* Licensed to the Apache Software Foundation (ASF) under one

* or more contributor license agreements.  See the NOTICE file

* distributed with this work for additional information

* regarding copyright ownership.  The ASF licenses this file

* to you under the Apache License, Version 2.0 (the

* "License"); you may not use this file except in compliance

* with the License.  You may obtain a copy of the License at

*

*   http://www.apache.org/licenses/LICENSE-2.0

*

* Unless required by applicable law or agreed to in writing,

* software distributed under the License is distributed on an

* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY

* KIND, either express or implied.  See the License for the

* specific language governing permissions and limitations

* under the License.

*/

* Finds tokens based on context. There are two major groupings or ranges that

* will be used to create the additional annotations needed to handle the drug

* mentions used to represent the status changes.

*

* @author Mayo Clinic

*/

  // LOG4J logger based on class name

  public static Logger iv_logger = Logger.getLogger(DrugMentionAnnotator.class);

  /**

   * This identifies the section ids that will be considered in generating DrugMentionAnnotaitons

   */

  public static final String PARAM_SEGMENTS_MEDICATION_RELATED = "medicationRelatedSection";

  public static String DISTANCE = "DISTANCE"; 

  /**

   * Annotation type that is used to count the distance.

   */

  public static String DISTANCE_ANN_TYPE = "DISTANCE_ANN_TYPE";

 

    /**

     * Annotation type that defines the boundary within which the dictionary hits should be present.

     */

    public static String BOUNDARY_ANN_TYPE = "STATUS_BOUNDARY_ANN_TYPE";

    public static int NO_WINDOW_SIZE_SPECIFIED = -1;

    public static int NO_ANNOTATION_TYPE_SPECIFIED = -1;

    private int iWindowSize = NO_WINDOW_SIZE_SPECIFIED;   //window size to identify pair of annotations as related

    private int iAnnotationType = NO_ANNOTATION_TYPE_SPECIFIED; //type used to define a window

    private int iBoundaryAnnType = NO_ANNOTATION_TYPE_SPECIFIED; //type used to define boundary across which pairs cannot exist.

  private FractionStrengthFSM iv_fractionFSM;

  private RangeStrengthFSM iv_rangeFSM;

  private SubSectionIndicatorFSM iv_subMedSectionFSM;

  private DosagesFSM iv_dosagesFSM;

  private SuffixStrengthFSM iv_suffixFSM;

  private DurationFSM iv_durationFSM;

  private RouteFSM iv_routeFSM;

  private FrequencyFSM iv_frequencyFSM;

  private DrugChangeStatusFSM iv_statusFSM;

  private DecimalStrengthFSM iv_decimalFSM;

  private StrengthFSM iv_strengthFSM;

  private StrengthUnitFSM iv_strengthUnitFSM;

  private FrequencyUnitFSM iv_frequencyUnitFSM;

  private FormFSM iv_formFSM;

  private static final int NERTypeIdentifier = 1;

  private static boolean handledRanges;

  private Set<String> iv_exclusionTagSet = null;

  private Set<String> iv_medicationRelatedSections = new HashSet<String>();

  public void initialize(UimaContext annotCtx)

  throws ResourceInitializationException

  {

    super.initialize(annotCtx);