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SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object | +--jadex.xml.SequenceMapXMLDump
Field Summary | |
static java.lang.String |
DTD_NAME
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static java.lang.String |
NAME_SPACE
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static java.lang.String |
ROOT_NAME
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Constructor Summary | |
SequenceMapXMLDump()
Default constructor: Creates new SequenceMapXMLDump |
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SequenceMapXMLDump(java.lang.String name)
Second constructor: Based on the name of the chromosome |
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SequenceMapXMLDump(java.lang.String host,
int port,
boolean withDTD)
Third constructor: provide the acedb server name and port number |
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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()
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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)
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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 |
public static final java.lang.String ROOT_NAME
public static final java.lang.String NAME_SPACE
public static final java.lang.String DTD_NAME
Constructor Detail |
public SequenceMapXMLDump()
public SequenceMapXMLDump(java.lang.String name)
public SequenceMapXMLDump(java.lang.String host, int port, boolean withDTD)
public SequenceMapXMLDump(java.lang.String name, java.lang.String host, int port, boolean withDTD)
Method Detail |
public void setName(java.lang.String name)
public void setAccessor(jade.db.JSAceAccessor acc)
public jade.db.JSAceAccessor getAccessor()
public void dump(java.lang.String name)
public void aqlSequenceDump(org.jdom.Element element, java.lang.String name)
public void geneDump(org.jdom.Element element, java.lang.String name)
public org.jdom.Document getDocument()
public void output(java.lang.String name)
public void output(java.io.OutputStream output)
public void zipIt(java.lang.String name)
public void dumpAll()
public void createXMLFile(java.lang.String name)
public static void main(java.lang.String[] args)
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