public void loadTable(Reader in) throws IOException, FormatException {
table = new ArrayList<Entry>(InitNumEntries);
String line = null;
LineNumberReader input = new LineNumberReader(in);
line = input.readLine();
if (line == null) throw new FormatException("Empty sample sheet");
// Verify that heading is as expected, ignoring quotes and case
if (!line.replaceAll("\"", "").toLowerCase().startsWith(ExpectedHeading))
throw new FormatException(
"Unexpected heading! Expected:\n" + ExpectedHeading + "\nFound:\n" + line);
line = input.readLine();
while (line != null) {
insertRecord(line);
line = input.readLine();
}
if (table.size() > 1) {
// Check for duplicates barcodes in the same lane
// start by sorting the table by lane
Collections.sort(
table,
new Comparator<Entry>() {
@Override
public int compare(Entry a, Entry b) {
return a.getLane() - b.getLane();
}
});
HashSet<String> samplesInLane = new HashSet<String>();
int currentLane = table.get(0).getLane();
for (Entry e : table) // table is an ArrayList of Entries
{
if (e.getLane() == currentLane) {
if (samplesInLane.contains(e.getIndex()))
throw new FormatException(
"index " + e.getIndex() + " appears twice for the same lane " + currentLane);
else samplesInLane.add(e.getIndex());
} else {
// lane change
samplesInLane.clear();
samplesInLane.add(e.getIndex());
currentLane = e.getLane();
}
}
}
}
public Set<String> getSamplesInLane(int lane) {
if (lane <= 0) throw new IllegalArgumentException("Invalid negative lane number " + lane);
HashSet<String> samples = new HashSet<String>(table.size() / 8);
for (Entry e : this) {
if (lane == e.getLane()) samples.add(e.getSampleId());
}
return samples;
}