org.emboss.jemboss.parser
Class Ajax

java.lang.Object
  org.emboss.jemboss.parser.Ajax

public class Ajax

extends java.lang.Object

Used with JNI to access EMBOSS ajax library. This is used to determine sequence attributes and authenticate the server methods.

Field Summary

private java.lang.String	errStd stderr
private int	fileok
java.lang.String	home user home dir
static int	length sequence length
int	length_soap sequence length
private java.lang.String	outStd stdout
private int	prnt
static boolean	protein true if the sequence is protein
boolean	protein_soap true if the sequence is protein
private int	size
static float	weight sequence weight
float	weight_soap sequence weight

Constructor Summary

Ajax()

Method Summary

boolean	delDir(java.lang.String username, byte[] password, java.lang.String environment, java.lang.String directory) delete a directory
boolean	delFile(java.lang.String username, byte[] password, java.lang.String environment, java.lang.String filename) delete a file
boolean	forkBatch(java.lang.String username, byte[] password, java.lang.String environment, java.lang.String commandline, java.lang.String directory) fork emboss batch proceess
boolean	forkEmboss(java.lang.String username, byte[] password, java.lang.String environment, java.lang.String commandline, java.lang.String directory) fork emboss proceess
java.lang.String	getErrStd() Get the stderr
byte[]	getFile(java.lang.String username, byte[] password, java.lang.String environment, java.lang.String filename) get the contents of a file
int	getFileok()
java.lang.String	getOutStd() Get the stdout
int	getPrnt()
int	getSize()
boolean	listDirs(java.lang.String username, byte[] password, java.lang.String environment, java.lang.String directory) list directorys
boolean	listFiles(java.lang.String username, byte[] password, java.lang.String environment, java.lang.String directory) list files in a directory
boolean	makeDir(java.lang.String username, byte[] password, java.lang.String environment, java.lang.String directory) make a directory
boolean	putFile(java.lang.String username, byte[] password, java.lang.String environment, java.lang.String filename, byte[] bytearray) create a file
boolean	renameFile(java.lang.String username, byte[] password, java.lang.String environment, java.lang.String filename, java.lang.String filename2) rename a file
boolean	seqAttrib(java.lang.String username, byte[] password, java.lang.String environment, java.lang.String usa) determine sequence attributes as the user
boolean	seqsetAttrib(java.lang.String username, byte[] password, java.lang.String environment, java.lang.String usa) determine sequence set attributes as the user
boolean	seqsetType(java.lang.String usa) determine sequence set attributes
boolean	seqType(java.lang.String usa) determine sequence attributes
void	setErrStd() Clear the stderr
void	setLength(int length) Sets the sequence length
void	setProtein(boolean protein) Sets whether sequence is protein (true)
void	setWeight(float weight) Sets the sequence weight
boolean	userAuth(java.lang.String username, byte[] password, java.lang.String environment) authentication method

Methods inherited from class java.lang.Object

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

Field Detail

protein

public static boolean protein

true if the sequence is protein

length

public static int length

sequence length

weight

public static float weight

sequence weight

protein_soap

public boolean protein_soap

true if the sequence is protein

length_soap

public int length_soap

sequence length

weight_soap

public float weight_soap

sequence weight

home

public java.lang.String home

user home dir

outStd

private java.lang.String outStd

stdout

errStd

private java.lang.String errStd

stderr

size

private int size

prnt

private int prnt

fileok

private int fileok

Constructor Detail

Ajax

public Ajax()

Method Detail

seqType

public boolean seqType(java.lang.String usa)

determine sequence attributes

seqsetType

public boolean seqsetType(java.lang.String usa)

determine sequence set attributes

seqAttrib

public boolean seqAttrib(java.lang.String username,
                         byte[] password,
                         java.lang.String environment,
                         java.lang.String usa)

determine sequence attributes as the user

seqsetAttrib

public boolean seqsetAttrib(java.lang.String username,
                            byte[] password,
                            java.lang.String environment,
                            java.lang.String usa)

determine sequence set attributes as the user

userAuth

public boolean userAuth(java.lang.String username,
                        byte[] password,
                        java.lang.String environment)

authentication method

forkEmboss

public boolean forkEmboss(java.lang.String username,
                          byte[] password,
                          java.lang.String environment,
                          java.lang.String commandline,
                          java.lang.String directory)

fork emboss proceess

forkBatch

public boolean forkBatch(java.lang.String username,
                         byte[] password,
                         java.lang.String environment,
                         java.lang.String commandline,
                         java.lang.String directory)

fork emboss batch proceess

makeDir

public boolean makeDir(java.lang.String username,
                       byte[] password,
                       java.lang.String environment,
                       java.lang.String directory)

make a directory

delFile

public boolean delFile(java.lang.String username,
                       byte[] password,
                       java.lang.String environment,
                       java.lang.String filename)

delete a file

renameFile

public boolean renameFile(java.lang.String username,
                          byte[] password,
                          java.lang.String environment,
                          java.lang.String filename,
                          java.lang.String filename2)

rename a file

delDir

public boolean delDir(java.lang.String username,
                      byte[] password,
                      java.lang.String environment,
                      java.lang.String directory)

delete a directory

listFiles

public boolean listFiles(java.lang.String username,
                         byte[] password,
                         java.lang.String environment,
                         java.lang.String directory)

list files in a directory

listDirs

public boolean listDirs(java.lang.String username,
                        byte[] password,
                        java.lang.String environment,
                        java.lang.String directory)

list directorys

getFile

public byte[] getFile(java.lang.String username,
                      byte[] password,
                      java.lang.String environment,
                      java.lang.String filename)

get the contents of a file

putFile

public boolean putFile(java.lang.String username,
                       byte[] password,
                       java.lang.String environment,
                       java.lang.String filename,
                       byte[] bytearray)

create a file

setLength

public void setLength(int length)

Sets the sequence length

Parameters:

length - sequence length

setWeight

public void setWeight(float weight)

Sets the sequence weight

Parameters:

weight - sequence weight

setProtein

public void setProtein(boolean protein)

Sets whether sequence is protein (true)

Parameters:

protein - sequence type

getOutStd

public java.lang.String getOutStd()

Get the stdout

Returns:

stdout

getErrStd

public java.lang.String getErrStd()

Get the stderr

Returns:

stderr

setErrStd

public void setErrStd()

Clear the stderr

getSize

public int getSize()

getPrnt

public int getPrnt()

getFileok

public int getFileok()