public Alignment bandedAlign(String ref, String query) throws Exception {
ACGTSequence r = new ACGTSequence(ref);
ACGTSequence q = new ACGTSequence(query);
Alignment alignment = SmithWatermanAligner.bandedAlign(r, q);
_logger.debug(alignment);
return alignment;
}
@Test
public void parseLine() throws IOException, RecognitionException {
DTDParser parser =
DTDParserUtil.createParser(
FileResource.find(DTDParserTest.class, "simple.dtd").openStream());
DTDParser.dtd_return r = parser.dtd();
CommonTree t = (CommonTree) r.getTree();
_logger.debug(ANTLRUtil.parseTree(t, DTDParser.tokenNames));
}
@Test
public void scan() throws Exception {
ACGTSequence q =
new ACGTSequence(
"TTTATACGTGTTTGAATAACTTGGCCAAATCGCCGAGAAGGAATAGAATACTGGACGACATTGTACATATTTTCCAAAAAATCAGAAAGTAGATGACGGG");
PrefixScan scan =
PrefixScan.scanRead(fmIndex, q, Strand.FORWARD, new StaircaseFilter(q.length(), 7));
_logger.debug(scan);
}
HashedArrayList<String, String> parse(String file) throws Exception {
JSONStreamReader reader =
new JSONStreamReader(FileResource.open(JSONStreamReaderTest.class, file));
TreeEvent e;
HashedArrayList<String, String> data = new HashedArrayList<String, String>();
while ((e = reader.next()) != null) {
_logger.debug(e);
if (e.isVisit()) data.put(e.nodeName, e.nodeValue);
}
return data;
}
public static void main(String[] args) throws OptionParserException, IOException {
Config config = new Config();
OptionParser optionParser = new OptionParser(config);
optionParser.parse(args);
if (config.displayHelp) {
optionParser.printUsage();
}
if (config.verbose) {
Logger.getRootLogger().setLogLevel(LogLevel.ALL);
}
if (config.searchFolderName == null) {
System.err.println("no search folder is specified");
return;
}
_logger.debug("search folder = " + config.searchFolderName);
if (config.packageName == null || config.className == null) {
System.err.println("no package or class name is given");
return;
}
// search track classes
File searchFolder = new File(config.searchFolderName);
TrackResourceFinder finder = new TrackResourceFinder(searchFolder);
finder.enter(searchFolder);
// template
Template template =
new Template(
FileResource.find(TrackLoaderGenerator.class, "TrackLoader.java.template")
.openStream());
Properties p = new Properties();
p.put("trackClasses", finder.trackClassFile);
p.put("trackGroupClasses", finder.trackGroupClassFile);
p.put("packageName", config.packageName);
p.put("className", config.className);
String result = template.apply(p);
System.out.print(result);
}
public void addRelation(Relation relation) {
_logger.debug("add relation: " + relation.toString());
}