public static void main(String[] args) throws Exception {
String sourceUrlString = "data/test.html";
if (args.length == 0)
System.err.println("Using default argument of \"" + sourceUrlString + '"');
else sourceUrlString = args[0];
if (sourceUrlString.indexOf(':') == -1) sourceUrlString = "file:" + sourceUrlString;
StreamedSource streamedSource = new StreamedSource(new URL(sourceUrlString));
// streamedSource.setBuffer(new char[65000]); // uncomment this to use a fixed buffer size
Writer writer = null;
try {
writer =
new OutputStreamWriter(
new FileOutputStream("StreamedSourceCopyOutput.html"), streamedSource.getEncoding());
System.out.println("Processing segments:");
int lastSegmentEnd = 0;
for (Segment segment : streamedSource) {
System.out.println(segment.getDebugInfo());
if (segment.getEnd() <= lastSegmentEnd)
continue; // if this tag is inside the previous tag (e.g. a server tag) then ignore it as
// it was already output along with the previous tag.
lastSegmentEnd = segment.getEnd();
if (segment instanceof Tag) {
Tag tag = (Tag) segment;
// HANDLE TAG
// Uncomment the following line to ensure each tag is valid XML:
// writer.write(tag.tidy()); continue;
} else if (segment instanceof CharacterReference) {
CharacterReference characterReference = (CharacterReference) segment;
// HANDLE CHARACTER REFERENCE
// Uncomment the following line to decode all character references instead of copying them
// verbatim:
// characterReference.appendCharTo(writer); continue;
} else {
// HANDLE PLAIN TEXT
}
// unless specific handling has prevented getting to here, simply output the segment as is:
writer.write(segment.toString());
}
writer.close();
System.err.println(
"\nA copy of the source document has been output to StreamedSourceCopyOuput.html");
} catch (Exception ex) {
if (writer != null)
try {
writer.close();
} catch (IOException ex2) {
}
throw ex;
}
}
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");
}
}
