Jirakjan bp rebase

Merge code by Jan Jirak that resulted from his BP

alib2algo/src/stringology/exact/CGR.h

+/*
+ * CGR.h
+ *
+ *  Created on: 19. 3. 2020
+ *      Author: Jan Jirak
+ */
+
+#ifndef _STRINGOLOGY_CGR_H_
+#define _STRINGOLOGY_CGR_H_
+
+#include <alib/measure>
+
+#include <alib/set>
+#include <alib/vector>
+
+#include <string/LinearString.h>
+#include <string/properties/Repetition.h>
+
+
+namespace stringology {
+
+    namespace exact {
+
+
+/**
+ * Implementation of the CGR algorithm from article "Constant-space string-matching in sublinear average time"
+ * Maxim Crochemore and Leszek Gasieniec and Wojciech Rytter
+ */
+        class CGR {
+        public:
+            /**
+             * Search for pattern in linear string.
+             * @return set set of occurences
+             */
+            template < class SymbolType >
+            static ext::set < unsigned > match ( const string::LinearString < SymbolType > & subject, const string::LinearString < SymbolType > & pattern );
+
+        };
+
+
+        template < class SymbolType >
+        ext::set < unsigned > CGR::match ( const string::LinearString < SymbolType > & subject, const string::LinearString < SymbolType > & pattern ) {
+            ext::set<unsigned> occ;
+            const auto & text = subject.getContent();
+            const auto & pat = pattern.getContent();
+            size_t n = text.size(), m = pat.size();
+
+            size_t repSize, p , q ;
+            measurements::start ( "Preprocess", measurements::Type::PREPROCESS );
+            std::tie( repSize , p , q ) = string::properties::Repetition::construct(pattern) ;
+            measurements::end ( );
+
+            measurements::start ( "Algorithm", measurements::Type::ALGORITHM );
+            // for repSize == 0 or 1 use naive solution
+            if ( repSize == 0 || repSize == 1 ) {
+                for ( size_t i = 0 ; i <= n - m ; ++ i ) {
+                    size_t j = 0 ;
+                    while ( j < m && text[i + j ] == pat[j] ) ++ j ;
+                    if ( j == m ) occ.insert(i) ;
+                }
+                measurements::end();
+                return occ ;
+            }
+
+            size_t i = repSize/2 ;
+            while ( i <= n - m ) {
+                bool leftmostMismatch = std::equal(text.begin() + i + p , text.begin() + i + p + repSize/2 , text.begin() + i + q ) ;
+                if ( leftmostMismatch ) {
+                    for ( size_t i_0 = i - repSize / 2 ; i_0 <= i ; ++ i_0 ){
+                        if ( std::equal( pat.begin() , pat.end() , text.begin() + i_0 ) ) occ.insert(i_0) ;
+                    }
+                }
+                i += repSize / 2 ;
+            }
+            // check last positions, where i jump into last window
+            for ( size_t j = i - repSize / 2 ; j <= n - m ; ++ j ) {
+                if ( std::equal( pat.begin() , pat.end() , text.begin() + j ) ) occ.insert(j) ;
+            }
+            measurements::end();
+            return occ ;
+        }
+
+
+    } /* namespace exact */
+
+} /* namespace stringology */
+
+#endif /* _STRINGOLOGY_TAILED_SUBSTRING_H_ */