private static final Map<String, Object> subsetAttributes(
final CommonInfo igc, final Collection<String> keysToPreserve) {
Map<String, Object> attributes = new HashMap<String, Object>(keysToPreserve.size());
for (final String key : keysToPreserve) {
if (igc.hasAttribute(key)) attributes.put(key, igc.getAttribute(key));
}
return attributes;
}
public int getAttributeAsInt(String key, int defaultValue) {
return commonInfo.getAttributeAsInt(key, defaultValue);
}
public String getAttributeAsString(String key, String defaultValue) {
return commonInfo.getAttributeAsString(key, defaultValue);
}
public Object getAttribute(String key, Object defaultValue) {
return commonInfo.getAttribute(key, defaultValue);
}
public Object getAttribute(String key) {
return commonInfo.getAttribute(key);
}
public boolean hasAttribute(String key) {
return commonInfo.hasAttribute(key);
}
public Map<String, Object> getAttributes() {
return commonInfo.getAttributes();
}
// ---------------------------------------------------------------------------------------------------------
//
// get routines to access context info fields
//
// ---------------------------------------------------------------------------------------------------------
public String getSource() {
return commonInfo.getName();
}
public double getLog10PError() {
return commonInfo.getLog10PError();
}
public boolean hasLog10PError() {
return commonInfo.hasLog10PError();
}
public boolean filtersWereApplied() {
return commonInfo.filtersWereApplied();
}
public boolean isNotFiltered() {
return commonInfo.isNotFiltered();
}
public Set<String> getFilters() {
return commonInfo.getFilters();
}
public Set<String> getFiltersMaybeNull() {
return commonInfo.getFiltersMaybeNull();
}
public double getAttributeAsDouble(String key, double defaultValue) {
return commonInfo.getAttributeAsDouble(key, defaultValue);
}
public boolean getAttributeAsBoolean(String key, boolean defaultValue) {
return commonInfo.getAttributeAsBoolean(key, defaultValue);
}
public double getPhredScaledQual() {
return commonInfo.getPhredScaledQual();
}