/**
* This method is called to execute the action that the StepInstance must perform.
*
* @param stepInstance containing the parameters for executing.
* @param temporaryFileDirectory
* @throws Exception could be anything thrown by the execute method.
*/
@Override
public void execute(StepInstance stepInstance, String temporaryFileDirectory) {
// Retrieve raw results for protein range.
Map<String, RawProtein<PfamHmmer3RawMatch>> rawMatches =
rawMatchDAO.getRawMatchesForProteinIdsInRange(
stepInstance.getBottomProtein(),
stepInstance.getTopProtein(),
getSignatureLibraryRelease());
if (LOGGER.isDebugEnabled()) {
LOGGER.debug("PfamA: Retrieved " + rawMatches.size() + " proteins to post-process.");
int matchCount = 0;
for (final RawProtein rawProtein : rawMatches.values()) {
matchCount += rawProtein.getMatches().size();
}
LOGGER.debug("PfamA: A total of " + matchCount + " raw matches.");
}
// Post process
try {
Map<String, RawProtein<PfamHmmer3RawMatch>> filteredMatches =
getPostProcessor().process(rawMatches);
if (LOGGER.isDebugEnabled()) {
LOGGER.debug(
"PfamA: " + filteredMatches.size() + " proteins passed through post processing.");
int matchCount = 0;
for (final RawProtein rawProtein : filteredMatches.values()) {
matchCount += rawProtein.getMatches().size();
}
LOGGER.debug("PfamA: A total of " + matchCount + " matches PASSED.");
}
filteredMatchDAO.persist(filteredMatches.values());
} catch (IOException e) {
throw new IllegalStateException(
"IOException thrown when attempting to post process filtered matches.", e);
}
}
