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java.lang.Object | +--org.emboss.jemboss.parser.Ajax
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 | homeuser home dir | 
| static int | lengthsequence length | 
|  int | length_soapsequence length | 
| private  java.lang.String | outStdstdout & stderr from fork | 
| private  int | prnt | 
| static boolean | proteintrue if the sequence is protein | 
|  boolean | protein_soaptrue if the sequence is protein | 
| private  int | size | 
| static float | weightsequence weight | 
|  float | weight_soapsequence 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 | 
public static boolean protein
public static int length
public static float weight
public boolean protein_soap
public int length_soap
public float weight_soap
public java.lang.String home
private java.lang.String outStd
private java.lang.String errStd
private int size
private int prnt
private int fileok
| Constructor Detail | 
public Ajax()
| Method Detail | 
public boolean seqType(java.lang.String usa)
public boolean seqsetType(java.lang.String usa)
public boolean seqAttrib(java.lang.String username,
                         byte[] password,
                         java.lang.String environment,
                         java.lang.String usa)
public boolean seqsetAttrib(java.lang.String username,
                            byte[] password,
                            java.lang.String environment,
                            java.lang.String usa)
public boolean userAuth(java.lang.String username,
                        byte[] password,
                        java.lang.String environment)
public boolean forkEmboss(java.lang.String username,
                          byte[] password,
                          java.lang.String environment,
                          java.lang.String commandline,
                          java.lang.String directory)
public boolean forkBatch(java.lang.String username,
                         byte[] password,
                         java.lang.String environment,
                         java.lang.String commandline,
                         java.lang.String directory)
public boolean makeDir(java.lang.String username,
                       byte[] password,
                       java.lang.String environment,
                       java.lang.String directory)
public boolean delFile(java.lang.String username,
                       byte[] password,
                       java.lang.String environment,
                       java.lang.String filename)
public boolean renameFile(java.lang.String username,
                          byte[] password,
                          java.lang.String environment,
                          java.lang.String filename,
                          java.lang.String filename2)
public boolean delDir(java.lang.String username,
                      byte[] password,
                      java.lang.String environment,
                      java.lang.String directory)
public boolean listFiles(java.lang.String username,
                         byte[] password,
                         java.lang.String environment,
                         java.lang.String directory)
public boolean listDirs(java.lang.String username,
                        byte[] password,
                        java.lang.String environment,
                        java.lang.String directory)
public byte[] getFile(java.lang.String username,
                      byte[] password,
                      java.lang.String environment,
                      java.lang.String filename)
public boolean putFile(java.lang.String username,
                       byte[] password,
                       java.lang.String environment,
                       java.lang.String filename,
                       byte[] bytearray)
public void setLength(int length)
public void setWeight(float weight)
public void setProtein(boolean protein)
public java.lang.String getOutStd()
public java.lang.String getErrStd()
public void setErrStd()
public int getSize()
public int getPrnt()
public int getFileok()
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