use of uk.ac.babraham.SeqMonk.DataTypes.DataStore in project SeqMonk by s-andrews.
the class WindowedReplicateStatsFilter method generateProbeList.
/* (non-Javadoc)
* @see uk.ac.babraham.SeqMonk.Filters.ProbeFilter#generateProbeList()
*/
@Override
protected void generateProbeList() {
Chromosome[] chromosomes = collection.genome().getAllChromosomes();
Vector<ProbeGroupTTestValue> newListProbesVector = new Vector<ProbeGroupTTestValue>();
for (int c = 0; c < chromosomes.length; c++) {
progressUpdated("Processing windows on Chr" + chromosomes[c].name(), c, chromosomes.length);
Probe[] probes = startingList.getProbesForChromosome(chromosomes[c]);
ProbeGroupGenerator gen = null;
if (windowType == DISTANCE_WINDOW) {
gen = new ProbeWindowGenerator(probes, windowSize);
} else if (windowType == CONSECUTIVE_WINDOW) {
gen = new ConsecutiveProbeGenerator(probes, windowSize);
} else if (windowType == FEATURE_WINDOW) {
gen = new FeatureProbeGroupGenerator(probes, collection.genome().annotationCollection().getFeaturesForType(optionsPanel.featureTypeBox.getSelectedItem().toString()));
}
while (true) {
if (cancel) {
cancel = false;
progressCancelled();
return;
}
Probe[] theseProbes = gen.nextSet();
if (theseProbes == null) {
// System.err.println("List of probes was null");
break;
}
// We need at least 3 probes in a set to calculate a p-value
if (theseProbes.length < 3) {
// System.err.println("Only "+theseProbes.length+" probes in the set");
continue;
}
double[][] values = new double[stores.length][];
for (int j = 0; j < stores.length; j++) {
if (splitReplicateSets & stores[j] instanceof ReplicateSet) {
values[j] = new double[theseProbes.length * ((ReplicateSet) stores[j]).dataStores().length];
} else {
values[j] = new double[theseProbes.length];
}
}
for (int j = 0; j < stores.length; j++) {
int index = 0;
for (int i = 0; i < theseProbes.length; i++) {
try {
if (splitReplicateSets & stores[j] instanceof ReplicateSet) {
DataStore[] localStores = ((ReplicateSet) stores[j]).dataStores();
for (int l = 0; l < localStores.length; l++) {
values[j][index] = localStores[l].getValueForProbe(theseProbes[i]);
index++;
}
} else {
values[j][index] = stores[j].getValueForProbe(theseProbes[i]);
index++;
}
} catch (SeqMonkException e) {
}
}
if (index != values[j].length) {
throw new IllegalStateException("Didn't fill all values total=" + values[j].length + " index=" + index);
}
}
double pValue = 0;
try {
if (stores.length == 1) {
pValue = TTest.calculatePValue(values[0], 0);
} else if (stores.length == 2) {
pValue = TTest.calculatePValue(values[0], values[1]);
} else {
pValue = AnovaTest.calculatePValue(values);
}
} catch (SeqMonkException e) {
throw new IllegalStateException(e);
}
newListProbesVector.add(new ProbeGroupTTestValue(theseProbes, pValue));
}
}
ProbeGroupTTestValue[] newListProbes = newListProbesVector.toArray(new ProbeGroupTTestValue[0]);
// Do the multi-testing correction if necessary
if (multiTest) {
BenjHochFDR.calculateQValues(newListProbes);
}
ProbeList newList;
// We need to handle duplicate hits internally since probe lists can't do
// this themselves any more.
Hashtable<Probe, Float> newListTemp = new Hashtable<Probe, Float>();
if (multiTest) {
newList = new ProbeList(startingList, "", "", "Q-value");
for (int i = 0; i < newListProbes.length; i++) {
if (newListProbes[i].q <= cutoff) {
Probe[] passedProbes = newListProbes[i].probes;
for (int p = 0; p < passedProbes.length; p++) {
if (newListTemp.containsKey(passedProbes[p])) {
// We always give a probe the lowest possible q-value
if (newListTemp.get(passedProbes[p]) <= newListProbes[i].q) {
continue;
}
}
newListTemp.put(passedProbes[p], (float) newListProbes[i].q);
}
}
}
} else {
newList = new ProbeList(startingList, "", "", "P-value");
for (int i = 0; i < newListProbes.length; i++) {
if (newListProbes[i].p <= cutoff) {
Probe[] passedProbes = newListProbes[i].probes;
for (int p = 0; p < passedProbes.length; p++) {
if (newListTemp.containsKey(passedProbes[p])) {
// We always give a probe the lowest possible p-value
if (newListTemp.get(passedProbes[p]) <= newListProbes[i].p) {
continue;
}
}
newListTemp.put(passedProbes[p], (float) newListProbes[i].p);
}
}
}
}
// Add the cached hits to the new list
Enumeration<Probe> en = newListTemp.keys();
while (en.hasMoreElements()) {
Probe p = en.nextElement();
newList.addProbe(p, newListTemp.get(p));
}
filterFinished(newList);
}
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