/**
* Construct new <code>Genotype</code> object from population in specified run XML data.
*
* @param runXml XML data from which to construct initial population
* @return new <code>Genotype</code>
* @throws Exception
*/
private Genotype genotypeFromRunXml(InputStream runXml, Configuration config) throws Exception {
DocumentBuilder builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
Document doc = builder.parse(runXml, baseDir.getAbsolutePath());
Node runNode = doc.getFirstChild();
if (XmlPersistableRun.RUN_TAG.equals(runNode.getNodeName()) == false)
throw new IllegalArgumentException("node name not " + XmlPersistableRun.RUN_TAG);
// loop through list to find last generation
Node generationNode = null;
for (int i = 0; i < runNode.getChildNodes().getLength(); ++i) {
Node nextNode = runNode.getChildNodes().item(i);
if (Generation.GENERATION_TAG.equals(nextNode.getNodeName())) generationNode = nextNode;
}
return genotypeFromXml(generationNode, config, this);
}
/**
* Create a <code>Genotype</code> from XML.
*
* @param generationNode XML
* @param config
* @param db persistence repository from which to read chromosomes
* @return new genotype
* @throws Exception
*/
private static Genotype genotypeFromXml(Node generationNode, Configuration config, Persistence db)
throws Exception {
if (Generation.GENERATION_TAG.equals(generationNode.getNodeName()) == false)
throw new IllegalArgumentException("node name not " + Generation.GENERATION_TAG);
// loop through list to find chromosomes
ArrayList chroms = new ArrayList();
for (int generationChildIdx = 0;
generationChildIdx < generationNode.getChildNodes().getLength();
++generationChildIdx) {
Node specieNode = generationNode.getChildNodes().item(generationChildIdx);
if (Specie.SPECIE_TAG.equals(specieNode.getNodeName())) {
// for each specie ...
NamedNodeMap specieAttrs = specieNode.getAttributes();
if (specieAttrs == null) throw new IllegalArgumentException("missing specie attributes");
// ... and loop through chromosomes
for (int specieChildIdx = 0;
specieChildIdx < specieNode.getChildNodes().getLength();
++specieChildIdx) {
Node chromNode = specieNode.getChildNodes().item(specieChildIdx);
if (Specie.CHROMOSOME_TAG.equals(chromNode.getNodeName())) {
NamedNodeMap chromAttrs = chromNode.getAttributes();
if (chromAttrs == null)
throw new IllegalArgumentException("missing chromosome attributes");
Node chromIdNode = chromAttrs.getNamedItem(Specie.ID_TAG);
if (chromIdNode == null) throw new IllegalArgumentException("missing chromosome id");
// get id and load chromosome from persistence (skip if representative since its
// already been added
Long chromId = Long.valueOf(chromIdNode.getNodeValue());
Chromosome c = db.loadChromosome(chromId.toString(), config);
if (c != null) chroms.add(c);
else logger.warn("chromosome in run not found: " + chromId);
}
}
}
}
// don't return empty genotype
if (chroms.size() <= 0) return null;
// sort in order of id so that they will be added in proper order (age)
Collections.sort(chroms);
return new Genotype(config, chroms);
}