docroot/WEB-INF/src/it/infn/ct/g_hmmer_portlet.java
void updateFiles(AppInput appInput) {
        // First of all remomve all possible ^Ms from Strings
        appInput.inputFileText=appInput.inputFileText.replaceAll("\r","");
        // Now save string content into files
        // This must be done for each input sandbox file
        try {            
            appInput.inputSandbox_inputFile="/tmp/"
                                                +appInput.timestamp
                                                +"_"
                                                +appInput.username
                                                +"_input_file.txt"
                                                ;
            FileWriter fwInput=new FileWriter(appInput.inputSandbox_inputFile);
            BufferedWriter bwInput = new BufferedWriter(fwInput);
            bwInput.write(appInput.inputFileText);
            bwInput.close();
        }
        catch (Exception e) {
            _log.error("Caught exception while creating inputSandbox files");
        }
    }
/**
     * Before to submit the job this method creates the inputSandbox files
     * starting from users' input fields (textareas or uploaded files)
     * 
     * @param appInput  AppInput instance storing the jobSubmission data
     */
Before to submit the job this method creates the inputSandbox files
starting from users' input fields (textareas or uploaded files)

@param appInput  AppInput instance storing the jobSubmission data
Before to submit the job this method creates the inputSandbox files starting from users ' input fields ( textareas or uploaded files ) @param appInput AppInput instance storing the jobSubmission data
void updateFiles(AppInput appInput) {
        appInput.inputFileText=appInput.inputFileText.replaceAll("\r","");
        try {            
            appInput.inputSandbox_inputFile="/tmp/"
                                                +appInput.timestamp
                                                +"_"
                                                +appInput.username
                                                +"_input_file.txt"
                                                ;
            FileWriter fwInput=new FileWriter(appInput.inputSandbox_inputFile);
            BufferedWriter bwInput = new BufferedWriter(fwInput);
            bwInput.write(appInput.inputFileText);
            bwInput.close();
        }
        catch (Exception e) {
            _log.error("Caught exception while creating inputSandbox files");
        }
    }
void updateFiles ( AppInput appInput ) { appInput . inputFileText = appInput . inputFileText . replaceAll ( "\r" , "" ) ; try { appInput . inputSandbox_inputFile = "/tmp/" + appInput . timestamp + "_" + appInput . username + "_input_file.txt" ; FileWriter fwInput = new FileWriter ( appInput . inputSandbox_inputFile ) ; BufferedWriter bwInput = new BufferedWriter ( fwInput ) ; bwInput . write ( appInput . inputFileText ) ; bwInput . close ( ) ; } catch ( Exception e ) { _log . error ( "Caught exception while creating inputSandbox files" ) ; } }
Before to submit the job this method creates the inputSandbox files
 starting from users' input fields (textareas or uploaded files)
Before to submit the job this method creates the inputSandbox files starting from users ' input fields ( textareas or uploaded files )
// First of all remomve all possible ^Ms from Strings // Now save string content into files // This must be done for each input sandbox file