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
           
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 & stderr from fork
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)
           
 boolean delFile(java.lang.String username, byte[] password, java.lang.String environment, java.lang.String filename)
           
 boolean forkBatch(java.lang.String username, byte[] password, java.lang.String environment, java.lang.String commandline, java.lang.String directory)
           
 boolean forkEmboss(java.lang.String username, byte[] password, java.lang.String environment, java.lang.String commandline, java.lang.String directory)
           
 java.lang.String getErrStd()
           
 byte[] getFile(java.lang.String username, byte[] password, java.lang.String environment, java.lang.String filename)
           
 int getFileok()
           
 java.lang.String getOutStd()
           
 int getPrnt()
           
 int getSize()
           
 boolean listDirs(java.lang.String username, byte[] password, java.lang.String environment, java.lang.String directory)
           
 boolean listFiles(java.lang.String username, byte[] password, java.lang.String environment, java.lang.String directory)
           
 boolean makeDir(java.lang.String username, byte[] password, java.lang.String environment, java.lang.String directory)
           
 boolean putFile(java.lang.String username, byte[] password, java.lang.String environment, java.lang.String filename, byte[] bytearray)
           
 boolean renameFile(java.lang.String username, byte[] password, java.lang.String environment, java.lang.String filename, java.lang.String filename2)
           
 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)
           
 boolean seqsetType(java.lang.String usa)
           
 boolean seqType(java.lang.String usa)
          determine sequence attributes
 void setErrStd()
           
 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 methods
 
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 & stderr from fork


errStd

private java.lang.String errStd

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)

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)

userAuth

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


forkEmboss

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

forkBatch

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

makeDir

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

delFile

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

renameFile

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

delDir

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

listFiles

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

listDirs

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

getFile

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

putFile

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

setLength

public void setLength(int length)
Sets the sequence length


setWeight

public void setWeight(float weight)
Sets the sequence weight


setProtein

public void setProtein(boolean protein)
Sets whether sequence is protein (true)


getOutStd

public java.lang.String getOutStd()

getErrStd

public java.lang.String getErrStd()

setErrStd

public void setErrStd()

getSize

public int getSize()

getPrnt

public int getPrnt()

getFileok

public int getFileok()