private static void addToSetIfNecessary(TaxonLabelSet tlSet, Collection<TaxonLabel> labels) {
Set<TaxonLabel> tlList = new HashSet<TaxonLabel>(tlSet.getTaxonLabelsReadOnly());
for (TaxonLabel label : labels) {
if (!tlList.contains(label)) {
tlList.add(label);
tlSet.addPhyloTaxonLabel(label);
}
}
}
public Set<TaxonLabelSet> createTaxonLabelSets(Study s, boolean justTrees, boolean justMatrices) {
bindSession();
Set<TaxonLabelSet> newSets = new HashSet<TaxonLabelSet>();
Set<TaxonLabelSet> oldSets = s.getTaxonLabelSets();
Hibernate.initialize(oldSets);
for (Analysis an : s.getAnalyses()) {
TaxonLabelSet theSet = new TaxonLabelSet();
theSet.setStudy(s);
theSet.setTitle(an.getName());
Collection<TreeBlock> treeBlocks = new LinkedList<TreeBlock>();
for (AnalysisStep as : an.getAnalysisStepsReadOnly()) {
for (AnalyzedData ad : as.getDataSetReadOnly()) {
Matrix m = ad.getMatrixData();
PhyloTree t = ad.getTreeData();
if (m != null && !justTrees) {
addToSetIfNecessary(theSet, m.getAllTaxonLabels());
m.setTaxa(theSet);
// tlService.updateStudyForAllLabels(m, s);
}
if (t != null && !justMatrices) {
addToSetIfNecessary(theSet, t.getAllTaxonLabels());
// tlService.updateStudyForAllLabels(t, s);
treeBlocks.add(t.getTreeBlock());
}
}
}
ContextManager.getTaxonLabelService().save(theSet);
for (TreeBlock tb : treeBlocks) {
tb.setTaxonLabelSet(theSet);
ContextManager.getTaxonLabelService().save(tb); // XXX Should be treeBlockService
}
newSets.add(theSet);
}
s.setTaxonLabelSets(newSets);
unbindSession();
return newSets;
}