrering parameters given by user and computed... */ session.setAttribute("maxHomology","none"); session.setAttribute("minHomology","none"); session.setAttribute("nbMinSequences","none"); session.setAttribute("nbMaxSequences","none"); session.setAttribute("delcrit","none"); session.setAttribute("idecrit","none"); session.setAttribute("homnum","none"); session.setAttribute("incertitude",""+incertitude); session.setAttribute("maxPredictions",""+this.maxPredictions); session.setAttribute("muchpredictions",""+this.muchpredictions); session.setAttribute("searchPseudoknots",""+this.searchPseudoknots);   /* J'ai enlever ici le rajout des séquences de P-DCFold dans le bean et l'ajout des séquences dans la session */   } else { session.setAttribute("P-DCFold", "notonly"); } if (requete.getParameter("OK_submit").equals("Re-Align (ClustalW)")) { /*origineInterface = 2;destinaInterface = 9; */} } }   /** ================================================================ */ /** Homologuous sequences have been choosen : compute main algorithm */ if ( (origineInterface == 2) && (destinaInterface == 3) ) {   if (requete.getParameter("OK_submit").equals("Previous")) { origineInterface = 3; destinaInterface = 6; } else { if (requete.getParameter("OK_submit").equals("Load new alignment")) { // session.invalidate(); origineInterface = 3; destinaInterface = 6; session.setAttribute("fileName", "Copy/paste was used"); session.setAttribute("isCopyPaste", true); } else { double incer = (double)Float.parseFloat((session.getAttribute("incertitude")).toString()); SequenceListe[] listes = new SequenceListe[0]; ListeBean bestSequensTemp = new ListeBean(); ListeBean bean = new ListeBean(); Sequence cible = new Sequence(); if (requete.getParameter("choose_cible") != null) { int choosenCible = Integer.parseInt(requete.getParameter("choose_cible")); bean = (ListeBean)session.getAttribute("generalbean"); bean.setCible(choosenCible); cible = bean.getSequence(choosenCible); session.setAttribute("cible",cible); ListeBean bestSequensOrig = (ListeBean)session.getAttribute("bestSequensOri"); bestSequensOrig.setCible(cible); this.bestSequensOri = bestSequensOrig; session.setAttribute("bestSequens",bestSequensOrig); session.setAttribute("bestSequensOri", bestSequensOrig); bestSequensTemp = this.bestSequensOri; } else { bestSequensTemp = (ListeBean)session.getAttribute("bestSequensOri"); } ListeBean bestSequens = bestSequensTemp;   String res = ""/** ,more_res = ""*/; String Logs = "";   /** for plain results to be save in bean */ String more_res_plain = "\nParameters\n"; more_res_plain += "----------\n\n"; more_res_plain += "Minimum Homology: "+session.getAttribute("minHomology")+"\n"; more_res_plain += "Maximum Homology: "+session.getAttribute("maxHomology")+"\n"; more_res_plain += "Minimal number of sequences: "+session.getAttribute("nbMinSequences")+"\n"; more_res_plain += "Maximal number of sequences: "+session.getAttribute("nbMaxSequences")+"\n"; more_res_plain += "Deletion criteria: "+session.getAttribute("delcrit")+"\n"; more_res_plain += "Homology criteria: "+session.getAttribute("idecrit")+"\n"; more_res_plain += "Optimal number (n): "+session.getAttribute("homnum")+"\n"; more_res_plain += "Maximum structures: "+session.getAttribute("maxPredictions")+"\n"; more_res_plain += "Several predictions: "+session.getAttribute("muchpredictions")+"\n"; more_res_plain += "Search pseudoKnots: "+session.getAttribute("searchPseudoknots")+"\n"; more_res_plain += "Resolution value: "+session.getAttribute("incertitude")+"\n"; more_res_plain += "\n"; // String Logs="";   if ( (requete.getParameter("optimalresult") == null) && (session.getAttribute("TFold").equals("stop")) ){ /** computing non-optimal results : selection */ // ListeBean bean = // (ListeBean)session.getAttribute("generalbean"); bestSequens = (ListeBean)session.getAttribute("bestSequens"); cible = bestSequens.getCible(); boolean tfold = true; if (session.getAttribute("P-DCFold").equals("only")) { tfold = false; } /** P-DCFold : see previous part : * bestSequens is all sequences without target... */ SequenceListe[] SSCAlistes = bestSequens.getMore(tfold);   /** (Sequence)session.getAttribute("cible"); */ int countNull = 0; /** To catch the selection of homologuous sequences ! */ if (session.getAttribute("P-DCFold").equals("notonly")) { /** Case of multiple selection form of TFold... */ SequenceListe[] seqtmp = new SequenceListe[0]; int l = 1; while (requete.getParameterValues("chooseHomo_"+l) != null) { /** catch if predictions are selected... */ if ( (requete.getParameter("selectHomo_"+l) != null) && (requete.getParameter("selectHomo_"+l).equals("on")) ) { countNull++; SequenceListe mortmp = SSCAlistes[(l-1)]; /** catch if list is not in... */ if (!mortmp.isIn(seqtmp)) { /** copy the new list... */ SequenceListe[] seqtmpbis = new SequenceListe[seqtmp.length+1]; for (int m = 0 ; m < seqtmp.length ; m++) { seqtmpbis[m] = seqtmp[m]; } seqtmpbis[seqtmp.length] = mortmp; seqtmp = seqtmpbis; } } l++; } listes = seqtmp; } else { /** running only P-DCFold with submitted sequences except cible */ countNull = 1; listes = new SequenceListe[1]; // bestSequens.addSequence(cible); bestSequens.removeSequence(cible); listes[0] = bestSequens; } if (countNull > 0) { /** a selection has been made by user... */ session.setAttribute("status",new Integer(4)); session.setAttribute("listes",listes);   /** calculating here... */ /** XXX BLACKBOX begin main launch */ /** Initializing variables */ // listes = bestSequens.getMore(false); OriginAlgorithmsStefan algo = new OriginAlgorithmsStefan(this.maxPredictions ,this.muchpredictions ,this.searchPseudoknots); algo.setUserPalindromesTableHTML(session.getAttribute("givenPalindromesHTML").toString()); if (incer != 0.) {algo.setIncertitude(incer);} /** adding some infos by user... */ algo.setUserPalindromesTable(this.userPalindromesTable); /** computing is here : here optimal is false... */ // Boolean TinU = (Boolean)session.getAttribute("TinU"); // System.out.println("TinU = "+TinU); algo.launch(cible, listes, false/*, TinU*/); /** Working about what will be on screen */ res = algo.getResultsHTML(); /** Here for recording */ bestSequens.setResults(cible, algo.getRecordingStructures(cible)); bestSequens.setResults(session.getAttribute("fileName").toString()+"\n\n"+algo.getResults()+more_res_plain); /** XXX BLACKBOX end main launch */   //* LOGS */ Logs = algo.logs+"</td></table>"; //* LOGS */ session.setAttribute("logs", Logs);   } } else { /** computing optimal results // whole TFold */ /** (session.getAttribute("TFold").equals("direct")) */ bestSequens = (ListeBean)session.getAttribute("bestSequens"); cible = bestSequens.getCible(); bestSequens.setCible(cible);   /** XXX BLACKBOX begin optimal... */ /** Initializing variables */ listes = bestSequens.getMore(true); // Logs += "<br><table><tr><td>On instancie l'algo ...</td>"; OriginAlgorithmsStefan algo = new OriginAlgorithmsStefan(this.maxPredictions ,this.muchpredictions ,this.searchPseudoknots); // Logs += "<td>On met la valeur de l'incertitude entré sauf s'il elle est nulle.</td>"; algo.setUserPalindromesTableHTML(session.getAttribute("givenPalindromesHTML").toString()); if (incer != 0.) {algo.setIncertitude(incer);} /** adding some infos by user... */ algo.setUserPalindromesTable(this.userPalindromesTable); /** computing is here : here optimal is TRUE... */ // Logs += "<td>On lance l'algo.</td></tr></table><br>"; // Boolean TinU = (Boolean)session.getAttribute("TinU"); // System.out.println("TinU = "+TinU); algo.launch(cible, listes, true/*, TinU*/); /** Working about what will be on screen */ res = algo.getResultsHTML(); /** Here for recording */ bestSequens.setResults(cible, algo.getRecordingStructures(cible)); bestSequens.setResults(session.getAttribute("fileName").toString()+"\n\n"+algo.getResults()+more_res_plain); /** XXX BLACKBOX end optimal */ //* LOGS */ Logs = algo.logs+"</table>"; } res += "<br><table><tr><td><table style=\"border:1px solid grey;\">\n" +"<th colspan=\"2\">Parameters: </th>\n"; /** remembering parameters given by user and computed... */ res += "<tr><td>Minimum Homology: </td><td>"+session.getAttribute("minHomology")+"</td></tr>\n"; res += "<tr><td>Maximum Homology: </td><td>"+session.getAttribute("maxHomology")+"</td></tr>\n"; res += "<tr><td>Minimal number of sequences: </td><td>"+session.getAttribute("nbMinSequences")+"</td></tr>\n"; res += "<tr><td>Maximal number of sequences: </td><td>"+session.getAttribute("nbMaxSequences")+"</td></tr>\n"; res += "<tr><td>Deletion criteria: </td><td>"+session.getAttribute("delcrit")+"</td></tr>\n"; res += "<tr><td>Homology criteria: </td><td>"+session.getAttribute("idecrit")+"</td></tr>\n"; res += "<tr><td>Optimal number (n): </td><td>"+session.getAttribute("homnum")+"</td></tr>\n"; res += "<tr><td>Maximum structures: </td><td>"+session.getAttribute("maxPredictions")+"</td></tr>\n"; res += "<tr><td>Several predictions: </td><td>"+session.getAttribute("muchpredictions")+"</td></tr>\n"; res += "<tr><td>Search pseudoKnots: </td><td>"+session.getAttribute("searchPseudoknots")+"</td></tr>\n"; res += "<tr><td>Resolution: </td><td>"+incer+"</td></tr>\n"; res += "</table></td><td style=\"padding-left:20px;\">\n"; // res += more_res; res += "</td></tr></table>\n"; /** remember results in session */ // session.setAttribute("res", res); session.setAttribute("results", res); /** for VARNA and Pseudoviewer in PDC-FOLD and T-FOLD *@author Mederich Besnard (2009)*/ RetrieveFormat rf = new RetrieveFormat(); rf.retrieveBracket(bestSequens.getBracketFile()); rf.retrievePositionPaire(bestSequens.getPositionspairedFile()); session.setAttribute("rf",rf); //* LOGS */ session.setAttribute("logs", Logs); } } } if ( ( (origineInterface == 4) || (origineInterface == 5) || (origineInterface == 3) || (origineInterface == 2) ) && (destinaInterface == 6) ) { String newDest = requete.getParameter("OK_submit"); newDest = newDest.replaceAll(" ", ""); // System.out.println("newDest = "+newDest); if (newDest.equals("Loadnewalignment")) { session.setAttribute("isCopyPaste", null); // session.invalidate(); origineInterface = -1; destinaInterface = 0; /** fileUsed = "Copy/paste was used."; isCopyPaste = true; session.setAttribute("fileName", fileUsed); session.setAttribute("isCopyPaste", isCopyPaste); **/ // System.out.println("Loadnewalignment, origineInterface = -1 et destinaInterface = 0"); } else if (newDest.equals("Previous") && ((origineInterface == 3) || (origineInterface == 2))) { if ( (session.getAttribute("TFold").equals("stop")) && (origineInterface == 3) && (session.getAttribute("P-DCFold").equals("notonly")) ) { origineInterface = 1; destinaInterface = 2; } else { origineInterface = 4; destinaInterface = 5; } // System.out.println("Previous, origineInterface = 4 et destinaInterface = 5"); } else if (newDest.equals("Previous") && (origineInterface == 5)) { origineInterface = 0; destinaInterface = 4; } else { /** fileUsed = "Copy/paste was used."; isCopyPaste = true; session.setAttribute("fileName", fileUsed); session.setAttribute("isCopyPaste", isCopyPaste); **/ origineInterface = -1; destinaInterface = 0; // System.out.println("1035 : Imposible Choice."); } }   }   /** ================================================================ */ /** ================================================================ */ /** ================================================================ */ /** ================================================================ */ /** ================================================================ */ /** MAIN TREATMENT HAD ENDED... */ /** To the next step... */   String pageDestination = "/interblackbox/test.jsp"; if ( (session.getAttribute("status") == null) ) { if ( (alignement != null) && (!alignement.equals(""))) { /** Bean use in destination : do not forget * elements in top of page and in... */ ListeBean bean = new ListeBean(); alignement += "\n\n"; /** XXX KNOWN BUG to avoid bug on last line */ // alignement = FichierFasta.ensureFastaAlignment(alignement); String[] tempo = alignement.split("\n"); String nom = "",sequence = ""; int commonlength = 0; if (tempo.length >= 2) { commonlength = tempo[1].length(); } for (int i = 0 ; (i < tempo.length) && (session.getAttribute("status") == null) ; i++) { if (i%2 == 0) { nom = tempo[i]; } /** name on odd / even line */ else { sequence = tempo[i]; /* if ( ( (i >= 2) && (i < (tempo.length-1)) ) && (commonlength != sequence.length()) ) { /** XXX KNOWN BUG sometimes bugs here : checking length */ /** alignment file must be : * - name on odd numbered lines (1,3,5,7...) * - aligned sequences on even numbered lines (2,4,6,8...) * - aligned sequences of same length * see the example file tmrna.fasta in web interface. */ /* session.setAttribute("status",new Integer(42)); session.setAttribute("error" ,"Alignment is not correct (length) !"); }*/ bean.addSequence(new Sequence(nom,sequence)); nom = "";sequence = ""; } } bean.computeContenuListe(); /** transmission */ if (session.getAttribute("status") == null) { session.setAttribute("status",new Integer(2)); session.setAttribute("alignment",alignement); session.setAttribute("generalbean",bean); session.setAttribute("length",""+bean.length()); } } else { /* if (alignement == null) { System.out.println("*****alignment is NULL* !!"); } else { if (alignement.equals("")) { System.out.println("*****alignment is EMPTY !!"); } } */ session.setAttribute("status",new Integer(42)); session.setAttribute("error","Alignment is not correct (upload) !"); } } /********************************************/ /*** PART FOR STRUCTURE COMPARISON IS HERE***/ /********************************************/ if(origineInterface==10 && destinaInterface==11){ /** Where you come, where you go**/ session.setAttribute("status",new Integer(4)); /** For initiate variables threatment**/ String reference = requete.getParameter("texte_sequence_reference"); String structure = requete.getParameter("texte_sequence_predicted"); String tailleString = requete.getParameter("taille"); int taillePerf=0;//we don't calcul MCC by default if(!tailleString.isEmpty()){// size enter, we calcul MCC try{ taillePerf = Integer.parseInt(tailleString); if(taillePerf<0){//wrong size session.setAttribute("status",new Integer(42)); session.setAttribute("error","You paste a wrong size.."); } }catch (NumberFormatException e){ session.setAttribute("status",new Integer(42)); session.setAttribute("error","You paste a wrong size.."); } }else{//don't calcul MCC taillePerf=-1; } /** threatment **/ Performance perf; try{ perf = new Performance(reference , structure , taillePerf); session.setAttribute("perf",perf); }catch (Exception e) { e.printStackTrace(); /** If Load problem **/ session.setAttribute("status",new Integer(42)); session.setAttribute("error","You paste a wrong format.."); }     }   /*********************************************/ /********END FOR STRUCTURE COMPARISON*********/ /*********************************************/ /******************************************************************************************************************/   /*********************************************/ /********BEGIN FOR GFOLD**********************/ /*********************************************/     if(origineInterface==0 && destinaInterface==13){ // CASE OF FILE UPLOADED session.setAttribute("status",new Integer(4)); }   /*********************************************/ /******** END FOR GFOLD ********************/ /*********************************************/     /******************************************************************************************************************/       if (session.getAttribute("status").equals(new Integer(42))) { /** If an error, we go back ... */ pageDestination = ProcessusNew.getScriptDestination(origineInterface); } else { /** ... else we continue to the destination ! */ pageDestination = ProcessusNew.getScriptDestination(destinaInterface); } RequestDispatcher rd = this.getServletContext().getRequestDispatcher(pageDestination); try { rd.forward(requete,reponse); } catch (ServletException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } }   /** * To get the page where to go... * @param numInterface number of the page * @return (String) Path to the JSP page to go... */ private static String getScriptDestination(int numInterface) { String scriptDestination = "/interblackbox/test.jsp"; switch(numInterface){ /** go to origine or destination */ case(-1):scriptDestination = "/interblackbox/formdefile.jsp";break; case(0):scriptDestination = "/interblackbox/formdepart.jsp";break; case(1):scriptDestination = "/interblackbox/formselectioncible.jsp";break; case(2):scriptDestination = "/interblackbox/formselectionhomol.jsp";break; case(3):scriptDestination = "/interblackbox/formresults.jsp";break; case(4):scriptDestination = "/interblackbox/formselectioncibleonly.jsp";break; case(5):scriptDestination = "/interblackbox/formselectionparameters.jsp";break; case(6):scriptDestination = "/interblackbox/formselectionparameters.jsp";break; case(9):scriptDestination = "/interblackbox/clustalwredirection.jsp";break; case(10):scriptDestination = "/interblackbox/comparaison_performance_submission.jsp";break; case(11):scriptDestination = "/interblackbox/comparaison_performance_results.jsp";break; case(12):scriptDestination = "/interblackbox/gFold/resultat.jsp";break; case(13):scriptDestination = "/interblackbox/gFold/resultat.jsp";break; default:scriptDestination = "/interblackbox/test.jsp"; } return scriptDestination; }   /** * Making the recording of alignment in a file. * Could be done with FichierFasta. * @param alignement (String) * @return (String) alignement * @see alonefichiers.FichierFasta * @since July / August 2008 */   /** * This method to cut a String by 80 characters length substring. * @param chaineDecoupe (String) * @return (String) * @see Processus#doPost(HttpServletRequest, HttpServletResponse) */ private static String decoupeString(String chaineDecoupe) { String tempo = ""; int i; for ( i = 0 ; i+80 < chaineDecoupe.length() ; i = (i+80)) { tempo += chaineDecoupe.substring(i,i+80)+"<br>\n"; } if ( (i < chaineDecoupe.length()) && (i+80 >= chaineDecoupe.length()) ) { tempo += chaineDecoupe.substring(i,chaineDecoupe.length())+"<br>\n"; } return tempo; }   }

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ya rien en PJ et rien dans ton post .. !???

Désolé la classe était trop importante j'ai du supprimer des centaines de lignes de commentaires,j 'ai édité au dessus.

Alors dans un premier temps, vérifie tes accolades { } dans la méthode doPost.. il doit t'en manquer quelques unes ..
Tu peux utiliser eclipse par exemple qui te facilitera la tache avec son editeur, où tu peux regrouper chaque bloc pour voir où c'est que t'as oublié des accolades.
Ensuite tu pourras y voir plus clair ..

j'ai modifié les accolades manquantes, seulement je suis toujours bloqué, pourquoi y'a t'il un conflit lorsque je met 2 RequestDispatcher dans mon test ? Car les 2 marches indépendamments mais pas en même temps :?