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java.lang.Object | +--org.emboss.jemboss.server.JembossAuthServer
Jemboss Authenticated Server for SOAP
| Field Summary | |
| (package private)  java.lang.String | acdDirToParse | 
| (package private)  java.lang.String | embossBin | 
| (package private)  java.lang.String | embossData | 
| (package private)  java.lang.String | embossPath | 
| private  java.lang.String[] | env | 
| private  java.lang.String | environ | 
| private  java.lang.String | errorLog | 
| private  java.lang.String | fs | 
| (package private)  JembossParams | jp | 
| private  java.lang.String | logFile | 
| (package private)  java.lang.String | plplot | 
| private  java.lang.String | ps | 
| private  java.lang.String | tmproot | 
| Constructor Summary | |
| JembossAuthServer() | |
| Method Summary | |
|  java.lang.String | about() | 
|  java.lang.String | abouturl() | 
| private  void | appendToLogFile(java.lang.String logEntry,
                java.lang.String logFileName)Appends a log entry to the log file | 
|  java.lang.String | appversion() | 
|  java.util.Vector | call_ajax(java.lang.String fileContent,
          java.lang.String seqtype)Uses JNI to calculate sequence attributes using EMBOSS library call. | 
|  java.util.Vector | call_ajax(java.lang.String fileContent,
          java.lang.String seqtype,
          java.lang.String userName,
          byte[] passwd)Uses JNI to calculate sequence attributes using EMBOSS library call. | 
|  java.lang.Object | clone() | 
|  java.util.Vector | delete_saved_results(java.lang.String project,
                     java.lang.String cl,
                     java.lang.String userName,
                     byte[] passwd)Private server Deletes a projects saved results. | 
|  java.lang.String | docurl() | 
| private  java.util.Hashtable | getHashtable(java.util.Vector v) | 
|  java.util.Vector | getWossname()Returns the output of the EMBOSS utility wossname | 
|  java.lang.String | helpurl() | 
|  java.util.Vector | list_saved_results(java.lang.String userName,
                   byte[] passwd)Private Server List of the saved results on the server. | 
| private  java.util.Vector | loadFilesContent(Ajax aj,
                 java.lang.String userName,
                 byte[] passwd,
                 java.io.File projectDir,
                 java.lang.String project,
                 java.util.Vector result,
                 java.util.Hashtable inFiles)Reads in files from EMBOSS output | 
|  java.lang.String | name() | 
| private  java.lang.String | quoteMe(java.lang.String s)Quote all tokens ready for shell scripts | 
| private  java.util.Vector | returnError(Ajax aj,
            java.lang.String msg)Report the stderr and stdout to error logs | 
|  java.util.Vector | run_prog(java.lang.String embossCommand,
         java.lang.String options,
         java.util.Hashtable inFiles,
         java.lang.String userName,
         byte[] passwd)Private Authenticated Server Run an EMBOSS application | 
|  java.util.Vector | run_prog(java.lang.String embossCommand,
         java.lang.String options,
         java.util.Vector inFiles,
         java.lang.String userName,
         byte[] passwd) | 
| private  void | runAsBatch(Ajax aj,
           java.lang.String userName,
           byte[] passwd,
           java.lang.String project,
           java.lang.String embossCommand) | 
| private  void | runAsGNQSBatch(Ajax aj,
               java.lang.String userName,
               byte[] passwd,
               java.lang.String project,
               java.lang.String embossCommand)Submit to a Generic NQS batch queue. | 
| private  void | runAsPBSBatch(Ajax aj,
              java.lang.String userName,
              byte[] passwd,
              java.lang.String project,
              java.lang.String embossCommand)Submit to a OpenPBS batch queue. | 
|  java.util.Vector | save_project_file(java.lang.String project,
                  java.lang.String filename,
                  java.lang.String notes,
                  java.lang.String userName,
                  byte[] passwd)Private server Save a file to a project directory on the server. | 
|  java.util.Hashtable | servicedesc() | 
|  java.util.Vector | show_acd(java.lang.String appName)Retrieves the ACD file of an application. | 
|  java.util.Vector | show_db()Returns the databases held on the server | 
|  java.util.Vector | show_help(java.lang.String applName)Returns the help for an application as given by 'tfm' | 
|  java.util.Vector | show_saved_results(java.lang.String project,
                   java.lang.String cl,
                   java.lang.String userName,
                   byte[] passwd)Private Server Returns the results for a saved project. | 
|  java.util.Vector | update_result_status(java.lang.String prog,
                     java.lang.String opt,
                     java.util.Hashtable resToQuery,
                     java.lang.String userName,
                     byte[] passwd) | 
|  java.util.Vector | update_result_status(java.lang.String prog,
                     java.lang.String opt,
                     java.util.Vector resToQuery,
                     java.lang.String userName,
                     byte[] passwd)Used to provide information on the batch/background processes. | 
| private  boolean | verifyUser(Ajax aj,
           java.lang.String userName,
           byte[] passwd,
           java.util.Vector res) | 
|  java.lang.String | version() | 
| Methods inherited from class java.lang.Object | 
| equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait | 
| Field Detail | 
private java.lang.String tmproot
private java.lang.String logFile
private java.lang.String errorLog
private java.lang.String fs
private java.lang.String ps
JembossParams jp
java.lang.String plplot
java.lang.String embossData
java.lang.String embossBin
java.lang.String embossPath
java.lang.String acdDirToParse
private java.lang.String[] env
private java.lang.String environ
| Constructor Detail | 
public JembossAuthServer()
| Method Detail | 
public java.lang.String name()
public java.lang.String version()
public java.lang.String appversion()
public java.lang.String about()
public java.lang.String helpurl()
public java.lang.String abouturl()
public java.lang.String docurl()
public java.util.Hashtable servicedesc()
public java.util.Vector show_acd(java.lang.String appName)
public java.util.Vector getWossname()
public java.util.Vector show_help(java.lang.String applName)
public java.util.Vector call_ajax(java.lang.String fileContent,
                                  java.lang.String seqtype,
                                  java.lang.String userName,
                                  byte[] passwd)
public java.util.Vector call_ajax(java.lang.String fileContent,
                                  java.lang.String seqtype)
public java.util.Vector show_db()
public java.util.Vector run_prog(java.lang.String embossCommand,
                                 java.lang.String options,
                                 java.util.Vector inFiles,
                                 java.lang.String userName,
                                 byte[] passwd)
private java.util.Hashtable getHashtable(java.util.Vector v)
public java.util.Vector run_prog(java.lang.String embossCommand,
                                 java.lang.String options,
                                 java.util.Hashtable inFiles,
                                 java.lang.String userName,
                                 byte[] passwd)
private java.lang.String quoteMe(java.lang.String s)
private void runAsPBSBatch(Ajax aj,
                           java.lang.String userName,
                           byte[] passwd,
                           java.lang.String project,
                           java.lang.String embossCommand)
private void runAsGNQSBatch(Ajax aj,
                            java.lang.String userName,
                            byte[] passwd,
                            java.lang.String project,
                            java.lang.String embossCommand)
private void runAsBatch(Ajax aj,
                        java.lang.String userName,
                        byte[] passwd,
                        java.lang.String project,
                        java.lang.String embossCommand)
public java.util.Vector show_saved_results(java.lang.String project,
                                           java.lang.String cl,
                                           java.lang.String userName,
                                           byte[] passwd)
public java.util.Vector save_project_file(java.lang.String project,
                                          java.lang.String filename,
                                          java.lang.String notes,
                                          java.lang.String userName,
                                          byte[] passwd)
public java.util.Vector delete_saved_results(java.lang.String project,
                                             java.lang.String cl,
                                             java.lang.String userName,
                                             byte[] passwd)
public java.util.Vector list_saved_results(java.lang.String userName,
                                           byte[] passwd)
private void appendToLogFile(java.lang.String logEntry,
                             java.lang.String logFileName)
private java.util.Vector loadFilesContent(Ajax aj,
                                          java.lang.String userName,
                                          byte[] passwd,
                                          java.io.File projectDir,
                                          java.lang.String project,
                                          java.util.Vector result,
                                          java.util.Hashtable inFiles)
public java.util.Vector update_result_status(java.lang.String prog,
                                             java.lang.String opt,
                                             java.util.Vector resToQuery,
                                             java.lang.String userName,
                                             byte[] passwd)
public java.util.Vector update_result_status(java.lang.String prog,
                                             java.lang.String opt,
                                             java.util.Hashtable resToQuery,
                                             java.lang.String userName,
                                             byte[] passwd)
private boolean verifyUser(Ajax aj,
                           java.lang.String userName,
                           byte[] passwd,
                           java.util.Vector res)
private java.util.Vector returnError(Ajax aj,
                                     java.lang.String msg)
public final java.lang.Object clone()
                             throws java.lang.CloneNotSupportedException
clone in class java.lang.Objectjava.lang.CloneNotSupportedException| 
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