/** {@inheritDoc} */
  @Override
  public Object read(final InputStream is) {
    final BasicNetwork result = new BasicNetwork();
    final FlatNetwork flat = new FlatNetwork();
    final EncogReadHelper in = new EncogReadHelper(is);
    EncogFileSection section;

    while ((section = in.readNextSection()) != null) {
      if (section.getSectionName().equals("BASIC")
          && section.getSubSectionName().equals("PARAMS")) {
        final Map<String, String> params = section.parseParams();
        result.getProperties().putAll(params);
      }
      if (section.getSectionName().equals("BASIC")
          && section.getSubSectionName().equals("NETWORK")) {
        final Map<String, String> params = section.parseParams();

        flat.setBeginTraining(EncogFileSection.parseInt(params, BasicNetwork.TAG_BEGIN_TRAINING));
        flat.setConnectionLimit(
            EncogFileSection.parseDouble(params, BasicNetwork.TAG_CONNECTION_LIMIT));
        flat.setContextTargetOffset(
            EncogFileSection.parseIntArray(params, BasicNetwork.TAG_CONTEXT_TARGET_OFFSET));
        flat.setContextTargetSize(
            EncogFileSection.parseIntArray(params, BasicNetwork.TAG_CONTEXT_TARGET_SIZE));
        flat.setEndTraining(EncogFileSection.parseInt(params, BasicNetwork.TAG_END_TRAINING));
        flat.setHasContext(EncogFileSection.parseBoolean(params, BasicNetwork.TAG_HAS_CONTEXT));
        flat.setInputCount(EncogFileSection.parseInt(params, PersistConst.INPUT_COUNT));
        flat.setLayerCounts(EncogFileSection.parseIntArray(params, BasicNetwork.TAG_LAYER_COUNTS));
        flat.setLayerFeedCounts(
            EncogFileSection.parseIntArray(params, BasicNetwork.TAG_LAYER_FEED_COUNTS));
        flat.setLayerContextCount(
            EncogFileSection.parseIntArray(params, BasicNetwork.TAG_LAYER_CONTEXT_COUNT));
        flat.setLayerIndex(EncogFileSection.parseIntArray(params, BasicNetwork.TAG_LAYER_INDEX));
        flat.setLayerOutput(section.parseDoubleArray(params, PersistConst.OUTPUT));
        flat.setLayerSums(new double[flat.getLayerOutput().length]);
        flat.setOutputCount(EncogFileSection.parseInt(params, PersistConst.OUTPUT_COUNT));
        flat.setWeightIndex(EncogFileSection.parseIntArray(params, BasicNetwork.TAG_WEIGHT_INDEX));
        flat.setWeights(section.parseDoubleArray(params, PersistConst.WEIGHTS));
        flat.setBiasActivation(section.parseDoubleArray(params, BasicNetwork.TAG_BIAS_ACTIVATION));
      } else if (section.getSectionName().equals("BASIC")
          && section.getSubSectionName().equals("ACTIVATION")) {
        int index = 0;

        flat.setActivationFunctions(new ActivationFunction[flat.getLayerCounts().length]);

        for (final String line : section.getLines()) {
          ActivationFunction af = null;
          final List<String> cols = EncogFileSection.splitColumns(line);

          // if this is a class name with a path, then do not default to inside of the Encog
          // package.
          String name;
          if (cols.get(0).indexOf('.') != -1) {
            name = cols.get(0);
          } else {
            name = "org.encog.engine.network.activation." + cols.get(0);
          }

          try {
            final Class<?> clazz = Class.forName(name);
            af = (ActivationFunction) clazz.newInstance();
          } catch (final ClassNotFoundException e) {
            throw new PersistError(e);
          } catch (final InstantiationException e) {
            throw new PersistError(e);
          } catch (final IllegalAccessException e) {
            throw new PersistError(e);
          }

          for (int i = 0; i < af.getParamNames().length; i++) {
            af.setParam(i, CSVFormat.EG_FORMAT.parse(cols.get(i + 1)));
          }

          flat.getActivationFunctions()[index++] = af;
        }
      }
    }

    result.getStructure().setFlat(flat);
    result.updateProperties();
    return result;
  }
  /** {@inheritDoc} */
  @Override
  public Object read(final InputStream is) {
    final RBFNetwork result = new RBFNetwork();
    final FlatNetworkRBF flat = (FlatNetworkRBF) result.getFlat();

    final EncogReadHelper in = new EncogReadHelper(is);
    EncogFileSection section;

    while ((section = in.readNextSection()) != null) {
      if (section.getSectionName().equals("RBF-NETWORK")
          && section.getSubSectionName().equals("PARAMS")) {
        final Map<String, String> params = section.parseParams();
        result.getProperties().putAll(params);
      }
      if (section.getSectionName().equals("RBF-NETWORK")
          && section.getSubSectionName().equals("NETWORK")) {
        final Map<String, String> params = section.parseParams();

        flat.setBeginTraining(EncogFileSection.parseInt(params, BasicNetwork.TAG_BEGIN_TRAINING));
        flat.setConnectionLimit(
            EncogFileSection.parseDouble(params, BasicNetwork.TAG_CONNECTION_LIMIT));
        flat.setContextTargetOffset(
            EncogFileSection.parseIntArray(params, BasicNetwork.TAG_CONTEXT_TARGET_OFFSET));
        flat.setContextTargetSize(
            EncogFileSection.parseIntArray(params, BasicNetwork.TAG_CONTEXT_TARGET_SIZE));
        flat.setEndTraining(EncogFileSection.parseInt(params, BasicNetwork.TAG_END_TRAINING));
        flat.setHasContext(EncogFileSection.parseBoolean(params, BasicNetwork.TAG_HAS_CONTEXT));
        flat.setInputCount(EncogFileSection.parseInt(params, PersistConst.INPUT_COUNT));
        flat.setLayerCounts(EncogFileSection.parseIntArray(params, BasicNetwork.TAG_LAYER_COUNTS));
        flat.setLayerFeedCounts(
            EncogFileSection.parseIntArray(params, BasicNetwork.TAG_LAYER_FEED_COUNTS));
        flat.setLayerContextCount(
            EncogFileSection.parseIntArray(params, BasicNetwork.TAG_LAYER_CONTEXT_COUNT));
        flat.setLayerIndex(EncogFileSection.parseIntArray(params, BasicNetwork.TAG_LAYER_INDEX));
        flat.setLayerOutput(section.parseDoubleArray(params, PersistConst.OUTPUT));
        flat.setLayerSums(new double[flat.getLayerOutput().length]);
        flat.setOutputCount(EncogFileSection.parseInt(params, PersistConst.OUTPUT_COUNT));
        flat.setWeightIndex(EncogFileSection.parseIntArray(params, BasicNetwork.TAG_WEIGHT_INDEX));
        flat.setWeights(section.parseDoubleArray(params, PersistConst.WEIGHTS));
        flat.setBiasActivation(section.parseDoubleArray(params, BasicNetwork.TAG_BIAS_ACTIVATION));
      } else if (section.getSectionName().equals("RBF-NETWORK")
          && section.getSubSectionName().equals("ACTIVATION")) {
        int index = 0;

        flat.setActivationFunctions(new ActivationFunction[flat.getLayerCounts().length]);

        for (final String line : section.getLines()) {
          ActivationFunction af = null;
          final List<String> cols = EncogFileSection.splitColumns(line);
          final String name = "org.encog.engine.network.activation." + cols.get(0);
          try {
            final Class<?> clazz = Class.forName(name);
            af = (ActivationFunction) clazz.newInstance();
          } catch (final ClassNotFoundException e) {
            throw new PersistError(e);
          } catch (final InstantiationException e) {
            throw new PersistError(e);
          } catch (final IllegalAccessException e) {
            throw new PersistError(e);
          }

          for (int i = 0; i < af.getParamNames().length; i++) {
            af.setParam(i, CSVFormat.EG_FORMAT.parse(cols.get(i + 1)));
          }

          flat.getActivationFunctions()[index++] = af;
        }

      } else if (section.getSectionName().equals("RBF-NETWORK")
          && section.getSubSectionName().equals("RBF")) {
        int index = 0;

        final int hiddenCount = flat.getLayerCounts()[1];
        final int inputCount = flat.getLayerCounts()[2];

        flat.setRBF(new RadialBasisFunction[hiddenCount]);

        for (final String line : section.getLines()) {
          RadialBasisFunction rbf = null;
          final List<String> cols = EncogFileSection.splitColumns(line);
          final String name = "org.encog.mathutil.rbf." + cols.get(0);
          try {
            final Class<?> clazz = Class.forName(name);
            rbf = (RadialBasisFunction) clazz.newInstance();
          } catch (final ClassNotFoundException e) {
            throw new PersistError(e);
          } catch (final InstantiationException e) {
            throw new PersistError(e);
          } catch (final IllegalAccessException e) {
            throw new PersistError(e);
          }

          rbf.setWidth(CSVFormat.EG_FORMAT.parse(cols.get(1)));
          rbf.setPeak(CSVFormat.EG_FORMAT.parse(cols.get(2)));
          rbf.setCenters(new double[inputCount]);

          for (int i = 0; i < inputCount; i++) {
            rbf.getCenters()[i] = CSVFormat.EG_FORMAT.parse(cols.get(i + 3));
          }

          flat.getRBF()[index++] = rbf;
        }
      }
    }

    return result;
  }