more doc

Doxyfile.in

@@ -45,7 +45,7 @@ PROJECT_BRIEF          =
 # exceed 55 pixels and the maximum width should not exceed 200 pixels.
 # Doxygen will copy the logo to the output directory.
 
-PROJECT_LOGO           =
+PROJECT_LOGO           = ../concordia.png
 
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
 # base path where the generated documentation will be put.

concordia-console/concordia-console.cpp

@@ -282,7 +282,7 @@ int main(int argc, char** argv) {
                 if (totalTimeElapsed == 0) {
                     totalTimeElapsed++;
                 }
-                
+
                 double totalSpeed =
                       static_cast<double>(1000 * lineCount / totalTimeElapsed);
                 std::cout << "\tReading finished. Read and added to index "

concordia/anubis_search_result.hpp

@@ -4,12 +4,17 @@
 #include "concordia/common/config.hpp"
 
 /*!
-  Class representing an example found by anubis search.
+  Class representing an example found by anubis search. Contains
+  the id of the example and anubis score of the search.
 
 */
 
 class AnubisSearchResult {
 public:
+    /*! Constructor.
+     \param exampleId the id of found example
+     \param score score of this example
+    */
     explicit AnubisSearchResult(const SUFFIX_MARKER_TYPE & exampleId,
                                 const double score);
 
@@ -17,14 +22,24 @@ public:
     */
     virtual ~AnubisSearchResult();
 
+    /*! Getter for example id.
+     \returns example id
+    */
     SUFFIX_MARKER_TYPE getExampleId() const {
         return _exampleId;
     }
 
+    /*! Getter for anubis score.
+     \returns anubis score of the example
+    */
     double getScore() const {
         return _score;
     }
 
+    /*! Operator "greater than", used to sort objects of this class.
+     \returns true if the score of the current result is larger than
+      the score of another result
+    */    
     bool operator > (const AnubisSearchResult & other) const {
         return (_score > other.getScore());
     }

concordia/common/text_utils.hpp

@@ -11,8 +11,13 @@
 */
 class TextUtils {
 public:
+    /*! Constructor
+    */
+
     TextUtils();
 
+    /*! Method for ensuring singleton.
+    */
     static TextUtils & getInstance() {
         static TextUtils instance;  // Guaranteed to be destroyed.
                                     // Instantiated on first use.

concordia/common/utils.hpp

@@ -13,61 +13,144 @@
 #include "concordia/matched_pattern_fragment.hpp"
 #include <divsufsort.h>
 
+/*!
+  Class offering a range of simple utility methods.
+
+*/
+
 class Utils {
 public:
+
+    /*! Constructor
+    */
     explicit Utils();
 
     /*! Destructor.
     */
     virtual ~Utils();
 
+    /*! Writes an index character to a binary file.
+        The character is written to the file as bytes, not necessarily in
+        the order in which they come in the character.
+     \param file file to write the character to
+     \param character character to write
+    */
     static void writeIndexCharacter(std::ofstream & file,
                                      INDEX_CHARACTER_TYPE character);
 
+    /*! Writes a marker to a binary file.
+        The marker is written to the file as bytes, not necessarily in
+        the order in which they come in the marker.
+     \param file file to write the marker to
+     \param marker marker to write
+    */
     static void writeMarker(std::ofstream & file,
                                      SUFFIX_MARKER_TYPE marker);
 
+    /*! Reads an index character from a binary file.
+        Reading restores the order of the bytes in the original
+        character, which was written to the file.
+     \param file file to read the character from
+     \returns read character
+    */
     static INDEX_CHARACTER_TYPE readIndexCharacter(std::ifstream & file);
 
+    /*! Reads a marker from a binary file.
+        Reading restores the order of the bytes in the original
+        marker, which was written to the file.
+     \param file file to read the marker from
+     \returns read marker
+    */
     static SUFFIX_MARKER_TYPE readMarker(std::ifstream & file);
 
+    /*! Converts a vector of index characters to higher resolution array.
+     \param input vector of index characters
+     \returns array of smaller parts of characters
+    */
     static sauchar_t * indexVectorToSaucharArray(
                        const std::vector<INDEX_CHARACTER_TYPE> & input);
 
+    /*! Converts a vector of index characters to higher resolution vector.
+     \param input vector of index characters
+     \returns vector of smaller parts of characters
+    */
     static std::vector<sauchar_t> indexVectorToSaucharVector(
                        const std::vector<INDEX_CHARACTER_TYPE> & input);
 
+    /*! Appends an index character to a high resolution vector.
+     \param vector vector to be appended to
+     \param character character to append
+    */
     static void appendCharToSaucharVector(
                              boost::shared_ptr<std::vector<sauchar_t> > vector,
                              INDEX_CHARACTER_TYPE character);
 
+    /*! Appends an index character to a high resolution vector.
+     \param vector vector to be appended to
+     \param character character to append
+    */
     static void appendCharToSaucharVector(
                              std::vector<sauchar_t> & vector,
                              INDEX_CHARACTER_TYPE character);
 
+    /*! Prints a given vector to standard output.
+     \param vector vector to be printed
+    */
     template <typename T>
     static void printVector(const std::vector<T> & vector);
 
+    /*! Retrieves sentence id from a marker.
+     \param marker input marker
+     \returns sentence id
+    */
     static SUFFIX_MARKER_TYPE getIdFromMarker(SUFFIX_MARKER_TYPE marker);
 
+    /*! Retrieves offset from a marker.
+     \param marker input marker
+     \returns offset
+    */
     static SUFFIX_MARKER_TYPE getOffsetFromMarker(SUFFIX_MARKER_TYPE marker);
 
+    /*! Retrieves example length from a marker.
+     \param marker input marker
+     \returns example length
+    */
     static SUFFIX_MARKER_TYPE getLengthFromMarker(SUFFIX_MARKER_TYPE marker);
 
+    /*! Creates a marker from given data.
+     \param id sentence id
+     \param offset offset
+     \param length example length
+     \returns generated marker
+    */
     static SUFFIX_MARKER_TYPE createMarker(SUFFIX_MARKER_TYPE id,
                                            SUFFIX_MARKER_TYPE offset,
                                            SUFFIX_MARKER_TYPE length);
 
+    /*! Computes overlay score based on a list of non-intersecting intervals.
+     \param intervalList list of the intervals
+     \param sentenceSize the total size of the sentence (or pattern)
+     \param k significance factor. When set to 1, the significance is neutral.
+     \returns score
+    */
     static double getLogarithmicOverlay(
                                   const std::vector<Interval> & intervalList,
                                   SUFFIX_MARKER_TYPE sentenceSize,
                                   double k);
 
+    /*! Computes overlay score based on a list of non-intersecting fragments.
+     \param intervalList list of the intervals
+     \param sentenceSize the total size of the sentence (or pattern)
+     \param k significance factor. When set to 1, the significance is neutral.
+     \returns score
+    */
     static double getLogarithmicOverlay(
                       const std::vector<MatchedPatternFragment> & fragmentList,
                       SUFFIX_MARKER_TYPE patternSize,
                       double k);
 
+    /*! Field holding the maximum sentence size allowed in the index.
+    */
     static SUFFIX_MARKER_TYPE maxSentenceSize;
 
 private:

concordia/concordia.hpp

@@ -39,23 +39,61 @@ public:
     */
     std::string & getVersion();
 
+    /*! Adds an Example to the index.
+      \param example example to be added
+      \throws ConcordiaException
+    */
     void addExample(const Example & example) throw(ConcordiaException);
 
+    /*! Adds multiple examples to the index.
+      \param examples vector of examples to be added
+      \throws ConcordiaException
+    */
     void addAllExamples(const std::vector<Example> & examples)
                                                    throw(ConcordiaException);
 
+    /*! Performs a simple substring lookup on the index.
+        For more info see \ref tutorial1_2.
+      \param pattern pattern to be searched in the index
+      \returns vector of matched results
+      \throws ConcordiaException
+    */
     std::vector<SubstringOccurence> simpleSearch(const std::string & pattern)
                                                  throw(ConcordiaException);
 
+    /*! \deprecated
+        Finds the examples from the index, whose resemblance to the
+        pattern is maximal. This method may perform very slow,
+        try using concordiaSearch instead.
+      \param pattern pattern to be searched in the index
+      \returns vector of anubis results
+      \throws ConcordiaException
+    */
     std::vector<AnubisSearchResult> anubisSearch(const std::string & pattern)
                                                  throw(ConcordiaException);
 
+    /*! Performs concordia lookup on the index. This is a unique library
+        functionality, designed to facilitate Computer-Aided Translation.
+        For more info see \ref tutorial1_3.
+      \param pattern pattern to be searched in the index
+      \returns concordia result
+      \throws ConcordiaException
+    */
     boost::shared_ptr<ConcordiaSearchResult> concordiaSearch(
                                                  const std::string & pattern)
                                                  throw(ConcordiaException);
 
+    /*! Loads HDD stored index files to RAM and generates
+        suffix array based on RAM stored data structures.
+        For more info see \ref tutorial2.
+      \throws ConcordiaException
+    */
     void loadRAMIndexFromDisk() throw(ConcordiaException);
 
+    /*! Generates suffix array based on RAM stored data structures.
+        For more info see \ref tutorial2.
+      \throws ConcordiaException
+    */
     void refreshSAfromRAM() throw(ConcordiaException);
 
 private:

concordia/concordia_config.hpp

@@ -24,42 +24,82 @@ public:
     */
     virtual ~ConcordiaConfig();
 
+    /*! Getter for word map file path.
+        For more information see \ref tutorial3.
+     \returns word map file path
+    */
     std::string & getWordMapFilePath() {
         return _wordMapFilePath;
     }
 
+    /*! Getter for hashed index file path.
+        For more information see \ref tutorial3.
+     \returns hashed index file path
+    */
     std::string & getHashedIndexFilePath() {
         return _hashedIndexFilePath;
     }
 
+    /*! Getter for markers file path.
+        For more information see \ref tutorial3.
+     \returns markers file path
+    */
     std::string & getMarkersFilePath() {
         return _markersFilePath;
     }
 
+    /*! Getter for html tags file path.
+        For more information see \ref tutorial3.
+     \returns html tags file path
+    */
     std::string & getHtmlTagsFilePath() {
         return _htmlTagsFilePath;
     }
 
+    /*! Getter for space symbols file path.
+        For more information see \ref tutorial3.
+     \returns space symbols file path
+    */
     std::string & getSpaceSymbolsFilePath() {
         return _spaceSymbolsFilePath;
     }
 
+    /*! Getter for stop symbols enabled parameter.
+        For more information see \ref tutorial3.
+     \returns true if stop words are enabled
+    */
     bool & isStopWordsEnabled() {
         return _stopWordsEnabled;
     }
 
+    /*! Getter for stop words file path.
+        For more information see \ref tutorial3.
+     \returns stop words file path
+    */
     std::string & getStopWordsFilePath() {
         return _stopWordsFilePath;
     }
 
+    /*! Getter for named entities file path.
+        For more information see \ref tutorial3.
+     \returns named entities file path
+    */
     std::string & getNamedEntitiesFilePath() {
         return _namedEntitiesFilePath;
     }
 
+    /*! Getter for stop symbols file path.
+        For more information see \ref tutorial3.
+     \returns stop symbols file path
+    */
     std::string & getStopSymbolsFilePath() {
         return _stopSymbolsFilePath;
     }
 
+    /*! Getter for anubis threshold. Anubis search results with
+        scores below that threshold will be discarded.        
+     \returns anubis threshold
+    */
     double getAnubisThreshold() {
         return _anubisThreshold;
     }