Exemplo n.º 1
1
 /*
  * public HashMap getLeafElements() { HashMap map = new HashMap(); Object[]
  * elts = dataElements.values().toArray(); for (int j=0; j<elts.length; j++)
  * { PDMDataElement data = (PDMDataElement) elts[j];
  * map.put(data.getID(),data); } Object[] ops =
  * operations.values().toArray(); for (int i=0; i<ops.length; i++){
  * PDMOperation op = (PDMOperation) ops[i]; if
  * (!(op.getInputElements().isEmpty())){ HashMap outs =
  * op.getOutputElements(); Object[] outArray = outs.values().toArray(); for
  * (int j=0; j<outArray.length; j++) { PDMDataElement d = (PDMDataElement)
  * outArray[j]; map.remove(d.getID()); } } } return map; }
  */
 public HashMap getLeafElements() {
   HashMap result = new HashMap();
   HashSet leafOps = getLeafOperations();
   if (!(leafOps.isEmpty())) {
     Iterator it = leafOps.iterator();
     while (it.hasNext()) {
       PDMOperation op = (PDMOperation) it.next();
       PDMDataElement data = op.getOutputElement();
       result.put(data.getID(), data);
     }
   } else {
     Object[] elts = dataElements.values().toArray();
     for (int j = 0; j < elts.length; j++) {
       PDMDataElement data = (PDMDataElement) elts[j];
       result.put(data.getID(), data);
     }
     Object[] ops = operations.values().toArray();
     for (int i = 0; i < ops.length; i++) {
       PDMOperation op = (PDMOperation) ops[i];
       HashMap outs = op.getOutputElements();
       Object[] outArray = outs.values().toArray();
       for (int j = 0; j < outArray.length; j++) {
         PDMDataElement d = (PDMDataElement) outArray[j];
         result.remove(d.getID());
       }
     }
   }
   return result;
 }
Exemplo n.º 2
0
  @Override
  public void execute() {
    Map<String, Set<CortexLinksMap>> links = new HashMap<String, Set<CortexLinksMap>>();
    Map<String, Set<String>> linkFilenames = new HashMap<String, Set<String>>();
    if (LINKS != null && !LINKS.isEmpty()) {
      for (CortexLinksMap cl : LINKS) {
        String name = cl.getCortexLinks().getColor(0).getSampleName();

        if (!links.containsKey(name)) {
          links.put(name, new HashSet<CortexLinksMap>());
          linkFilenames.put(name, new HashSet<String>());
        }

        links.get(name).add(cl);
        linkFilenames.get(name).add(cl.getCortexLinks().getCortexLinksFile().getAbsolutePath());
      }
      log.info("Loaded {} links", LINKS.size());

      for (CortexLinksMap clm : LINKS) {
        log.info(
            "  {}: {}",
            clm.getCortexLinks().getCortexLinksFile().getAbsolutePath(),
            clm.getCortexLinks().getNumLinks());
      }
    }

    log.info("Loaded {} graphs", GRAPHS.size());
    for (CortexGraph cg : GRAPHS) {
      String name = cg.getColor(0).getSampleName();
      graphs.put(cg.getCortexFile().getName(), cg);

      log.info(
          "  {}: {} {}", cg.getCortexFile().getName(), cg.getKmerSize(), linkFilenames.get(name));
    }

    loadContigs();
    log.info("Loaded {} contigs", contigs.size());

    log.info("Listening on port {}", PORT);

    try {
      HttpServer server = HttpServer.create(new InetSocketAddress(PORT), 0);
      server.createContext("/", new PageHandler());
      server.createContext("/graphlist", new GraphList());
      server.createContext("/search", new SearchHandler());
      server.createContext("/cr", new CtxRecordHandler());
      server.createContext("/links", new LinksHandler());
      server.setExecutor(null);
      server.start();
    } catch (IOException e) {
      throw new IndianaException("Unable to start server", e);
    }
  }
Exemplo n.º 3
0
 public boolean hashSetContainsSameOperations(HashSet set1, HashSet set2) {
   boolean result = false;
   HashSet s1 = (HashSet) set1.clone();
   HashSet s2 = (HashSet) set2.clone();
   // first part, are all elements of s1 also in s2?
   boolean one = false;
   Iterator it = set1.iterator();
   while (it.hasNext()) {
     PDMOperation d = (PDMOperation) it.next();
     if (s2.contains(d)) {
       s1.remove(d);
     }
   }
   if (s1.isEmpty()) {
     one = true;
   }
   // second part, are all elements of s21 also in s1?
   boolean two = false;
   HashSet s3 = (HashSet) set1.clone();
   HashSet s4 = (HashSet) set2.clone();
   Iterator it2 = set2.iterator();
   while (it2.hasNext()) {
     PDMOperation d = (PDMOperation) it2.next();
     if (s3.contains(d)) {
       s4.remove(d);
     }
   }
   if (s4.isEmpty()) {
     two = true;
   }
   // administrative stuff
   s1.clear();
   s2.clear();
   s3.clear();
   s4.clear();
   result = one && two;
   return result;
 }
Exemplo n.º 4
0
 void remove() {
   UFNode root = this.find();
   if (root != this) for (UFNode child : children) child.parent = root;
   else if (!children.isEmpty()) {
     Iterator<UFNode> it = children.iterator();
     root = it.next();
     root.parent = null;
     while (it.hasNext()) it.next().parent = root;
     root.size = this.size;
   }
   root.size--;
   this.parent = null;
   this.size = 1;
 }
Exemplo n.º 5
0
  synchronized void updateAll() {
    HashSet<Node> seenNodes = new HashSet<Node>();
    for (int i = 0; i < _all.size(); i++) {
      Node n = _all.get(i);
      n.update(seenNodes);
    }

    if (!seenNodes.isEmpty()) {
      // not empty, means that at least 1 server gave node list
      // remove unused hosts
      Iterator<Node> it = _all.iterator();
      while (it.hasNext()) {
        if (!seenNodes.contains(it.next())) it.remove();
      }
    }
  }
Exemplo n.º 6
0
    private void unpackSegment(InputStream in, JarOutputStream out) throws IOException {
      _props.setProperty(java.util.jar.Pack200.Unpacker.PROGRESS, "0");
      // Process the output directory or jar output.
      new PackageReader(pkg, in).read();

      if (_props.getBoolean("unpack.strip.debug")) pkg.stripAttributeKind("Debug");
      if (_props.getBoolean("unpack.strip.compile")) pkg.stripAttributeKind("Compile");
      _props.setProperty(java.util.jar.Pack200.Unpacker.PROGRESS, "50");
      pkg.ensureAllClassFiles();
      // Now write out the files.
      HashSet classesToWrite = new HashSet(pkg.getClasses());
      for (Iterator i = pkg.getFiles().iterator(); i.hasNext(); ) {
        Package.File file = (Package.File) i.next();
        String name = file.nameString;
        JarEntry je = new JarEntry(Utils.getJarEntryName(name));
        boolean deflate;

        deflate =
            (keepDeflateHint)
                ? (((file.options & Constants.FO_DEFLATE_HINT) != 0)
                    || ((pkg.default_options & Constants.AO_DEFLATE_HINT) != 0))
                : deflateHint;

        boolean needCRC = !deflate; // STORE mode requires CRC

        if (needCRC) crc.reset();
        bufOut.reset();
        if (file.isClassStub()) {
          Package.Class cls = file.getStubClass();
          assert (cls != null);
          new ClassWriter(cls, needCRC ? crcOut : bufOut).write();
          classesToWrite.remove(cls); // for an error check
        } else {
          // collect data & maybe CRC
          file.writeTo(needCRC ? crcOut : bufOut);
        }
        je.setMethod(deflate ? JarEntry.DEFLATED : JarEntry.STORED);
        if (needCRC) {
          if (verbose > 0)
            Utils.log.info("stored size=" + bufOut.size() + " and crc=" + crc.getValue());

          je.setMethod(JarEntry.STORED);
          je.setSize(bufOut.size());
          je.setCrc(crc.getValue());
        }
        if (keepModtime) {
          je.setTime(file.modtime);
          // Convert back to milliseconds
          je.setTime((long) file.modtime * 1000);
        } else {
          je.setTime((long) modtime * 1000);
        }
        out.putNextEntry(je);
        bufOut.writeTo(out);
        out.closeEntry();
        if (verbose > 0) Utils.log.info("Writing " + Utils.zeString((ZipEntry) je));
      }
      assert (classesToWrite.isEmpty());
      _props.setProperty(java.util.jar.Pack200.Unpacker.PROGRESS, "100");
      pkg.reset(); // reset for the next segment, if any
    }
Exemplo n.º 7
0
  public PDMStateSpace calculateSimpleStateSpace(
      boolean root, boolean failure, boolean input, boolean colored, int numStates, int breadth) {
    PDMStateSpace result = new PDMStateSpace(this, colored);
    HashSet states = new HashSet();
    int j = (operations.size() + 1);

    if (!input) {
      HashSet empty = new HashSet();
      PDMState st = new PDMState(result, "state" + i, empty, empty, empty);
      result.addState(st);
      states.add(st);
      i++;
    } else {
      // Start with the complete set of input data elements available
      HashSet empty = new HashSet();
      String name = new String("state" + i);
      HashSet ins = new HashSet(); // this hashSet contains the input
      // elements to the process (input
      // elements of PDM)
      HashSet execOps = new HashSet();
      // Fill the hashSet with the leaf elements
      HashMap leafs = getLeafElements();
      Object[] leafElts = leafs.values().toArray();
      for (int i = 0; i < leafElts.length; i++) {
        PDMDataElement d = (PDMDataElement) leafElts[i];
        ins.add(d);
      }
      HashSet leafOps = getLeafOperations();
      Iterator it = leafOps.iterator();
      while (it.hasNext()) {
        PDMOperation op = (PDMOperation) it.next();
        execOps.add(op);
      }

      PDMState start = new PDMState(result, name, ins, execOps, empty); // start
      // state
      // of
      // the
      // statespace
      result.addState(start);
      i++;
      states.add(start);
    }
    while (!states.isEmpty()) {
      HashSet states2 = (HashSet) states.clone();
      Iterator it = states2.iterator();
      while (it.hasNext()) {
        PDMState state = (PDMState) it.next();
        HashSet nextStates = calculateNextStates(state, result, root, failure, numStates, breadth);
        Iterator it2 = nextStates.iterator();
        // Add the new states to iterator
        while (it2.hasNext()) {
          PDMState st = (PDMState) it2.next();
          states.add(st);
        }
        states.remove(state);
      }
    }
    i = 0;
    j = 0;
    Message.add("<PDMMDPStateSpace>", Message.TEST);
    Message.add("<NumberOfStates = " + result.getNumberOfStates() + " >", Message.TEST);
    Message.add("</PDMMDPStateSpace>", Message.TEST);
    return result;
  }