private static PirsfDatRecord parseSubFamilyLine(String line) {
PirsfDatRecord instance = null;
String[] chunks = line.split(" ");
for (int i = 0; i < chunks.length; i++) {
if (i == 0) {
if (chunks[i].length() > 1) {
final String modelAccession = chunks[i].substring(1);
instance = new PirsfDatRecord(modelAccession);
if (LOGGER.isDebugEnabled()) {
LOGGER.debug("Found a new model accession with sub families: " + modelAccession);
}
}
} else if (i > 1) {
final String subfamily = chunks[i];
if (LOGGER.isDebugEnabled()) {
LOGGER.debug(
"Found a new subfamily named "
+ subfamily
+ " for model accession: "
+ instance.getModelAccession());
}
instance.addSubFamily(subfamily);
}
}
return instance;
}
public static Map<String, PirsfDatRecord> parse(final Resource pirsfDatFileResource)
throws IOException {
LOGGER.debug("Running PIRSF data file parser...");
if (pirsfDatFileResource == null) {
throw new NullPointerException("Resource to the PIRSF dat file is null");
}
if (!pirsfDatFileResource.exists()) {
throw new IllegalStateException(pirsfDatFileResource.getFilename() + " does not exist");
}
if (!pirsfDatFileResource.isReadable()) {
throw new IllegalStateException(pirsfDatFileResource.getFilename() + " is not readable");
}
// Result map
final Map<String, PirsfDatRecord> data = new HashMap<String, PirsfDatRecord>();
BufferedReader reader = null;
try {
// Read input file line by line
reader = new BufferedReader(new InputStreamReader(pirsfDatFileResource.getInputStream()));
String line;
PirsfDatRecord pirsfDatRecord = null;
int row = 1;
while ((line = reader.readLine()) != null) {
Matcher modelStart = PIRSF_DAT_PATTERN_SUPERFAM.matcher(line);
if (modelStart.find()) {
// New accession without sub families
final String modelAccession = line.substring(1);
pirsfDatRecord = new PirsfDatRecord(modelAccession);
if (LOGGER.isDebugEnabled()) {
LOGGER.debug("Found a new model accession without sub families: " + modelAccession);
}
// Reset row attributes
row = 1;
} else if (row == 2) {
// Model name
final String modelName = line;
pirsfDatRecord.setModelName(modelName);
if (LOGGER.isDebugEnabled()) {
LOGGER.debug("Set model name to " + modelName);
}
} else if (row == 3) {
final String[] values = line.split("\\s+");
pirsfDatRecord.setValues(values);
} else if (row == 4 && line.startsWith("BLAST: ")) {
int index = line.indexOf(":");
if (index > -1 && line.length() >= index + 1) {
line = line.substring(index + 1).trim();
}
final boolean isBlastRequired = line.equalsIgnoreCase("YES");
pirsfDatRecord.setBlastRequired(isBlastRequired);
data.put(pirsfDatRecord.getModelAccession(), pirsfDatRecord);
} else {
modelStart = PIRSF_DAT_PATTERN_SUBFAM.matcher(line);
if (modelStart.find()) {
// New accession with sub families
row = 1;
pirsfDatRecord = parseSubFamilyLine(line);
} else {
LOGGER.warn("Unexpected line in pirsf.dat: " + line);
}
}
row++;
}
} finally {
if (reader != null) {
reader.close();
}
}
return data;
}
