/**
* Returns the taxonomy hierarchy of this taxon entry in the form: most specific; less specific;
* ...; least specific. It follows the chain up the tree as far as it can, and will stop at the
* first one it comes to that returns null for getParentNCBITaxID(). If this taxon entry has no
* scientific name, you will get the string ".".
*
* @return the display name as described above.
*/
public String getNameHierarchy() {
StringBuffer sb = new StringBuffer();
boolean first = true;
Integer parent = this.getParentNCBITaxID();
while (parent != null) {
NCBITaxon t =
(NCBITaxon) RichObjectFactory.getObject(SimpleNCBITaxon.class, new Object[] {parent});
Set sciNames = t.getNames(NCBITaxon.SCIENTIFIC);
// System.out.println("SimpleNCBITaxon2.getNameHierarchy-t:"+t+", t.isTaxonHidden?
// "+t.isTaxonHidden()+", isRoot? "+isRoot(t)+", sciNames:"+sciNames);
if (sciNames.size() > 0) {
if (!t.isTaxonHidden() && !isRoot(t)) { // root is NOT hidden - but also not displayed
if (!first) sb.insert(0, "; ");
else first = false;
sb.insert(0, (String) sciNames.iterator().next());
}
// Don't get into endless loop if child's parent is itself.
if (t.getParentNCBITaxID().equals(new Integer(t.getNCBITaxID()))) parent = null;
else parent = t.getParentNCBITaxID();
}
// Also don't go up past a parent that doesn't have a name.
else parent = null;
}
sb.append(".");
return sb.toString();
}
/** {@inheritDoc} NCBITaxon objects are equal if their NCBITaxID fields match. */
public boolean equals(Object obj) {
if (this == obj) return true;
if (obj == null || !(obj instanceof NCBITaxon)) return false;
NCBITaxon them = (NCBITaxon) obj;
return this.NCBITaxID == them.getNCBITaxID();
}
/** {@inheritDoc} NCBITaxon objects are compared only by their NCBITaxID fields. */
public int compareTo(Object o) {
if (o == this) return 0;
NCBITaxon them = (NCBITaxon) o;
return this.NCBITaxID - them.getNCBITaxID();
}
private static final boolean isRoot(final NCBITaxon theTaxon) {
return isRoot(theTaxon.getNCBITaxID());
}
