Example #1
0
 private void writeState(XMLWriter writer) {
   writer.startTag(RepositoriesViewContentHandler.REPOSITORIES_VIEW_TAG, null, true);
   // Write the repositories
   Collection repos = Arrays.asList(getKnownRepositoryLocations());
   Iterator it = repos.iterator();
   while (it.hasNext()) {
     CVSRepositoryLocation location = (CVSRepositoryLocation) it.next();
     RepositoryRoot root = getRepositoryRootFor(location);
     root.writeState(writer);
   }
   writer.endTag(RepositoriesViewContentHandler.REPOSITORIES_VIEW_TAG);
 }
 public void startElement(
     SimplePath path, String name, AttributesImpl attributes, String leadingCDdata) {
   previousCallbackWasCDATA = false;
   log(path.toString() + ":");
   String startTag = XMLWriter.createStartTag(name, attributes);
   log(startTag);
   if (leadingCDdata != null) {
     String encodedText = XMLEncode.xmlEncodeText(leadingCDdata);
     log(encodedText);
   }
 }
Example #3
0
 protected void saveState() throws TeamException {
   IPath pluginStateLocation = CVSUIPlugin.getPlugin().getStateLocation();
   File tempFile =
       pluginStateLocation.append(REPOSITORIES_VIEW_FILE + ".tmp").toFile(); // $NON-NLS-1$
   File stateFile = pluginStateLocation.append(REPOSITORIES_VIEW_FILE).toFile();
   try {
     XMLWriter writer = new XMLWriter(new BufferedOutputStream(new FileOutputStream(tempFile)));
     try {
       writeState(writer);
     } finally {
       writer.close();
     }
     if (stateFile.exists()) {
       stateFile.delete();
     }
     boolean renamed = tempFile.renameTo(stateFile);
     if (!renamed) {
       throw new TeamException(
           new Status(
               IStatus.ERROR,
               CVSUIPlugin.ID,
               TeamException.UNABLE,
               NLS.bind(
                   CVSUIMessages.RepositoryManager_rename,
                   new String[] {tempFile.getAbsolutePath()}),
               null));
     }
   } catch (IOException e) {
     throw new TeamException(
         new Status(
             IStatus.ERROR,
             CVSUIPlugin.ID,
             TeamException.UNABLE,
             NLS.bind(
                 CVSUIMessages.RepositoryManager_save, new String[] {stateFile.getAbsolutePath()}),
             e));
   }
 }
Example #4
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");
    }
  }
Example #5
0
 private void writeCommentHistory(XMLWriter writer) {
   writer.startTag(ELEMENT_COMMIT_HISTORY, null, false);
   for (int i = 0; i < previousComments.length && i < maxComments; i++)
     writer.printSimpleTag(ELEMENT_COMMIT_COMMENT, previousComments[i]);
   writer.endTag(ELEMENT_COMMIT_HISTORY);
 }
Example #6
0
 private void writeCommentTemplates(XMLWriter writer) {
   writer.startTag(ELEMENT_COMMENT_TEMPLATES, null, false);
   for (int i = 0; i < commentTemplates.length; i++)
     writer.printSimpleTag(ELEMENT_COMMIT_COMMENT, commentTemplates[i]);
   writer.endTag(ELEMENT_COMMENT_TEMPLATES);
 }