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;
   }
 }
Beispiel #2
0
  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");
    }
  }