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java.lang.Objectmanipulator.Converter
public class Converter
Converter class for exporting the XML structure into objects.
Field Summary | |
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private core.XMLBurger |
burger
|
private java.lang.String |
outputPath
|
private pid.PID |
pid
|
Constructor Summary | |
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Converter(java.lang.String pathToXml)
Construction of the converter from the XML file of the PID. |
|
Converter(java.lang.String pathToXml,
java.lang.String pathToOutputFile)
Construction of the converter and outputting the serialised objects. |
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Converter(java.net.URL pidUrl,
java.lang.String pathToOutputFile)
Preferred constructor. |
Method Summary | |
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core.XMLBurger |
getBurger()
|
java.lang.String |
getOutputPath()
|
pid.PID |
getPid()
|
static void |
main(java.lang.String[] args)
|
private void |
parseInteractions(pid.Model model)
Parse the interactions |
private void |
parseMolecules(pid.Model model)
Parse the molecule bit. |
private void |
parseOntology()
Parse the "Ontology" section. |
private void |
parsePathways(pid.Model model)
Parse the pathway section |
(package private) void |
save()
Save the created objects in ".pid" file. |
void |
setBurger(core.XMLBurger burger)
|
void |
setOutputPath(java.lang.String outputPath)
|
void |
setPid(pid.PID pid)
|
void |
start()
Start the parsing of the document |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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private core.XMLBurger burger
private pid.PID pid
private java.lang.String outputPath
Constructor Detail |
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public Converter(java.lang.String pathToXml)
pathToXml
- public Converter(java.lang.String pathToXml, java.lang.String pathToOutputFile)
pathToXml
- pathToOutputFile
- public Converter(java.net.URL pidUrl, java.lang.String pathToOutputFile) throws java.io.IOException
pidUrl
- pathToOutputFile
-
java.io.IOException
Method Detail |
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public void setOutputPath(java.lang.String outputPath)
public java.lang.String getOutputPath()
public void setBurger(core.XMLBurger burger)
public core.XMLBurger getBurger()
public void setPid(pid.PID pid)
public pid.PID getPid()
public static void main(java.lang.String[] args) throws javax.xml.stream.XMLStreamException, javax.xml.stream.FactoryConfigurationError, java.io.IOException
javax.xml.stream.XMLStreamException
javax.xml.stream.FactoryConfigurationError
java.io.IOException
void save() throws java.io.IOException
java.io.IOException
public void start() throws javax.xml.stream.XMLStreamException
javax.xml.stream.XMLStreamException
private void parsePathways(pid.Model model)
model
- private void parseInteractions(pid.Model model) throws javax.xml.stream.XMLStreamException
model
-
javax.xml.stream.XMLStreamException
private void parseMolecules(pid.Model model) throws java.lang.NumberFormatException, javax.xml.stream.XMLStreamException
model
-
javax.xml.stream.XMLStreamException
java.lang.NumberFormatException
private void parseOntology() throws java.lang.NumberFormatException, javax.xml.stream.XMLStreamException
javax.xml.stream.XMLStreamException
java.lang.NumberFormatException
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