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 Collection<Experiment> findExpts(CellLine cells, ExptCondition cond) throws SQLException {
LinkedList<Integer> dbids = new LinkedList<Integer>();
String tables = "experiment e";
if (genome != null) {
tables += ", probe_platform_to_genome p2g";
}
String query = "select e.id from " + tables;
Vector<String> conds = new Vector<String>();
if (genome != null) {
int gid = genome.getDBID();
conds.add("e.platform=p2g.platform and p2g.genome=" + gid);
}
if (cells != null) {
conds.add("e.cells=" + cells.getDBID());
}
if (cond != null) {
conds.add("e.condition=" + cond.getDBID());
}
for (int i = 0; i < conds.size(); i++) {
if (i == 0) {
query += " where ";
} else {
query += " and ";
}
query += conds.get(i);
}
System.out.println("Final Query: \"" + query + "\"");
java.sql.Connection cxn = loader.getConnection();
Statement s = cxn.createStatement();
ResultSet rs = s.executeQuery(query);
while (rs.next()) {
int dbid = rs.getInt(1);
dbids.addLast(dbid);
}
rs.close();
s.close();
Collection<Experiment> expts = loader.loadExperiments(dbids);
return expts;
}
public void addCDS(GFFRecord rec, Map<String, List<String>> attrs) {
if (!rec.getFeature().equals("CDS")) {
throw new IllegalArgumentException();
}
if (attrs == null) {
attrs = decodeAttrMap(rec);
}
if (!attrs.containsKey("Parent")) {
throw new IllegalArgumentException();
}
if (!attrs.get("Parent").contains(id)) {
throw new IllegalArgumentException();
}
cds.addLast(rec);
}
public static Pair<String, List<String>> decodeKeyValues(String str) {
int index = str.indexOf("=");
if (index == -1) {
return null;
}
String k = str.substring(0, index);
LinkedList<String> vlist = new LinkedList<String>();
try {
String vstr = URLDecoder.decode(str.substring(index + 1, str.length()), "UTF-8");
String[] array = vstr.split(",");
for (int i = 0; i < array.length; i++) {
vlist.addLast(array[i]);
}
return new Pair<String, List<String>>(k, vlist);
} catch (UnsupportedEncodingException e) {
System.err.println("BAD STRING " + str);
e.printStackTrace();
return null;
} catch (Exception e) {
System.err.println("BAD STRING " + str);
return null;
}
}
static synchronized void pushConnectionBackToPool(ConnectionWrapper con) {
boolean exist = m_usedUsedConnection.remove(con);
if (exist) {
m_notUsedConnection.addLast(con);
}
}
