public static int close() {
int count = 0;
Iterator iterator = m_notUsedConnection.iterator();
while (iterator.hasNext()) {
try {
((ConnectionWrapper) iterator.next()).close();
count++;
} catch (Exception e) {
}
}
m_notUsedConnection.clear();
iterator = m_usedUsedConnection.iterator();
while (iterator.hasNext()) {
try {
ConnectionWrapper wrapper = (ConnectionWrapper) iterator.next();
wrapper.close();
if (DEBUG) {
wrapper.debugInfo.printStackTrace();
}
count++;
} catch (Exception e) {
}
}
m_usedUsedConnection.clear();
return count;
}
public void parseInputFile(File inputFile) throws IOException {
geneFeatures.clear();
otherRecords.clear();
try {
GFFEntrySet gffEntries = GFFTools.readGFF(inputFile);
Iterator itr = gffEntries.lineIterator();
int count = 0;
int intronFeatures = 0;
LinkedList<GFFRecord> cdsRecs = new LinkedList<GFFRecord>();
while (itr.hasNext()) {
Object val = itr.next();
if (val instanceof GFFRecord) {
GFFRecord rec = (GFFRecord) val;
count += 1;
if (rec.getFeature().endsWith("gene")) {
GeneFeatures gf = new GeneFeatures(rec);
geneFeatures.put(gf.id, gf);
} else if (rec.getFeature().equals("CDS")) {
cdsRecs.addLast(rec);
} else {
otherRecords.add(rec);
}
}
}
for (GFFRecord rec : cdsRecs) {
Map<String, List<String>> attrs = decodeAttrMap(rec);
if (geneFeatures.containsKey(attrs.get("Parent").get(0))) {
geneFeatures.get(attrs.get("Parent").get(0)).addCDS(rec, attrs);
} else {
System.err.println("Unknown CDS Parent: " + attrs.get("Parent").get(0));
}
}
for (String k : geneFeatures.keySet()) {
GeneFeatures gf = geneFeatures.get(k);
if (gf.cds != null && gf.cds.size() > 1) {
intronFeatures++;
}
}
System.err.println("# GFF Records: " + count);
System.err.println("# Gene Feature Sets: " + geneFeatures.size());
System.err.println("\t# Intron-Features: " + intronFeatures);
} catch (ParserException e) {
e.printStackTrace();
} catch (BioException e) {
e.printStackTrace();
}
}
public static synchronized Connection getConnection() {
clearClosedConnection();
while (m_notUsedConnection.size() > 0) {
try {
ConnectionWrapper wrapper = (ConnectionWrapper) m_notUsedConnection.removeFirst();
if (wrapper.connection.isClosed()) {
continue;
}
m_usedUsedConnection.add(wrapper);
if (DEBUG) {
wrapper.debugInfo = new Throwable("Connection initial statement");
}
return wrapper.connection;
} catch (Exception e) {
}
}
int newCount = getIncreasingConnectionCount();
LinkedList list = new LinkedList();
ConnectionWrapper wrapper = null;
for (int i = 0; i < newCount; i++) {
wrapper = getNewConnection();
if (wrapper != null) {
list.add(wrapper);
}
}
if (list.size() == 0) {
return null;
}
wrapper = (ConnectionWrapper) list.removeFirst();
m_usedUsedConnection.add(wrapper);
m_notUsedConnection.addAll(list);
list.clear();
return wrapper.connection;
}