// This is VERY slow.
// ABout 50% from DNATools.dnaToke
// About 30% from StringBuffer.toString
// About 20% from StringBuffer.<init>
protected static String keyFromSyms(Symbol[] syms) {
StringBuffer buf = new StringBuffer(syms.length);
try {
for (int i = 0; i < syms.length; i++) {
buf.append(DNATools.dnaToken(syms[i]));
}
} catch (Exception e) {
System.err.println("NmerCounter called with non-DNA symbol");
System.exit(1);
}
return buf.toString();
}
@Override
protected void processResults() throws ServiceException {
String seqs[] = getOutputs().get("sequences").split(">");
String seq1 = seqs[0].substring(seqs[0].indexOf('\n')).replace("\n", "").trim();
String seq2 = seqs[1].substring(seqs[1].indexOf('\n')).replace("\n", "").trim();
try {
if (isAa()) {
setAlignedSequence1(
ProteinTools.createGappedProteinSequence(seq1, getSequence1().getName()));
setAlignedSequence2(
ProteinTools.createGappedProteinSequence(seq2, getSequence2().getName()));
} else {
setAlignedSequence1(DNATools.createGappedDNASequence(seq1, getSequence1().getName()));
setAlignedSequence2(DNATools.createGappedDNASequence(seq2, getSequence2().getName()));
}
} catch (IllegalSymbolException e) {
e.printStackTrace();
throw new AlignServiceException(getService(), getUrl(), e);
}
setScore(Double.parseDouble(getOutputs().get("score")));
}
/**
* Test constructor to create a non-empty database.
*
* @throws BioException if iterator fails.
*/
public void testNonEmptyConstructor() throws BioException {
SimpleSymbolPropertyTableDB dbInit = new SimpleSymbolPropertyTableDB();
SymbolPropertyTable t1 = new SimpleSymbolPropertyTable(ProteinTools.getAlphabet(), "protein");
SymbolPropertyTable t2 = new SimpleSymbolPropertyTable(DNATools.getDNA(), "dna");
dbInit.addTable(t1);
dbInit.addTable(t2);
SymbolPropertyTableDB db = new SimpleSymbolPropertyTableDB(dbInit.tableIterator());
assertEquals("Database has wrong number of tables.", 2, db.numTables());
SymbolPropertyTableIterator iterator = db.tableIterator();
ArrayList tables = new ArrayList(2);
while (iterator.hasNext()) {
tables.add(iterator.nextTable());
}
assertEquals("Iterator returned wrong number of tables.", 2, tables.size());
assertEquals("Iterator returned wrong table.", t1, tables.get(0));
assertEquals("Iterator returned wrong table.", t2, tables.get(1));
}
/**
* Test for {@link SimpleSymbolPropertyTableDB#addTable(SymbolPropertyTable)}.
*
* @throws IllegalIDException if {@link SymbolPropertyTableDB#table(String)} fails.
*/
public void testAddTable() throws IllegalIDException {
SimpleSymbolPropertyTableDB db = new SimpleSymbolPropertyTableDB();
SymbolPropertyTable t1 = new SimpleSymbolPropertyTable(ProteinTools.getAlphabet(), "protein");
SymbolPropertyTable t2 = new SimpleSymbolPropertyTable(DNATools.getDNA(), "dna");
db.addTable(t1);
assertEquals("Database has wrong number of tables.", 1, db.numTables());
db.addTable(t2);
assertEquals("Database has wrong number of tables.", 2, db.numTables());
assertEquals("Database returned wrong table.", t1, db.table("protein"));
assertEquals("Database returned wrong table.", t2, db.table("dna"));
Set names = db.names();
assertTrue("Table is missing.", names.contains("protein"));
assertTrue("Table is missing.", names.contains("dna"));
assertEquals("Database has wrong number of tables.", 2, names.size());
try {
db.addTable(null);
fail("addTable must throw NullPointerException.");
} catch (NullPointerException e) {
e.printStackTrace();
}
}
@Override
public boolean elementPasses(AlignmentPosStreamerPosition streamPos) {
return streamPos.currentAp.getRef().equals(DNATools.c());
}
private void dnaCommand(HttpServletRequest req, DazzleResponse resp, DazzleDataSource dds)
throws IOException, DataSourceException, ServletException, DazzleException {
DazzleReferenceSource drs = (DazzleReferenceSource) dds;
List segments = DazzleTools.getSegments(dds, req, resp);
if (segments.size() == 0) {
throw new DazzleException(
DASStatus.STATUS_BAD_COMMAND_ARGUMENTS, "No segments specified for dna command");
}
// Fetch and validate the requests.
Map segmentResults = new HashMap();
for (Iterator i = segments.iterator(); i.hasNext(); ) {
Segment seg = (Segment) i.next();
try {
Sequence seq = drs.getSequence(seg.getReference());
if (seq.getAlphabet() != DNATools.getDNA()) {
throw new DazzleException(
DASStatus.STATUS_SERVER_ERROR,
"Sequence " + seg.toString() + " is not in the DNA alphabet");
}
if (seg.isBounded()) {
if (seg.getMin() < 1 || seg.getMax() > seq.length()) {
throw new DazzleException(
DASStatus.STATUS_BAD_COORDS,
"Segment " + seg.toString() + " doesn't fit sequence of length " + seq.length());
}
}
segmentResults.put(seg, seq);
} catch (NoSuchElementException ex) {
throw new DazzleException(DASStatus.STATUS_BAD_REFERENCE, ex);
} catch (DataSourceException ex) {
throw new DazzleException(DASStatus.STATUS_SERVER_ERROR, ex);
}
}
//
// Looks okay -- generate the response document
//
XMLWriter xw = resp.startDasXML("DASDNA", "dasdna.dtd");
try {
xw.openTag("DASDNA");
for (Iterator i = segmentResults.entrySet().iterator(); i.hasNext(); ) {
Map.Entry me = (Map.Entry) i.next();
Segment seg = (Segment) me.getKey();
Sequence seq = (Sequence) me.getValue();
xw.openTag("SEQUENCE");
xw.attribute("id", seg.getReference());
xw.attribute("version", drs.getLandmarkVersion(seg.getReference()));
if (seg.isBounded()) {
xw.attribute("start", "" + seg.getStart());
xw.attribute("stop", "" + seg.getStop());
} else {
xw.attribute("start", "" + 1);
xw.attribute("stop", "" + seq.length());
}
SymbolList syms = seq;
if (seg.isBounded()) {
syms = syms.subList(seg.getMin(), seg.getMax());
}
if (seg.isInverted()) {
syms = DNATools.reverseComplement(syms);
}
xw.openTag("DNA");
xw.attribute("length", "" + syms.length());
for (int pos = 1; pos <= syms.length(); pos += 60) {
int maxPos = Math.min(syms.length(), pos + 59);
xw.println(syms.subStr(pos, maxPos));
}
xw.closeTag("DNA");
xw.closeTag("SEQUENCE");
}
xw.closeTag("DASDNA");
xw.close();
} catch (Exception ex) {
throw new DazzleException(ex, "Error writing DNA document");
}
}