kmp for tree patterns on prefix ranked notation

alib2algo/src/arbology/exact/BorderArrayNaive.cpp

@@ -10,6 +10,7 @@
 #include <exception/AlibException.h>
 #include <tree/ranked/PrefixRankedBarPattern.h>
+#include <tree/ranked/PrefixRankedPattern.h>
 namespace arbology {
@@ -62,6 +63,49 @@ std::vector < size_t > BorderArrayNaive::ba ( const tree::PrefixRankedBarPattern
 auto BorderArrayPrefixRankedBarPattern = BorderArrayNaive::RegistratorWrapper < std::vector < size_t >, tree::PrefixRankedBarPattern > ( BorderArrayNaive::getInstance ( ), BorderArrayNaive::ba );
+bool BorderArrayNaive::matches ( const tree::PrefixRankedPattern & pattern, const std::vector < int > & subtreeJumpTable, int stop, int offset ) {
+	unsigned i = 1;
+
+	while ( offset < stop && i < pattern.getContent ( ).size ( ) )
+		if ( pattern.getContent ( )[i] == pattern.getContent ( )[offset] ) {
+			i++;
+			offset++;
+		} else if ( ( pattern.getContent ( )[i] == pattern.getSubtreeWildcard ( ) ) || ( pattern.getContent ( )[offset] == pattern.getSubtreeWildcard ( ) ) ) {
+			i = subtreeJumpTable[i];
+			offset = subtreeJumpTable[offset];
+		} else {
+			return false;
+		}
+
+	return true;
+}
+
+std::vector < size_t > BorderArrayNaive::ba ( const tree::PrefixRankedPattern & pattern ) {
+	std::vector < int > patternSubtreeJumpTable = SubtreeJumpTable::compute ( pattern );
+	std::vector < size_t > res;
+
+	for ( unsigned i = 0; i <= pattern.getContent ( ).size ( ); i++ )
+		res.push_back ( 0 );
+
+	res[0] = -1;
+
+	for ( unsigned i = 1; i <= pattern.getContent ( ).size ( ); i++ ) {
+		int min = i;
+
+		for ( unsigned j = 1; j < i; j++ )
+			if ( matches ( pattern, patternSubtreeJumpTable, i, j ) ) {
+				min = j;
+				break;
+			}
+
+		res[i] = i - min;
+	}
+
+	return res;
+}
+
+auto BorderArrayPrefixRankedPattern = BorderArrayNaive::RegistratorWrapper < std::vector < size_t >, tree::PrefixRankedPattern > ( BorderArrayNaive::getInstance ( ), BorderArrayNaive::ba );
+
 } /* namespace exact */
 } /* namespace arbology */

alib2algo/src/arbology/exact/BorderArrayNaive.h

@@ -25,6 +25,8 @@ namespace exact {
 class BorderArrayNaive : public std::SingleDispatch < std::vector < size_t >, tree::RankedTreeBase > {
 	static bool matches ( const tree::PrefixRankedBarPattern & pattern, const std::vector < int > & subtreeJumpTable, int stop, int offset );
+	static bool matches ( const tree::PrefixRankedPattern & pattern, const std::vector < int > & subtreeJumpTable, int stop, int offset );
+
 public:
 	/**
 	 * Search for pattern in linear string.
@@ -38,6 +40,12 @@ public:
 	 */
 	static std::vector < size_t > ba ( const tree::PrefixRankedBarPattern & pattern );
+	/**
+	 * Search for pattern in linear string.
+	 * @return set set of occurences
+	 */
+	static std::vector < size_t > ba ( const tree::PrefixRankedPattern & pattern );
+
 	static BorderArrayNaive & getInstance ( ) {
 		static BorderArrayNaive res;

alib2algo/src/arbology/exact/KnuthMorrisPratt.cpp

@@ -13,6 +13,8 @@
 #include <tree/Tree.h>
 #include <tree/ranked/PrefixRankedBarTree.h>
 #include <tree/ranked/PrefixRankedBarPattern.h>
+#include <tree/ranked/PrefixRankedTree.h>
+#include <tree/ranked/PrefixRankedPattern.h>
 #include <alphabet/RankedSymbol.h>
 #include <map>
@@ -74,6 +76,55 @@ std::set < unsigned > KnuthMorrisPratt::match ( const tree::PrefixRankedBarTree
 auto KnuthMorrisPrattPrefixRankedBarTreePrefixRankedBarPattern = KnuthMorrisPratt::RegistratorWrapper < std::set < unsigned >, tree::PrefixRankedBarTree, tree::PrefixRankedBarPattern > ( KnuthMorrisPratt::getInstance ( ), KnuthMorrisPratt::match );
+std::set < unsigned > KnuthMorrisPratt::match ( const tree::PrefixRankedTree & subject, const tree::PrefixRankedTree & pattern ) {
+	return match ( subject, tree::PrefixRankedPattern ( pattern ) );
+}
+
+auto KnuthMorrisPrattPrefixRankedTreePrefixRankedTree = KnuthMorrisPratt::RegistratorWrapper < std::set < unsigned >, tree::PrefixRankedTree, tree::PrefixRankedTree > ( KnuthMorrisPratt::getInstance ( ), KnuthMorrisPratt::match );
+
+std::set < unsigned > KnuthMorrisPratt::match ( const tree::PrefixRankedTree & subject, const tree::PrefixRankedPattern & pattern ) {
+	std::set < unsigned > occ;
+	std::vector < size_t > ba = BorderArrayNaive::ba ( pattern );
+	std::vector < int > subjectSubtreeJumpTable = SubtreeJumpTable::compute ( subject );
+
+	 // index to the subject
+	unsigned i = 0;
+
+	 // main loop of the algorithm over all possible indexes where the pattern can start
+	while ( i + pattern.getContent ( ).size ( ) <= subject.getContent ( ).size ( ) ) {
+
+		 // index to the pattern
+		unsigned j = 0;
+
+		 // offset to the subject
+		unsigned offset = i;
+
+		while ( ( j < pattern.getContent ( ).size ( ) ) && ( offset < subject.getContent ( ).size ( ) ) ) {
+			if ( subject.getContent ( )[offset] == pattern.getContent ( )[j] ) {
+				 // match of symbol
+				offset++;
+				j++;
+			} else if ( ( pattern.getContent ( )[j] == pattern.getSubtreeWildcard ( ) ) ) {
+				 // match of variable with subtree
+				offset = subjectSubtreeJumpTable[offset];
+				j++;
+			} else {
+				break;
+			}
+		}
+
+		 // match was found
+		if ( j >= pattern.getContent ( ).size ( ) ) occ.insert ( i );
+
+		 // shift heristics
+		i += j - ba[j];
+	}
+
+	return occ;
+}
+
+auto KnuthMorrisPrattPrefixRankedTreePrefixRankedPattern = KnuthMorrisPratt::RegistratorWrapper < std::set < unsigned >, tree::PrefixRankedTree, tree::PrefixRankedPattern > ( KnuthMorrisPratt::getInstance ( ), KnuthMorrisPratt::match );
+
 } /* namespace exact */
 } /* namespace arbology */

alib2algo/src/arbology/exact/KnuthMorrisPratt.h

@@ -31,6 +31,9 @@ public:
 	static std::set < unsigned > match ( const tree::PrefixRankedBarTree & subject, const tree::PrefixRankedBarTree & pattern );
 	static std::set < unsigned > match ( const tree::PrefixRankedBarTree & subject, const tree::PrefixRankedBarPattern & pattern );
+	static std::set < unsigned > match ( const tree::PrefixRankedTree & subject, const tree::PrefixRankedTree & pattern );
+	static std::set < unsigned > match ( const tree::PrefixRankedTree & subject, const tree::PrefixRankedPattern & pattern );
+
 	static KnuthMorrisPratt & getInstance ( ) {
 		static KnuthMorrisPratt res;

alib2data/src/tree/ranked/PrefixRankedPattern.cpp

@@ -13,6 +13,7 @@
 #include <deque>
 #include "RankedPattern.h"
+#include "PrefixRankedTree.h"
 #include "../../sax/FromXMLParserHelper.h"
 #include "../common/TreeFromXMLParser.h"
@@ -23,6 +24,8 @@
 #include "../../XmlApi.hpp"
 #include "../../CastApi.hpp"
+#include "../../alphabet/SubtreeWildcardSymbol.h"
+
 namespace tree {
 PrefixRankedPattern::PrefixRankedPattern ( alphabet::RankedSymbol subtreeWildcard, std::set < alphabet::RankedSymbol > alphabet, std::vector < alphabet::RankedSymbol > data ) : RankedPatternAlphabet ( std::move ( subtreeWildcard ) ) {
@@ -37,6 +40,9 @@ PrefixRankedPattern::PrefixRankedPattern ( alphabet::RankedSymbol subtreeWildcar
 	m_Data = std::move ( data );
 }
+PrefixRankedPattern::PrefixRankedPattern ( const PrefixRankedTree & tree ) : PrefixRankedPattern ( alphabet::RankedSymbol ( alphabet::Symbol ( alphabet::SubtreeWildcardSymbol::SUBTREE_WILDCARD ), 0 ), tree.getAlphabet ( ), tree.getContent ( ) ) {
+}
+
 PrefixRankedPattern::PrefixRankedPattern ( const RankedPattern & tree ) : RankedPatternAlphabet ( tree.getSubtreeWildcard ( ) ) {
 	toPrefixRanked ( tree.getRoot ( ) );
 	addSymbolsToAlphabet ( tree.getAlphabet ( ) );

alib2data/src/tree/ranked/PrefixRankedPattern.h

@@ -19,6 +19,7 @@
 namespace tree {
 class RankedPattern;
+class PrefixRankedTree;
 /**
  * Represents regular expression parsed from the XML. Regular expression is stored
@@ -32,6 +33,7 @@ class PrefixRankedPattern : public RankedTreeBase, public RankedPatternAlphabet
 public:
 	explicit PrefixRankedPattern ( alphabet::RankedSymbol subtreeWildcard, std::set < alphabet::RankedSymbol > alphabet, std::vector < alphabet::RankedSymbol > data );
 	explicit PrefixRankedPattern ( alphabet::RankedSymbol subtreeWildcard, std::vector < alphabet::RankedSymbol > data );
+	explicit PrefixRankedPattern ( const PrefixRankedTree & tree );
 	explicit PrefixRankedPattern ( const RankedPattern & tree );
 	virtual RankedTreeBase * clone ( ) const;

tests.aarbology.sh

@@ -214,4 +214,5 @@ runTestSubtree "Exact Subtree Automaton" "./arun2 -t occurrences -a <(./aarbolog
 runTestPattern "Exact Boyer Moore Horspool" "./aarbology2 -a boyerMooreHorspool -s <( ./acast2 -t PrefixRankedBarTree -i \"\$SUBJECT_FILE\" ) -p <( ./acast2 -t PrefixRankedBarPattern -i <(./alphabetManip2 -o add -i \"\$PATTERN_FILE\" -a <(./alphabetManip2 -o get -i \"\$SUBJECT_FILE\"))) | ./astat2 -p size --set"
 runTestPattern "Exact Knuth Morris Pratt" "./aarbology2 -a knuthMorrisPratt -s <( ./acast2 -t PrefixRankedBarTree -i \"\$SUBJECT_FILE\" ) -p <( ./acast2 -t PrefixRankedBarPattern -i \"\$PATTERN_FILE\" ) | ./astat2 -p size --set"
+runTestPattern "Exact Knuth Morris Pratt" "./aarbology2 -a knuthMorrisPratt -s <( ./acast2 -t PrefixRankedTree -i \"\$SUBJECT_FILE\" ) -p <( ./acast2 -t PrefixRankedPattern -i \"\$PATTERN_FILE\" ) | ./astat2 -p size --set"
 runTestPattern "Exact Pattern Automaton" "./arun2 -t occurrences -a <(./aarbology2 -a exactPatternMatchingAutomaton -p <(./alphabetManip2 -o add -i \"\$PATTERN_FILE\" -a <(./alphabetManip2 -o get -i \"\$SUBJECT_FILE\")) | ./adeterminize2) -i \"\$SUBJECT_FILE\" | ./astat2 -p size --set"