org.emboss.jemboss.server
Class JembossServer

java.lang.Object
  org.emboss.jemboss.server.JembossServer

public class JembossServer

extends java.lang.Object

Jemboss Non-authenticated Server for Apache Axis (SOAP) web services

Field Summary

(package private) java.lang.String	acdDirToParse acd directory
(package private) java.lang.String	embossBin emboss binary directory
(package private) java.lang.String	embossData emboss data directory
(package private) java.lang.String	embossPath emboss path
private java.lang.String[]	envp emboss run environment
private java.lang.String[]	envp_emboss emboss run environment
private java.lang.String	fs file separator
private java.lang.String	homeDirectory user home directory
(package private) JembossParams	jp jemboss properties
(package private) java.lang.String	plplot plplot path
private java.lang.String	tmproot results directory
private java.io.File	tmprootDir results directory
private java.lang.String	username user name

Constructor Summary

JembossServer()

Method Summary

java.lang.String	about()
java.lang.String	abouturl()
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) Uses JNI to calculate sequence attributes using EMBOSS library call.
java.lang.Object	clone()
private void	createFinishedFile(java.lang.String project) Creates a file named "finished" in the project directory, that contains a time stamp.
java.util.Vector	delete_saved_results(java.lang.String project, java.lang.String cl) Deletes a projects saved results.
java.util.Vector	delete_saved_results(java.lang.String project, java.lang.String cl, java.lang.String userName) Deletes a projects saved results.
java.lang.String	docurl()
private java.util.Hashtable	getHashtable(java.util.Vector v) Convert contents from a Vector to a Hashtable
java.util.Vector	getWossname() Returns the output of the EMBOSS utility wossname
java.lang.String	helpurl()
java.util.Vector	list_saved_results() List of the saved results on the server.
java.util.Vector	list_saved_results(java.lang.String userName) List of the saved results on the server.
private java.util.Vector	loadFilesContent(java.io.File projectDir, java.lang.String project, java.util.Vector result, java.util.Hashtable inFiles) Reads in files from EMBOSS output
private java.util.Vector	loadPNGContent(java.io.File projectDir, java.lang.String project, java.util.Vector result) Reads in png files from EMBOSS output
java.lang.String	name()
protected static byte[]	readByteFile(java.lang.String filename) Read a file into a byte array.
java.util.Vector	run_prog(java.lang.String embossCommand, java.lang.String options, java.util.Hashtable inFiles) Run an EMBOSS application
java.util.Vector	run_prog(java.lang.String embossCommand, java.lang.String options, java.lang.String[] inFiles) 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) Run an EMBOSS application
java.util.Vector	save_project_file(java.lang.String project, java.lang.String filename, java.lang.String notes, java.lang.String userName) 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) Returns the results for a saved project.
java.util.Vector	show_saved_results(java.lang.String project, java.lang.String cl, java.lang.String userName) 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) Used to provide information on the batch/background processes.
java.util.Vector	update_result_status(java.lang.String prog, java.lang.String opt, java.util.Hashtable resToQuery, java.lang.String userName) Used to provide information on the batch/background processes.
java.util.Vector	update_result_status(java.lang.String prog, java.lang.String opt, java.util.Vector resToQuery, java.lang.String userName) Used to provide information on the batch/background processes.
java.lang.String	version()

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

fs

private java.lang.String fs

file separator

jp

JembossParams jp

jemboss properties

plplot

java.lang.String plplot

plplot path

embossData

java.lang.String embossData

emboss data directory

embossBin

java.lang.String embossBin

emboss binary directory

embossPath

java.lang.String embossPath

emboss path

acdDirToParse

java.lang.String acdDirToParse

acd directory

homeDirectory

private java.lang.String homeDirectory

user home directory

username

private java.lang.String username

user name

tmproot

private java.lang.String tmproot

results directory

tmprootDir

private java.io.File tmprootDir

results directory

envp_emboss

private java.lang.String[] envp_emboss

emboss run environment

envp

private java.lang.String[] envp

emboss run environment

Constructor Detail

JembossServer

public JembossServer()

Method Detail

name

public java.lang.String name()

version

public java.lang.String version()

appversion

public java.lang.String appversion()

about

public java.lang.String about()

helpurl

public java.lang.String helpurl()

abouturl

public java.lang.String abouturl()

docurl

public java.lang.String docurl()

servicedesc

public java.util.Hashtable servicedesc()

show_acd

public java.util.Vector show_acd(java.lang.String appName)

Retrieves the ACD file of an application.

Parameters:

appName - application name

Returns:

ACD string

getWossname

public java.util.Vector getWossname()

Returns the output of the EMBOSS utility wossname

Returns:

wossname output

show_help

public java.util.Vector show_help(java.lang.String applName)

Returns the help for an application as given by 'tfm'

Parameters:

applName - application name

Returns:

help

call_ajax

public java.util.Vector call_ajax(java.lang.String fileContent,
                                  java.lang.String seqtype,
                                  java.lang.String userName)

Uses JNI to calculate sequence attributes using EMBOSS library call.

Parameters:

fileContent - sequence filename or database entry

seqtype - sequence type (seqset/sequence)

userName - username

Returns:

sequence length, weight & type (protein/nucleotide)

call_ajax

public java.util.Vector call_ajax(java.lang.String fileContent,
                                  java.lang.String seqtype)

Uses JNI to calculate sequence attributes using EMBOSS library call.

Parameters:

fileContent - sequence filename or database entry

seqtype - sequence type (seqset/sequence)

Returns:

sequence length, weight & type (protein/nucleotide)

show_db

public java.util.Vector show_db()

Returns the databases held on the server

Returns:

output from 'showdb'

run_prog

public java.util.Vector run_prog(java.lang.String embossCommand,
                                 java.lang.String options,
                                 java.lang.String[] inFiles)

Run an EMBOSS application

Parameters:

embossCommand - command line to run

options - unused

inFiles - input files and names

Returns:

output files from application run

run_prog

public java.util.Vector run_prog(java.lang.String embossCommand,
                                 java.lang.String options,
                                 java.util.Vector inFiles,
                                 java.lang.String userName)

Run an EMBOSS application

Parameters:

embossCommand - command line to run

options - unused

inFiles - input files and names

userName - username

Returns:

output files from application run

run_prog

public java.util.Vector run_prog(java.lang.String embossCommand,
                                 java.lang.String options,
                                 java.util.Hashtable inFiles)

Run an EMBOSS application

Parameters:

embossCommand - command line to run

options - unused

inFiles - input files

Returns:

output files from application run

createFinishedFile

private void createFinishedFile(java.lang.String project)

Creates a file named "finished" in the project directory, that contains a time stamp.

Parameters:

project - project directory name

show_saved_results

public java.util.Vector show_saved_results(java.lang.String project,
                                           java.lang.String cl,
                                           java.lang.String userName)

Returns the results for a saved project.

Parameters:

project - project directory name

cl - unused if showing all results otherwise this is the name of the file to display

userName - username

Returns:

saved results files

show_saved_results

public java.util.Vector show_saved_results(java.lang.String project,
                                           java.lang.String cl)

Returns the results for a saved project.

Parameters:

project - project directory name

cl - unused if showing all results otherwise this is the name of the file to display

Returns:

saved results files

save_project_file

public java.util.Vector save_project_file(java.lang.String project,
                                          java.lang.String filename,
                                          java.lang.String notes,
                                          java.lang.String userName)

Save a file to a project directory on the server.

Parameters:

project - project directory to save file in

filename - filename

notes - text to write to file

userName - username

Returns:

message

delete_saved_results

public java.util.Vector delete_saved_results(java.lang.String project,
                                             java.lang.String cl,
                                             java.lang.String userName)

Deletes a projects saved results.

Parameters:

project - project directory name

cl - unused

userName - username

Returns:

message

delete_saved_results

public java.util.Vector delete_saved_results(java.lang.String project,
                                             java.lang.String cl)

Deletes a projects saved results.

Parameters:

project - project directory name

cl - unused

Returns:

message

list_saved_results

public java.util.Vector list_saved_results(java.lang.String userName)

List of the saved results on the server.

Parameters:

userName - username

Returns:

list of the saved results.

list_saved_results

public java.util.Vector list_saved_results()

List of the saved results on the server.

Returns:

list of the saved results.

loadFilesContent

private java.util.Vector loadFilesContent(java.io.File projectDir,
                                          java.lang.String project,
                                          java.util.Vector result,
                                          java.util.Hashtable inFiles)

Reads in files from EMBOSS output

Parameters:

projectDir - project directory

project - project name

result - results

inFiles - input files

Returns:

result

loadPNGContent

private java.util.Vector loadPNGContent(java.io.File projectDir,
                                        java.lang.String project,
                                        java.util.Vector result)

Reads in png files from EMBOSS output

Parameters:

projectDir - project directory

project - project name

result - results

Returns:

result

readByteFile

protected static byte[] readByteFile(java.lang.String filename)

Read a file into a byte array.

Parameters:

filename - file name

Returns:

byte[] contents of file

update_result_status

public java.util.Vector update_result_status(java.lang.String prog,
                                             java.lang.String opt,
                                             java.util.Vector resToQuery,
                                             java.lang.String userName)

Used to provide information on the batch/background processes.

Parameters:

prog - program

opt - options

resToQuery - results to query

userName - username

update_result_status

public java.util.Vector update_result_status(java.lang.String prog,
                                             java.lang.String opt,
                                             java.util.Hashtable resToQuery,
                                             java.lang.String userName)

Used to provide information on the batch/background processes.

Parameters:

prog - program

opt - options

resToQuery - results to query

userName - username

update_result_status

public java.util.Vector update_result_status(java.lang.String prog,
                                             java.lang.String opt,
                                             java.util.Hashtable resToQuery)

Used to provide information on the batch/background processes.

Parameters:

prog - program

opt - options

resToQuery - results to query

getHashtable

private java.util.Hashtable getHashtable(java.util.Vector v)

Convert contents from a Vector to a Hashtable

Parameters:

v - Vector

clone

public final java.lang.Object clone()
                             throws java.lang.CloneNotSupportedException

Throws:

java.lang.CloneNotSupportedException