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java.lang.Object | +--org.emboss.jemboss.server.JembossServer
Jemboss Non-authenticating 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[] |
envp
|
private java.lang.String[] |
envp_emboss
|
private java.lang.String |
fs
|
private java.lang.String |
homeDirectory
|
(package private) JembossParams |
jp
|
(package private) java.lang.String |
plplot
|
private java.lang.String |
tmproot
|
private java.io.File |
tmprootDir
|
private java.lang.String |
username
|
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)
|
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)
Private server Deletes a projects saved results. |
java.util.Vector |
delete_saved_results(java.lang.String project,
java.lang.String cl,
java.lang.String userName)
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()
Private Server List of the saved results on the server. |
java.util.Vector |
list_saved_results(java.lang.String userName)
Private Server 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)
Private 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)
|
java.util.Vector |
save_project_file(java.lang.String project,
java.lang.String filename,
java.lang.String notes,
java.lang.String userName)
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)
Private Server 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)
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)
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)
|
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 |
private java.lang.String fs
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 homeDirectory
private java.lang.String username
private java.lang.String tmproot
private java.io.File tmprootDir
private java.lang.String[] envp_emboss
private java.lang.String[] envp
Constructor Detail |
public JembossServer()
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)
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.lang.String[] inFiles)
public java.util.Vector run_prog(java.lang.String embossCommand, java.lang.String options, java.util.Vector inFiles, java.lang.String userName)
public java.util.Vector run_prog(java.lang.String embossCommand, java.lang.String options, java.util.Hashtable inFiles)
private void createFinishedFile(java.lang.String project)
public java.util.Vector show_saved_results(java.lang.String project, java.lang.String cl, java.lang.String userName)
public java.util.Vector show_saved_results(java.lang.String project, java.lang.String cl)
public java.util.Vector save_project_file(java.lang.String project, java.lang.String filename, java.lang.String notes, java.lang.String userName)
public java.util.Vector delete_saved_results(java.lang.String project, java.lang.String cl, java.lang.String userName)
public java.util.Vector delete_saved_results(java.lang.String project, java.lang.String cl)
public java.util.Vector list_saved_results(java.lang.String userName)
public java.util.Vector list_saved_results()
private java.util.Vector loadFilesContent(java.io.File projectDir, java.lang.String project, java.util.Vector result, java.util.Hashtable inFiles)
private java.util.Vector loadPNGContent(java.io.File projectDir, java.lang.String project, java.util.Vector result)
protected static byte[] readByteFile(java.lang.String filename)
public java.util.Vector update_result_status(java.lang.String prog, java.lang.String opt, java.util.Vector resToQuery, java.lang.String userName)
public java.util.Vector update_result_status(java.lang.String prog, java.lang.String opt, java.util.Hashtable resToQuery, java.lang.String userName)
public java.util.Vector update_result_status(java.lang.String prog, java.lang.String opt, java.util.Hashtable resToQuery)
private java.util.Hashtable getHashtable(java.util.Vector v)
public final java.lang.Object clone() throws java.lang.CloneNotSupportedException
clone
in class java.lang.Object
java.lang.CloneNotSupportedException
|
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