private void createColumns() {
// Create columns if necessary
final GeneAssociationTag[] tags = GeneAssociationTag.values();
int index = 0;
for (GeneAssociationTag tag : tags) {
index++;
// Special cases: handled in the last part
if (tag == GeneAssociationTag.GO_ID
|| tag == GeneAssociationTag.EVIDENCE
|| tag == GeneAssociationTag.DB_REFERENCE
|| tag == GeneAssociationTag.ASPECT) continue;
final String tagString = tag.toString();
if (table.getColumn(tagString) == null) {
if (LIST_INDEX.contains(index)) {
table.createListColumn(tagString, String.class, false);
} else {
table.createColumn(tagString, String.class, false);
}
}
}
// Create one column per namespace
for (String name : NAMESPACE_MAP.keySet()) {
table.createListColumn(NAMESPACE_MAP.get(name), String.class, false);
table.createListColumn(NAMESPACE_MAP.get(name) + EVIDENCE_SUFFIX, String.class, false);
table.createListColumn(NAMESPACE_MAP.get(name) + REFERENCE_SUFFIX, String.class, false);
}
// Consolidated entry name list
table.createListColumn(SYNONYM_COL_NAME, String.class, true);
}
private void mapEntry(final String[] entries) {
// Set primary key for the table, which is DB Object ID
final String primaryKeyValue = entries[DB_OBJ_ID];
final CyRow row = table.getRow(primaryKeyValue);
row.set(CyNetwork.NAME, primaryKeyValue);
// Check namespace
final String namespace = NAMESPACE_MAP.get(entries[ASPECT]);
for (int i = 0; i < EXPECTED_COL_COUNT; i++) {
final GeneAssociationTag tag = GeneAssociationTag.values()[i];
switch (tag) {
// Evidence code and GO ID should be organized by namespace.
case GO_ID:
String goidString = entries[i];
if (this.termIDList != null) goidString = convertToName(goidString);
List<String> currentList = row.getList(namespace, String.class);
if (currentList == null) currentList = new ArrayList<String>();
if (currentList.contains(goidString) == false) currentList.add(goidString);
row.set(namespace, currentList);
break;
case EVIDENCE:
case DB_REFERENCE:
final String value = entries[i];
String columnName = namespace;
if (tag == GeneAssociationTag.EVIDENCE) columnName = columnName + EVIDENCE_SUFFIX;
else columnName = columnName + REFERENCE_SUFFIX;
List<String> valueList = row.getList(columnName, String.class);
if (valueList == null) valueList = new ArrayList<String>();
if (valueList.contains(value) == false) valueList.add(value);
row.set(columnName, valueList);
break;
case TAXON:
final String taxID = entries[i].split(":")[1];
final String taxName = speciesMap.get(taxID);
if (taxName != null) row.set(tag.toString(), taxName);
else if (taxID != null) row.set(tag.toString(), taxID);
break;
case ASPECT:
// Ignore these lines
break;
case DB_OBJECT_ID:
case DB_OBJECT_SYMBOL:
case DB_OBJECT_SYNONYM:
// Create consolidated id list attribute.
List<String> synList = row.getList(SYNONYM_COL_NAME, String.class);
if (synList == null) synList = new ArrayList<String>();
if (tag == GeneAssociationTag.DB_OBJECT_SYNONYM) {
final String[] vals = entries[i].split(LIST_DELIMITER);
for (String val : vals) {
if (synList.contains(val) == false) synList.add(val);
}
} else {
if (synList.contains(entries[i]) == false) synList.add(entries[i]);
}
row.set(SYNONYM_COL_NAME, synList);
break;
default:
if (LIST_INDEX.contains(i + 1)) {
final String[] vals = entries[i].split(LIST_DELIMITER);
List<String> listVals = row.getList(tag.toString(), String.class);
if (listVals == null) listVals = new ArrayList<String>();
for (String val : vals) {
if (listVals.contains(val) == false) listVals.add(val);
}
row.set(tag.toString(), listVals);
} else row.set(tag.toString(), entries[i]);
break;
}
}
}
