jadex.xml
Class SequenceMapXMLDump

java.lang.Object
  |
  +--jadex.xml.SequenceMapXMLDump

public class SequenceMapXMLDump
extends java.lang.Object


Field Summary
static java.lang.String DTD_NAME
           
static java.lang.String NAME_SPACE
           
static java.lang.String ROOT_NAME
           
 
Constructor Summary
SequenceMapXMLDump()
          Default constructor: Creates new SequenceMapXMLDump
SequenceMapXMLDump(java.lang.String name)
          Second constructor: Based on the name of the chromosome
SequenceMapXMLDump(java.lang.String host, int port, boolean withDTD)
          Third constructor: provide the acedb server name and port number
SequenceMapXMLDump(java.lang.String name, java.lang.String host, int port, boolean withDTD)
          Fourth constructor: Name and Acedb information as the argument
 
Method Summary
 void aqlSequenceDump(org.jdom.Element element, java.lang.String name)
          Dump sequence by aql from acedb
 void createXMLFile(java.lang.String name)
          A template to create xml files
 void dump(java.lang.String name)
          A template method to dump the sequnece from acedb
 void dumpAll()
          This method to dump all chromosomes from acedb into six xml and six jar files
 void geneDump(org.jdom.Element element, java.lang.String name)
          Dump a possible gene
 jade.db.JSAceAccessor getAccessor()
           
 org.jdom.Document getDocument()
          Get the document to display the contents
static void main(java.lang.String[] args)
          A tester
 void output(java.io.OutputStream output)
           
 void output(java.lang.String name)
          A utility to print out document at any time
 void setAccessor(jade.db.JSAceAccessor acc)
          Set and get AceAccessor: Query engine
 void setName(java.lang.String name)
          Get and set the chromosome name
 void zipIt(java.lang.String name)
          A utility to zip the xml files
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

ROOT_NAME

public static final java.lang.String ROOT_NAME

NAME_SPACE

public static final java.lang.String NAME_SPACE

DTD_NAME

public static final java.lang.String DTD_NAME
Constructor Detail

SequenceMapXMLDump

public SequenceMapXMLDump()
Default constructor: Creates new SequenceMapXMLDump

SequenceMapXMLDump

public SequenceMapXMLDump(java.lang.String name)
Second constructor: Based on the name of the chromosome

SequenceMapXMLDump

public SequenceMapXMLDump(java.lang.String host,
                          int port,
                          boolean withDTD)
Third constructor: provide the acedb server name and port number

SequenceMapXMLDump

public SequenceMapXMLDump(java.lang.String name,
                          java.lang.String host,
                          int port,
                          boolean withDTD)
Fourth constructor: Name and Acedb information as the argument
Method Detail

setName

public void setName(java.lang.String name)
Get and set the chromosome name

setAccessor

public void setAccessor(jade.db.JSAceAccessor acc)
Set and get AceAccessor: Query engine

getAccessor

public jade.db.JSAceAccessor getAccessor()

dump

public void dump(java.lang.String name)
A template method to dump the sequnece from acedb

aqlSequenceDump

public void aqlSequenceDump(org.jdom.Element element,
                            java.lang.String name)
Dump sequence by aql from acedb

geneDump

public void geneDump(org.jdom.Element element,
                     java.lang.String name)
Dump a possible gene

getDocument

public org.jdom.Document getDocument()
Get the document to display the contents

output

public void output(java.lang.String name)
A utility to print out document at any time

output

public void output(java.io.OutputStream output)

zipIt

public void zipIt(java.lang.String name)
A utility to zip the xml files

dumpAll

public void dumpAll()
This method to dump all chromosomes from acedb into six xml and six jar files

createXMLFile

public void createXMLFile(java.lang.String name)
A template to create xml files

main

public static void main(java.lang.String[] args)
A tester