@Override
public boolean equals(Object obj) {
if (this == obj) {
return true;
}
// DO NOT call super.equals(); because ID could be null.
// if (!super.equals(obj)) {
// return false;
// }
if (getClass() != obj.getClass()) {
return false;
}
RestaurantPrefixTable other = (RestaurantPrefixTable) obj;
if (restaurant == null) {
if (other.restaurant != null) {
return false;
}
} else if (restaurant.getId() == null) {
if (other.restaurant.getId() != null) {
return false;
}
} else if (other.restaurant == null || !restaurant.getId().equals(other.restaurant.getId())) {
return false;
}
if (prefix == null) {
if (other.prefix != null) {
return false;
}
} else if (prefix.getId() == null) {
if (other.prefix.getId() != null) {
return false;
}
} else if (other.prefix == null || !prefix.getId().equals(other.prefix.getId())) {
return false;
}
if (type == null) {
if (other.type != null) {
return false;
}
} else if (type.getId() == null) {
if (other.type.getId() != null) {
return false;
}
} else if (other.type == null || !type.getId().equals(other.type.getId())) {
return false;
}
return true;
}
@Override
public int hashCode() {
final int prime = 31;
int result = 1; // DO NOT call super.hashCode(); because ID could be
// null.
result =
prime * result
+ ((restaurant == null || restaurant.getId() == null)
? 0
: restaurant.getId().hashCode());
result =
prime * result
+ ((prefix == null || prefix.getId() == null) ? 0 : prefix.getId().hashCode());
result =
prime * result + ((type == null || type.getId() == null) ? 0 : type.getId().hashCode());
return result;
}
/**
* Output the finalized report
*
* @param result an integer that doesn't get used for anything
*/
public void onTraversalDone(Integer result) {
logger.info("Finalizing variant report");
for (StateKey stateKey : evaluationContexts.keySet()) {
NewEvaluationContext nec = evaluationContexts.get(stateKey);
for (VariantEvaluator ve : nec.getEvaluationClassList().values()) {
ve.finalizeEvaluation();
AnalysisModuleScanner scanner = new AnalysisModuleScanner(ve);
Map<Field, DataPoint> datamap = scanner.getData();
for (Field field : datamap.keySet()) {
try {
field.setAccessible(true);
if (field.get(ve) instanceof TableType) {
TableType t = (TableType) field.get(ve);
String subTableName = ve.getClass().getSimpleName() + "." + field.getName();
final DataPoint dataPointAnn = datamap.get(field);
GATKReportTable table;
if (!report.hasTable(subTableName)) {
report.addTable(subTableName, dataPointAnn.description());
table = report.getTable(subTableName);
table.addPrimaryKey("entry", false);
table.addColumn(subTableName, subTableName);
for (VariantStratifier vs : stratificationObjects) {
table.addColumn(vs.getName(), "unknown");
}
table.addColumn("row", "unknown");
for (Object o : t.getColumnKeys()) {
String c;
if (o instanceof String) {
c = (String) o;
} else {
c = o.toString();
}
table.addColumn(c, 0.0);
}
} else {
table = report.getTable(subTableName);
}
for (int row = 0; row < t.getRowKeys().length; row++) {
String r = (String) t.getRowKeys()[row];
for (VariantStratifier vs : stratificationObjects) {
final String columnName = vs.getName();
table.set(stateKey.toString() + r, columnName, stateKey.get(columnName));
}
for (int col = 0; col < t.getColumnKeys().length; col++) {
String c;
if (t.getColumnKeys()[col] instanceof String) {
c = (String) t.getColumnKeys()[col];
} else {
c = t.getColumnKeys()[col].toString();
}
String newStateKey = stateKey.toString() + r;
table.set(newStateKey, c, t.getCell(row, col));
table.set(newStateKey, "row", r);
}
}
} else {
GATKReportTable table = report.getTable(ve.getClass().getSimpleName());
for (VariantStratifier vs : stratificationObjects) {
String columnName = vs.getName();
table.set(stateKey.toString(), columnName, stateKey.get(vs.getName()));
}
table.set(stateKey.toString(), field.getName(), field.get(ve));
}
} catch (IllegalAccessException e) {
throw new StingException("IllegalAccessException: " + e);
}
}
}
}
report.print(out);
}
