/** Read a file that has all proteins in fasta format */
void readProteinFile() {
if (verbose) Timer.showStdErr("Reading proteins from file '" + proteinFile + "'...");
proteinByTrId = new HashMap<String, String>();
if (proteinFile.endsWith("txt") || proteinFile.endsWith("txt.gz")) readProteinFileTxt();
else if (proteinFile.endsWith(SnpEffPredictorFactoryGenBank.EXTENSION_GENBANK))
readProteinFileGenBank();
else if (proteinFile.endsWith(SnpEffPredictorFactoryEmbl.EXTENSION_EMBL)) readProteinFileEmbl();
else readProteinFileFasta();
if (verbose) Timer.showStdErr("done (" + proteinByTrId.size() + " Proteins).");
}
/** Check proteins using all possible codon tables */
void checkCodonTables() {
if (verbose) Timer.showStdErr("Comparing Proteins...");
createTrByChromo(); // Create lists of transcripts by chromosome
// For each chromosome...
for (Chromosome chromo : genome) {
String chr = chromo.getId();
// Check against each codon table
for (CodonTable codonTable : CodonTables.getInstance()) {
setCodonTable(chromo, codonTable);
proteinCompare(chr, false, false);
}
}
if (verbose) Timer.showStdErr("done");
}
/** Run command */
@Override
public boolean run() {
if (verbose) Timer.showStdErr("Checking database using protein sequences");
loadConfig(); // Load config
readProteinFile(); // Read proteins
loadDb(); // Load database
checkProteins(); // Compare proteins
return true;
}
/** Check proteins */
void checkProteins() {
if (verbose) Timer.showStdErr("Comparing Proteins...");
if (codonTables) {
// Compare proteins using ALL codon tables
checkCodonTables();
} else {
// Compare proteins
proteinCompare(null, true, true);
}
}
/**
* Read data from input stream
*
* @return true on success
*/
@SuppressWarnings("unchecked")
public boolean load(DataInputStream in) {
try {
chromosome = in.readUTF();
size = in.readInt();
if (verbose)
Timer.showStdErr(
"\tReading index for chromosome '" + chromosome + "' (index size: " + size + " )");
// Sanity cgheck
if (size < 0) return false;
// Allocate arrays
left = new int[size];
right = new int[size];
mid = new int[size];
intersectFilePosStart = new long[size][];
intersectFilePosEnd = new long[size][];
intersect = new List[size];
// Read array data
for (int i = 0; i < size; i++) {
left[i] = in.readInt();
right[i] = in.readInt();
mid[i] = in.readInt();
int len = in.readInt();
if (len > 0) {
// Allocate
intersectFilePosStart[i] = new long[len];
intersectFilePosEnd[i] = new long[len];
// Read values
for (int j = 0; j < len; j++) {
intersectFilePosStart[i][j] = in.readLong();
intersectFilePosEnd[i][j] = in.readLong();
}
} else {
intersectFilePosStart[i] = intersectFilePosEnd[i] = null;
}
}
} catch (EOFException e) {
return false;
} catch (IOException e) {
throw new RuntimeException(e);
}
return true;
}