// file: $isip/class/mmedia/TranscriptionDatabase/trans_05.cc
// version: $Id: trans_05.cc 9421 2004-03-10 20:11:33Z parihar $
//

// isip include files
//
#include "TranscriptionDatabase.h"

// method: assign
//
// arguments:
//  const TranscriptionDatabase& arg: (input) transDB object
//
// return: logical error status
//
// this method has assigns the input transcription database
//
bool8 TranscriptionDatabase::assign(const TranscriptionDatabase& arg_a) {

  // declare local variables
  //
  bool8 status = false;

  // determine if the TranscriptionDatabase objects are equal
  //
  status = name_d.assign(arg_a.name_d);
  status &= hash_index_d.assign(arg_a.hash_index_d);

  // return the status
  //
  return status;
}

// method: sofSize
//
// arguments: none
//
// return: logical error status
//
// this method determines the size of the object
//
int32 TranscriptionDatabase::sofSize() const {

  // declare local variables
  //
  int32 size = 0;

  // get the size of the object
  //
  size = name_d.sofSize();
  size += hash_index_d.sofSize();

  // return the size
  //
  return size;
}

// method: eq
//
// arguments:
//  const TranscriptionDatabase& arg: (input) transDB object
//
// return: logical error status
//
// this method has determines if the transcription databases are equal
//
bool8 TranscriptionDatabase::eq(const TranscriptionDatabase& arg_a) const {
  
  // declare local variables
  //
  bool8 status = false;

  // determine if the TranscriptionDatabase objects are equal
  //
  status = name_d.eq(arg_a.name_d);
  status &= hash_index_d.eq(arg_a.hash_index_d);

  // return the status
  //
  return status;
}

// method: clear
//
// arguments:
//  Integral::CMODE cmode: (input) clear mode
//
// return: logical error status
//
// this method clears the content of the current object
//
bool8 TranscriptionDatabase::clear(Integral::CMODE cmode_a) {

  // declare local variables
  //
  bool8 status = false;  

  // clear the data members
  //
  status = name_d.clear(cmode_a);
  status &= hash_d.clear(cmode_a);  
  status &= hash_index_d.clear(cmode_a);
  
  // return the status
  //
  return status;
}

// method: insertRecord
//
// arguments:
//  String& identifier: (input) annotation graph id
//  AnnotationGraph& graph: (input) desired annotation graph
//
// return: logical error status
//
// this method inserts the record into the database
//
bool8 TranscriptionDatabase::insertRecord(String& identifier_a,
					    AnnotationGraph& graph_a) {

  // make sure the name of the graph matches the database name
  //
  if (!graph_a.getId().eq(name_d)) {
    return Error::handle(name(), L"insertRecord", Error::ARG, __FILE__, __LINE__);
  }

  Long values;

  // get the keys associated with the hash table
  //
  Vector<String> keys;
  if (!hash_d.keys(keys)) {
    return Error::handle(name(), L"insertRecord", Error::ARG, __FILE__, __LINE__);
  }
  
  values.assign(keys.length());
  
  hash_index_d.insert(identifier_a, &values);
  
  // insert the record into the database
  //
  return hash_d.insert(identifier_a, &graph_a);
}

// method: getRecord
//
// arguments:
//  String& identifier: (input) annotation graph id
//  AnnotationGraph& graph: (output) desired annotation graph
//
// return: logical error status
//
// this method retrieves the record from the database
//
bool8 TranscriptionDatabase::getRecord(String& identifier_a,
					 AnnotationGraph& graph_a) {

  // declare local variables
  //
  Long* tag;
  
  // determine if the identifier exists in the database
  //
  tag = hash_index_d.get(identifier_a);
  if (tag == (Long*)NULL) {
    return false;
  }
  
  // when the identifier exists in the database return a copy of the record
  //
  else {
    graph_a.clear();
    if (!graph_a.read(database_sof_d, (int32)*tag)) {
      Error::handle(name(), L"getReord", Error::NO_PARAM_FILE,
		    __FILE__, __LINE__);      
    }
  }

  // exit gracefully
  //
  return true;
}

// method: getRecord
//
// arguments:
//  String& identifier: (input) annotation graph id
//  String& feature: (input) annotation feature
//  String& value: (input) annotation feature value
//  DoubleLinkedList<String>& records: (output) list of records
//
// return: logical error status
//
// this method retrieves the record from the database
//
bool8 TranscriptionDatabase::getRecord(String& identifier_a,
					 String& feature_a, String& value_a,
					 DoubleLinkedList<String>& records_a) {

  // declare local variables
  //
  String tmpstr;
  DoubleLinkedList<Annotation> annos;
  AnnotationGraph graph;  

  // declare local variables
  //
  Long* tag;
  
  // determine if the identifier exists in the database
  //
  tag = hash_index_d.get(identifier_a);
  if (tag == (Long*)NULL) {
    return false;
  }
  
  // when the identifier exists in the database return a copy of the record
  //
  else {
    graph.clear();
    if (!graph.read(database_sof_d, (int32)*tag)) {
      Error::handle(name(), L"getReord", Error::NO_PARAM_FILE,
		    __FILE__, __LINE__);      
    }

    // retrieve the list of records from the database that contains
    // the features
    //

    // get the annotations with the given features
    //
    if (!graph.getAnnotationSetByFeature(feature_a, value_a, annos)) {
      return Error::handle(name(), L"getRecord - unable to find the annotation for the given feature and the value", Error::ARG, __FILE__, __LINE__);      
    }

    // add the annotation labels to the list
    //
    for (bool8 more=annos.gotoFirst(); more; more=annos.gotoNext()) {
      tmpstr.assign(annos.getCurr()->getType());
      records_a.insert(&tmpstr);
    }
  }

  // clean up memory
  //
  graph.clear();
  
  // exit gracefully
  //
  return true;
}

// method: getRecord
//
// arguments:
//  String& identifier: (input) annotation graph id
//  String& feature: (input) annotation feature
//  String& value: (input) annotation feature value
//  DoubleLinkedList<Annotation>& records: (output) list of records
//
// return: logical error status
//
// this method retrieves the record from the database
//
bool8 TranscriptionDatabase::getRecord(String& identifier_a,
					 String& feature_a, String& value_a,
				  DoubleLinkedList<Annotation>& records_a) {

  // declare local variables
  //
  AnnotationGraph graph;
  DoubleLinkedList<Annotation> records;
  
  // declare local variables
  //
  Long* tag;
  
  // determine if the identifier exists in the database
  //
  tag = hash_index_d.get(identifier_a);
  if (tag == (Long*)NULL) {
    return false;
  }
  
  // when the identifier exists in the database return a copy of the record
  //
  else {
    graph.clear();
    if (!graph.read(database_sof_d, (int32)*tag)) {
      Error::handle(name(), L"getRecord", Error::NO_PARAM_FILE,
		    __FILE__, __LINE__);      
    }
    
    // retrieve the list of records from the database that contains
    // the features
    //
    else {

      // get the annotations with the given features
      //
      if (!graph.getAnnotationSetByFeature(feature_a, value_a, records)) {
	return false;
      }
    }
  }

  records_a.assign(records);

  // clean up memory
  //
  graph.clear();
  
  // exit gracefully
  //
  return true;
}

// method: getRecord
//
// arguments:
//  String& identifier: (input) annotation graph id
//  String& feature_name: (input) feature name
//  Vector<String>& values: (input) annotation feature values corresponding
//                          to  feature-name
//  String& record: (output) alignments
//
// return: logical error status
//
// this method retrieves the alignment from the database
//
bool8 TranscriptionDatabase::getRecord(String& identifier_a,
					 String& feature_name_a,
					 Vector<String>& values_a,
					 String& record_a) {
  
  // declare local variables
  //
  DoubleLinkedList<Annotation> annos;
  AnnotationGraph graph;  
  Long* tag;
  String fea_score(L"score");
  
  // check for input values
  //
  if (values_a.length() <= int32(0)) {
    Error::handle(name(), L"getRecord - levels missing", Error::ARG,
		  __FILE__, __LINE__);      
  }
  
  // determine if the identifier exists in the database
  //
  tag = hash_index_d.get(identifier_a);
  if (tag == (Long*)NULL) {
    Error::handle(name(), L"getRecord - annotation-graph missing", Error::ARG,
		  __FILE__, __LINE__);      
  }
  
  // when the identifier exists in the database return a copy of the record
  //
  else {
    graph.clear();
    if (!graph.read(database_sof_d, (int32)*tag)) {
      Error::handle(name(), L"getRecord", Error::ARG,
		    __FILE__, __LINE__);      
    }

    // loop over all the required levels
    //
    for (int32 i = 0; i < values_a.length(); i++) {
    
      // get all the annotations at feature "level" and value starting
      // with the top-most level
      //
      if (!graph.getAnnotationSetByFeature(feature_name_a, values_a(i),
					   annos)) {
	return Error::handle(name(), L"getRecord - unable to find the annotations for the given feature and the value", Error::ARG, __FILE__, __LINE__);
      }

      // update the output alignment format
      //
      record_a.concat(L"\n");
      record_a.concat(L"  ");
      record_a.concat(feature_name_a);
      record_a.concat(L": ");
      record_a.concat(values_a(i));
    
      // loop over each annotation at this level
      //
      Annotation* anno = (Annotation*)NULL;
      for (bool8 more = annos.gotoFirst(); more; more = annos.gotoNext()) {
	anno = (Annotation*)NULL;
	anno = annos.getCurr();

	// check the annotation for NULL
	//
	if (anno == (Annotation*)NULL) {
	  return Error::handle(name(), L"getRecord - NULL Annotation",
			       Error::ARG, __FILE__, __LINE__);
	}
	
	// get the type and the score at this annotation
	//
	String type;
	String score;
	type.assign(anno->getType());
	score.assign(anno->getFeature(fea_score));
	
	// get start and end anchors for the current annotation
	//
	Anchor* anch_start = (Anchor*)NULL;
	Anchor* anch_end = (Anchor*)NULL;
	anch_start = anno->getStartAnchor();
	anch_end = anno->getEndAnchor();
	
	// check for NULL anchors
	//
	if ((anch_start == (Anchor*)NULL) || (anch_end == (Anchor*)NULL)) {
	  return Error::handle(name(), L"getRecord - NULL Anchors",
			       Error::ARG, __FILE__, __LINE__);
	}
	
	// get the unit and offset from the start and end anchors
	//
	String unit_start;
	String unit_end;
	unit_start.assign(anch_start->getUnit());
	unit_end.assign(anch_end->getUnit());
	float32 offset_start;
	float32 offset_end;
	offset_start = anch_start->getOffset();
	offset_end = anch_end->getOffset();

	// update the output alignment format
	//
	record_a.concat(L"\n");
	record_a.concat(L"    from");
	record_a.concat(L": ");
	record_a.concat(offset_start);
	record_a.concat(L" ");
	record_a.concat(unit_start);
	record_a.concat(L"  to");
	record_a.concat(L": ");
	record_a.concat(offset_end);
	record_a.concat(L" ");
	record_a.concat(unit_end);
	record_a.concat(L"  ");
	record_a.concat(type);
	record_a.concat(L"  ");
	record_a.concat(score);
      }

      // update the output alignment format
      //
      record_a.concat(L"\n");
    }
    
    // update the output alignment format
    //
    record_a.concat(L"\n");
  }

  // clean up memory
  //
  graph.clear();
  
  // exit gracefully
  //
  return true;
}

// method: getHypothesesNistTrn
//
// arguments:
//  Sdb& ident_list_sdb: (input) list of identifier
//  Sdb& exlude_symbols_sdb: (input) list of exclude_symbols
//  String& fvalue: (input) annotation feature value (transcription level)
//  Vector<String>& nist_hypotheses: (output) vector of NIST_TRN format
//                                    hypotheses
//
// return: logical error status
//
// this method retrieves the hypotheses at a given feature (level)
// from the database in NIST_TRN format
//
bool8 TranscriptionDatabase::getHypothesesNistTrn(Sdb& ident_list_sdb_a,
						    Sdb& exclude_symbols_sdb_a,
						    String& fvalue_a,
						    Vector<String>&
						    nist_hypotheses_a) {
  
  // declare local variables
  //
  Filename input_ID;
  int32 num_ident = (int32)0;
  Vector<String> identifiers;
    
  // default feature name for transcriptions
  //
  String fname(L"level");

  //  default feature name for level-index and highest level-index
  //
  if (fvalue_a.length() < (int32)1) {
    fname.assign(L"level_index");
    fvalue_a.assign(L"0");
  }

  // if no identifiers are specified, extract all the transcriptions
  // contained in the database
  //
  int32 len = ident_list_sdb_a.length();
  if (len < (int32)1) {
    getIdentifiers(identifiers);
  }
  else {
    identifiers.setLength(len);
  }
  
  // loop over all the identifiers
  //
  int32 i = (int32)0;
  for (ident_list_sdb_a.gotoFirst(); ident_list_sdb_a.getName(input_ID);
       ident_list_sdb_a.gotoNext()) {
    
    // get the identifier
    //
    identifiers(i).assign(input_ID);
    i++;
  }
  
  // set the capacity of the output vector to the length of the input
  // identifiers
  //
  nist_hypotheses_a.setCapacity(identifiers.length());
  
  // loop over all the identifiers and extract the hypotheses
  // corresponding to each
  //
  for (int32 j = 0; j < identifiers.length(); j++) {
    
    // local variables
    //
    DoubleLinkedList<String> records;
      
    if (debug_level_d >= Integral::NONE) {      
      Console::increaseIndention();
      String output;
      output.assign(L"\nretrieving transcription for identifier: ");
      output.concat(identifiers(j));
      output.concat(L", ");
      output.concat(fname);
      output.concat(L": ");
      output.concat(fvalue_a);
      Console::put(output);
      Console::decreaseIndention();
    }
    
    // get the transcription at the given level
    //
    if (!getRecord(identifiers(j), fname, fvalue_a, records)) {
      identifiers(j).debug(L"identifier");
      return Error::handle(name(), L"getHypothesesNistTrn - unable to find transcription for identifier", Error::ARG, __FILE__, __LINE__);
    }

    // concat all the records to get the hypothesis
    //
    nist_hypotheses_a.setLength(nist_hypotheses_a.length() + (int32)1);
    for (bool8 more = records.gotoFirst(); more;
	 more = records.gotoNext()) {

      // get the record
      //
      String* record = records.getCurr();

      // local variables
      //
      String exclude_symbol;
      Filename input_exclude_symbol;
      bool8 exclude = false;
      
      // see if this record is included in the exclude-symbols list
      //
      for (exclude_symbols_sdb_a.gotoFirst();
	   exclude_symbols_sdb_a.getName(input_exclude_symbol);
	   exclude_symbols_sdb_a.gotoNext()) {
	
	// get the exclude-symbol
	//
	exclude_symbol.assign(input_exclude_symbol);
	
	if (exclude_symbol.eq(*record)) {
	  exclude = true;
	}
      }
      
      // add this record only if it is not included in the
      // exclude-symbols list
      //
      if (!exclude) {
	nist_hypotheses_a(num_ident).concat(*record);
	nist_hypotheses_a(num_ident).concat(L" ");
      }
    }
    
    // concat the identifier within braces
    //
    nist_hypotheses_a(num_ident).concat(L"(");
    nist_hypotheses_a(num_ident).concat(identifiers(j));
    nist_hypotheses_a(num_ident).concat(L")\n");

    // increment the counter
    //
    num_ident++;
  }
  
  // exit gracefully
  //
  return true;
}

// method: getAlignmentsHypAlign
//
// arguments:
//  Sdb& ident_list_sdb: (input) list of identifiers
//  String& levels: (input) transcription levels in format (word : state)
//  Vector<String>& alignments: (output) alignments in HYP_ALIGN format
//
// return: logical error status
//
// this method retrieves the hypotheses at a given level(s) from the
// database in HYP_ALIGN format
//
bool8 TranscriptionDatabase::getAlignmentsHypAlign(Sdb& ident_list_sdb_a,
						     String& levels_a,
						     Vector<String>&
						     alignments_a) {
  
  // declare local variables
  //
  Vector<String> levels;
  String identifier;
  Filename input_ID;
  Vector<String> identifiers;
  
  // default feature name for transcriptions
  //
  String fname(L"level");

  // parse the input level string and get the number of levels
  //
  if (levels_a.length() > (int32)0) {
    if (!parseLevels(levels_a, levels)) {
      return Error::handle(name(), L"getAlignmentsHypAlign - unable to parse the input level", Error::ARG, __FILE__, __LINE__);
    }
  }
  
  // default feature name for level-index and highest level-index
  //
  else {
    fname.assign(L"level_index");
    levels.setLength((int32)1);
    levels((int32)0).assign(L"0");
  }
  
  // if no identifiers are specified, extract alignments for all the
  // transcriptions contained in the database
  //
  int32 len = ident_list_sdb_a.length();
  if (len < (int32)1) {
    getIdentifiers(identifiers);
  }
  else {
    identifiers.setLength(len);
  }
  
  // loop over all the identifiers
  //
  int32 i = (int32)0;
  for (ident_list_sdb_a.gotoFirst(); ident_list_sdb_a.getName(input_ID);
       ident_list_sdb_a.gotoNext()) {
    
    // get the identifier
    //
    identifiers(i).assign(input_ID);
    i++;
  }
  
  // set the capacity of the output vector to the length of the input
  // identifiers
  //
  alignments_a.setCapacity(identifiers.length());
  
  // loop over all the identifiers and extract the alignments at
  // required levels corresponding to each
  //
  for (int32 j = 0; j < identifiers.length(); j++) {
    
    // get the identifier
    //
    if (debug_level_d >= Integral::NONE) {      
      Console::increaseIndention();
      String output;
      output.assign(L"\nretrieving alignments for identifier: ");
      output.concat(identifiers(j));
      output.concat(L", ");
      output.concat(fname);
      output.concat(L": ");
      for (int32 i = 0; i < levels.length(); i++) {
	output.concat(levels(i));
      }
      
      Console::put(output);
      Console::decreaseIndention();
    }
    
    // update the alignment string
    //
    String alignment;
    alignment.concat(L"alignments for identier: ");
    alignment.concat(identifiers(j));
      
    // get the alignments at the given level(s)
    //    
    if (!getRecord(identifiers(j), fname, levels, alignment)) {
      identifiers(j).debug(L"identifier");
      return Error::handle(name(), L"getAlignmentsHypAlign - unable to find transcription for identifier", Error::ARG, __FILE__, __LINE__);
    }

    // store the alignment in the vector
    //
    int32 temp_len = alignments_a.length();
    alignments_a.setLength(temp_len + (int32)1);
    alignments_a(temp_len).assign(alignment);
  }

  // exit gracefully
  //
  return true;
}

// method: parseLevels
//
// arguments:
//  const String& input: (input) transcription levels in format (word : state)
//  Vector<String>& levels: (output) parsed levels
//
// return: logical error status
//
// this method parses the input string for the levels
//
bool8 TranscriptionDatabase::parseLevels(const String& input_a,
					   Vector<String>& levels_a) {
  
  // error if the input string in empty
  //
  if (input_a.length() == (int32)0) {
    return Error::handle(name(), L"parseLevels - empty string", Error::ARG, __FILE__, __LINE__);
  }
  
  // count the number of sub-strings separated by ','
  //
  int32 tokens = input_a.countTokens(L',');

  // get all the sub-strings separated by ','
  //
  String vals[tokens];
  for (int32 i = 0, pos = 0; i < tokens; i++) {
    input_a.tokenize(vals[i], pos, L",");
  }

  // compute the number of all the sub-strings (levels) in input
  // string seperated by the delimiter ':'
  //
  int32 num = 0;
  for (int32 i = 0; i < tokens; i++) {
    num += vals[i].countTokens(L':');
  }

  // allocate the minimun space for these levels
  //
  levels_a.clear(Integral::RELEASE);
  levels_a.setCapacity(num);

  // local variables
  //
  Vector<String> levels_in;
  Vector<String> levels_out;
      
  // loop through all the sub-strings
  //
  for (int32 i = 0; i < tokens; i++) {

    // local variables
    //
    String level;
    int32 pos = 0;

    // clear the levels from the previous loop
    //
    levels_in.clear(Integral::RELEASE);
    levels_out.clear(Integral::RELEASE);
    
    // parse the input in the format based on the endlimiter ":"
    //
    while (vals[i].tokenize(level, pos, L":")) {
      
      // get rid of white spaces if any
      //
      level.trim();
      
      // get the levels in numericals
      //      
      int32 len = levels_in.length();
      levels_in.setLength(len + (int32)1);
      levels_in(len).assign(level);
    }

    // get the levels in numericals from the first annotation-graph in
    // the transcription database
    //
    
    // declare local variables
    //
    Vector<String> ident;
    AnnotationGraph graph;
    
    // get all the identifiers in the database
    //
    if (!hash_index_d.keys(ident)) {
      Error::handle(name(), L"parseLevels -  no transcriptions in the database", Error::ARG, __FILE__, __LINE__);
    }
    
    // return a copy of the record corresponding to first tag in the
    // vector
    //
    graph.clear();
    if (!graph.read(database_sof_d, *hash_index_d.get(ident(0)))) {
      Error::handle(name(), L"parseLevels - transcription missing",
		    Error::ARG, __FILE__, __LINE__);
    }
    
    // local variables
    //
    Vector<String> values;
    VectorLong indices;
    DoubleLinkedList<Annotation> temp_annos;
    Annotation* temp_anno = (Annotation*)NULL;
    
    // set the capacity of the variables
    //
    int32 len = levels_in.length();
    values.setCapacity(len);
    indices.setCapacity(len);
    
    // declare the feature "index" and the feature "level" as string
    // objects
    //
    String fea_index(L"level_index");
    String fea_level(L"level");
    
    // get the level values corresponding to the features
    //
    for (int32 i = 0; i < len; i++) {
      
      // set length
      //
      values.setLength(i+1);
      indices.setLength(i+1);
      
      // get all the annotations from the graph at a given level and
      // then find the index from the first annotation
      //    
      if (!graph.getAnnotationSetByFeature(fea_level, levels_in(i),
					   temp_annos)) {
	Error::handle(name(), L"parseLevels - transcription missing",
		      Error::ARG, __FILE__, __LINE__);
      }

      // get the first annotation
      // 
      if (temp_annos.length() > (int32)0) {
	temp_anno = temp_annos.getFirst();
      }
      else      
	Error::handle(name(), L"parseLevels - level missing",
		      Error::ARG, __FILE__, __LINE__);
      
      // get the corresponding level index 
      //
      values(i).assign((*temp_anno).getFeature(fea_index));
      indices(i).assign(values(i));
    }
    
    // find the minimum and maximum index of the levels
    //
    Long min_index = indices.min();
    Long max_index = indices.max();
    
    // set the minimum capacity of the output levels
    //
    levels_out.setCapacity(levels_in.length());
    
    // get the missing levels between the min and max indices
    //
    for (int32 j = (int32)min_index; j <= (int32)max_index; j++) {
      
      // local variables
      //
      String temp_level;
      Long index = (Long)-1;
      String temp_index;
      
      // get the Annotations from the AnnotationGraph
      //
      if (!graph.getAnnotationSet(temp_annos)) {
	Error::handle(name(), L"parseLevels - transcription missing",
		      Error::ARG, __FILE__, __LINE__);
      }
      
      // loop over all the annotations to find the corresponding level
      // name
      //
      for (bool8 more = temp_annos.gotoFirst(); more;
	   more = temp_annos.gotoNext()) {
	
	// get the current annotation
	//
	temp_anno = temp_annos.getCurr();
	
	// check for NULL condition
	//
	if (temp_anno == (Annotation*)NULL) {
	  Error::handle(name(), L"parseLevels - NULL Annotation",
			Error::ARG, __FILE__, __LINE__);
	}
	
	// get the level and then get the corresponding index
	//
	temp_level = (*temp_anno).getFeature(fea_level);
	temp_index = (*temp_anno).getFeature(fea_index);
	index.assign(temp_index);
	
	// see if the index matches
	//
	if ((int32)index == j) {
	  int32 temp_len = levels_out.length();
	  levels_out.setLength(temp_len + (int32)1);
	  levels_out(temp_len).assign(temp_level);
	  break;
	}
      }
    }

    // add the sub-string levels to the total numner of output levels
    //
    for ( int32 k = 0; k < levels_out.length(); k++) {
      int32 length_tmp = levels_a.length();
      levels_a.setLength(length_tmp + (int32)1);
      levels_a(length_tmp).assign(levels_out(k));
    }

    // clean up memory
    //
    graph.clear();    
  }

  // exit gracefully
  //
  return true;  
}

// method: getRecord
//
// arguments:
//  String& identifier: (input) annotation graph id
//  String& feature: (input) annotation feature
//  String& value: (input) annotation value
//  Vector<String>& annotations: (output) annotations for the feature
//  VectorFloat& start_times: (output) start timming information (alignments)
//  VectorFloat& end_times: (output) end timming information (alignments)
//
// return: logical error status
//
// this method retrieves the alignments from the database
//
bool8 TranscriptionDatabase::getRecord(String& identifier_a,
					 String& feature_a,
					 String& value_a,
					 Vector<String>& annotations_a,
					 VectorFloat& start_times_a,
					 VectorFloat& end_times_a){
  
  // declare local variables
  //
  DoubleLinkedList<Annotation> annos;
  AnnotationGraph graph;  
  Long* tag;

  // check for input values
  //
  if (value_a.length() <= int32(0)) {
    Error::handle(name(), L"getRecord - levels missing", Error::ARG,
		  __FILE__, __LINE__);      
  }
  
  // determine if the identifier exists in the database
  //
  tag = hash_index_d.get(identifier_a);
  if (tag == (Long*)NULL) {
    Error::handle(name(), L"getRecord - annotation-graph missing", Error::ARG,
		  __FILE__, __LINE__);      
  }
  
  // when the identifier exists in the database return a copy of the record
  //
  else {
    graph.clear();
    if (!graph.read(database_sof_d, (int32)*tag)) {
      Error::handle(name(), L"getRecord", Error::ARG,
		    __FILE__, __LINE__);      
    }

    // get all the annotations at feature "level" and value starting
    // with the top-most level
    //
    if (!graph.getAnnotationSetByFeature(feature_a, value_a, annos)) {
      return Error::handle(name(), L"getRecord - unable to find the annotations for the given feature and the value", Error::ARG, __FILE__, __LINE__);
    }
    
    // loop over each annotation at this level
    //
    Annotation* anno = (Annotation*)NULL;
    int32 temp = (int32)0;
    for (bool8 more = annos.gotoFirst(); more; more = annos.gotoNext()) {
      anno = (Annotation*)NULL;
      anno = annos.getCurr();
      
      // check the annotation for NULL
      //
      if (anno == (Annotation*)NULL) {
	return Error::handle(name(), L"getRecord - NULL Annotation",
			     Error::ARG, __FILE__, __LINE__);
      }
      
      // get start and end anchors for the current annotation
      //
      Anchor* anch_start = (Anchor*)NULL;
      Anchor* anch_end = (Anchor*)NULL;
      anch_start = anno->getStartAnchor();
      anch_end = anno->getEndAnchor();

      String annotation;
      annotation.assign(anno->getType());
      
      // check for NULL anchors
      //
      if ((anch_start == (Anchor*)NULL) || (anch_end == (Anchor*)NULL)) {
	return Error::handle(name(), L"getRecord - NULL Anchors",
			     Error::ARG, __FILE__, __LINE__);
      }
      
      // get the unit and offset from the start and end anchors
      //
      String unit_start;
      String unit_end;
      unit_start.assign(anch_start->getUnit());
      unit_end.assign(anch_end->getUnit());
      
      start_times_a.setLength(++temp);
      end_times_a.setLength(temp);
      annotations_a.setLength(temp);

      start_times_a(temp-(int32)1) = anch_start->getOffset();
      end_times_a(temp-(int32)1) = anch_end->getOffset();
      annotations_a(temp-(int32)1).assign(annotation);
    }
  }
  
  // clean up memory
  //
  graph.clear();
  
  // exit gracefully
  //
  return true;
}

// method: getRecord
//
// arguments:
//  String& identifier: (input) annotation graph id
//  String& feature: (input) annotation feature
//  String& value: (input) annotation value
//  const String& type: (input) annotation type
//  Vector<String>& annotations: (output) annotations for the feature
//  VectorFloat& start_times: (output) start timming information (alignments)
//  VectorFloat& end_times: (output) end timming information (alignments)
//
// return: logical error status
//
// this method retrieves the alignments from the database on the basis
// of the feature-value pair and type
//
bool8 TranscriptionDatabase::getRecord(String& identifier_a,
					 String& feature_a, String& value_a,
					 String& type_a,
					 Vector<String>& annotations_a,
					 VectorFloat& start_times_a,
					 VectorFloat& end_times_a) {
  
  // declare local variables
  //
  DoubleLinkedList<Annotation> annos;
  AnnotationGraph graph;  
  Long* tag;
  
  // check for input values
  //
  if (value_a.length() <= int32(0)) {
    Error::handle(name(), L"getRecord - levels missing", Error::ARG,
		  __FILE__, __LINE__);      
  }
  
  // determine if the identifier exists in the database
  //
  tag = hash_index_d.get(identifier_a);
  if (tag == (Long*)NULL) {
    Error::handle(name(), L"getRecord - annotation-graph missing", Error::ARG,
		  __FILE__, __LINE__);      
  }
  
  // when the identifier exists in the database return a copy of the record
  //
  else {
    graph.clear();
    if (!graph.read(database_sof_d, (int32)*tag)) {
      Error::handle(name(), L"getRecord", Error::ARG,
		    __FILE__, __LINE__);      
    }

    // get all the annotations at feature "level" and value starting
    // with the top-most level
    //
    if (!graph.getAnnotationSetByFeature(feature_a, value_a, annos)) {
      return Error::handle(name(), L"getRecord - unable to find the annotations for the given feature and the value", Error::ARG, __FILE__, __LINE__);
    }
    
    // loop over each annotation at this level
    //
    Annotation* anno = (Annotation*)NULL;
    int32 temp = (int32)0;
    for (bool8 more = annos.gotoFirst(); more; more = annos.gotoNext()) {
      anno = (Annotation*)NULL;
      anno = annos.getCurr();
      
      // check the annotation for NULL
      //
      if (anno == (Annotation*)NULL) {
	return Error::handle(name(), L"getRecord - NULL Annotation",
			     Error::ARG, __FILE__, __LINE__);
      }

      // insert the annotation and its respective start-end times only
      // when the type matches
      //
      if (anno->getType().eq(type_a)) {
	
	// get start and end anchors for the current annotation
	//
	Anchor* anch_start = (Anchor*)NULL;
	Anchor* anch_end = (Anchor*)NULL;
	anch_start = anno->getStartAnchor();
	anch_end = anno->getEndAnchor();
	
	String annotation;
	annotation.assign(anno->getType());
	
	// check for NULL anchors
	//
	if ((anch_start == (Anchor*)NULL) || (anch_end == (Anchor*)NULL)) {
	  return Error::handle(name(), L"getRecord - NULL Anchors",
			       Error::ARG, __FILE__, __LINE__);
	}
	
	// get the unit and offset from the start and end anchors
	//
	String unit_start;
	String unit_end;
	unit_start.assign(anch_start->getUnit());
	unit_end.assign(anch_end->getUnit());
	
	start_times_a.setLength(++temp);
	end_times_a.setLength(temp);
	annotations_a.setLength(temp);
	
	start_times_a(temp-(int32)1) = anch_start->getOffset();
	end_times_a(temp-(int32)1) = anch_end->getOffset();
	annotations_a(temp-(int32)1).assign(annotation);
      }
    }
  }
  
  // clean up memory
  //
  graph.clear();
  
  // exit gracefully
  //
  return true;
}

// method: getIdentifiers
//
// arguments:
//  Sdb& identifiers_a: (output) list of identifier
//
// return: logical error status
//
// this method retrieves all the identifiers in the database
//
bool8 TranscriptionDatabase::getIdentifiers(Vector<String>& identifiers_a) {
  
  // clear all the elements in the sdb object
  //
  identifiers_a.clear();
  
  // get all the keys (identifiers) from the hash table
  //
  return hash_index_d.keys(identifiers_a);
}