public float[] weight(Collection<String> features) {
float[] scores = new float[index.size()];
for (String feature : features) {
if (!data.containsKey(feature)) {
continue;
}
if (isAveraged || data.get(feature).used > opts.minupdate) {
data.get(feature).sumScoresForAllTransitions(scores);
}
}
return scores;
}
/**
* Return all Genbank IDs associated to this probeset.
*
* @param probesetID
* @return Genbank IDs associated to this probeset.
*/
public String[] getGenbankList(final String probesetID) {
final String gbList = (String) probesetId2GenbankList.get(probesetID);
if (gbList == null) {
return ArrayUtils.EMPTY_STRING_ARRAY;
} else {
return gbList.split("[ ]");
}
}
private void increment(List<String> features, int transition, float delta) {
for (String feat : features) {
if (!data.containsKey(feat)) {
data.put(feat, new FeatureWeights());
}
data.get(feat).increment(transition, delta, i);
}
}
public float weight(Collection<String> features, int trans) {
float score = 0.0f;
for (String feature : features) {
if (data.containsKey(feature)) {
score += data.get(feature).scoreForTransition(trans);
}
}
return score;
}
public Weights<T> average() {
System.err.print("averaging (this may take a while)... ");
Weights<T> result = new Weights<T>(opts, true);
result.data = new Object2ObjectOpenHashMap<>();
result.index = index;
result.gram = gram;
int cnt = 0;
for (String feat : data.keySet()) {
FeatureWeights dw = data.get(feat);
if (dw.used > opts.minupdate) {
cnt++;
FeatureWeights fw = new FeatureWeights();
for (int trans : index.indices()) {
float averaged = dw.getAveraged(trans, i);
if (!Float.isNaN(averaged)) {
fw.increment(trans, averaged, 0);
}
}
result.data.put(feat, fw);
}
}
System.err.println("done, averaged " + cnt + " features.");
return result;
}
/**
* Utility method to pull up the version number at which an annotation was deprecated and the
* suggested replacement, if any
*
* @param annotationName the annotation class name (not the full package) to check
*/
public static String getAnnotationDeprecationInfo(final String annotationName) {
return deprecatedGATKAnnotations.get(annotationName).toString();
}
/**
* Utility method to pull up the version number at which a walker was deprecated and the suggested
* replacement, if any
*
* @param walkerName the walker class name (not the full package) to check
*/
public static String getWalkerDeprecationInfo(final String walkerName) {
return deprecatedGATKWalkers.get(walkerName).toString();
}