bcs on nonlinear tree patterns

alib2algo/src/arbology/exact/BadCharacterShiftTable.cpp

@@ -8,6 +8,7 @@
 #include "BadCharacterShiftTable.h"
 #include <tree/ranked/PrefixRankedBarPattern.h>
+#include <tree/ranked/PrefixRankedBarNonlinearPattern.h>
 namespace arbology {
@@ -18,13 +19,19 @@ std::map < alphabet::RankedSymbol, size_t > BadCharacterShiftTable::bcs ( const
 }
 std::map < alphabet::RankedSymbol, size_t > BadCharacterShiftTable::bcs ( const tree::PrefixRankedBarPattern & pattern ) {
+	return bcs ( tree::PrefixRankedBarNonlinearPattern ( pattern ) );
+}
+
+auto BadCharacterShiftTablePrefixRankedBarPattern = BadCharacterShiftTable::RegistratorWrapper < std::map < alphabet::RankedSymbol, size_t >, tree::PrefixRankedBarPattern > ( BadCharacterShiftTable::bcs );
+
+std::map < alphabet::RankedSymbol, size_t > BadCharacterShiftTable::bcs ( const tree::PrefixRankedBarNonlinearPattern & pattern ) {
 	const std::set < alphabet::RankedSymbol > & alphabet = pattern.getAlphabet ( );
 	std::map < alphabet::RankedSymbol, size_t > bcs;
 	 // initialisation of bcs table to the size of the pattern
 	for ( const alphabet::RankedSymbol & symbol : alphabet ) {
-		if ( ( symbol == pattern.getSubtreeWildcard ( ) ) || ( symbol == pattern.getVariablesBar ( ) ) ) continue;
+		if ( ( symbol == pattern.getSubtreeWildcard ( ) ) || ( pattern.getNonlinearVariables ( ).count ( symbol ) ) || ( symbol == pattern.getVariablesBar ( ) ) ) continue;
 		bcs.insert ( std::make_pair ( symbol, pattern.getContent ( ).size ( ) ) );
 	}
@@ -34,13 +41,13 @@ std::map < alphabet::RankedSymbol, size_t > BadCharacterShiftTable::bcs ( const
 	unsigned lastSOffset = pattern.getContent ( ).size ( );
 	for ( unsigned i = 0; i < pattern.getContent ( ).size ( ); i++ )
-		if ( pattern.getContent ( )[i] == pattern.getSubtreeWildcard ( ) )
+		if ( pattern.getContent ( )[i] == pattern.getSubtreeWildcard ( ) || pattern.getNonlinearVariables ( ).count ( pattern.getContent ( )[i] ) )
 			lastSOffset = pattern.getContent ( ).size ( ) - i - 1;
 	// limit the shift by occurrence of the last variable
 	for ( const alphabet::RankedSymbol & symbol : alphabet ) {
-		if ( ( symbol == pattern.getSubtreeWildcard ( ) ) || ( symbol == pattern.getVariablesBar ( ) ) ) continue;
+		if ( ( symbol == pattern.getSubtreeWildcard ( ) ) || ( pattern.getNonlinearVariables ( ).count ( symbol ) ) || ( symbol == pattern.getVariablesBar ( ) ) ) continue;
 		size_t tmp = lastSOffset;
@@ -60,7 +67,7 @@ std::map < alphabet::RankedSymbol, size_t > BadCharacterShiftTable::bcs ( const
 	 // limit the shift by position of symbols within the pattern
 	for ( unsigned i = 0; i < pattern.getContent ( ).size ( ) - 1; i++ ) { // last symbol is not concerned
-		if ( ( pattern.getContent ( )[i] == pattern.getSubtreeWildcard ( ) ) || ( pattern.getContent ( )[i] == pattern.getVariablesBar ( ) ) ) continue;
+		if ( ( pattern.getContent ( )[i] == pattern.getSubtreeWildcard ( ) ) || ( pattern.getNonlinearVariables ( ).count ( pattern.getContent ( )[i] ) ) || ( pattern.getContent ( )[i] == pattern.getVariablesBar ( ) ) ) continue;
 		size_t tmp = pattern.getContent ( ).size ( ) - i - 1;
@@ -71,7 +78,7 @@ std::map < alphabet::RankedSymbol, size_t > BadCharacterShiftTable::bcs ( const
 	return bcs;
 }
-auto BadCharacterShiftTablePrefixRankedBarPattern = BadCharacterShiftTable::RegistratorWrapper < std::map < alphabet::RankedSymbol, size_t >, tree::PrefixRankedBarPattern > ( BadCharacterShiftTable::bcs );
+auto BadCharacterShiftTablePrefixRankedBarNonlinearPattern = BadCharacterShiftTable::RegistratorWrapper < std::map < alphabet::RankedSymbol, size_t >, tree::PrefixRankedBarNonlinearPattern > ( BadCharacterShiftTable::bcs );
 } /* namespace exact */

alib2algo/src/arbology/exact/BadCharacterShiftTable.h

@@ -33,6 +33,7 @@ public:
 	static std::map < alphabet::RankedSymbol, size_t > bcs ( const tree::RankedTreeWrapper & pattern );
 	static std::map < alphabet::RankedSymbol, size_t > bcs ( const tree::PrefixRankedBarPattern & pattern );
+	static std::map < alphabet::RankedSymbol, size_t > bcs ( const tree::PrefixRankedBarNonlinearPattern & pattern );
 };

alib2algo/src/arbology/exact/BoyerMooreHorspool.cpp

@@ -8,10 +8,12 @@
 #include "BoyerMooreHorspool.h"
 #include "BadCharacterShiftTable.h"
 #include "SubtreeJumpTable.h"
+#include "ExactSubtreeRepeatsNaive.h"
 #include <tree/Tree.h>
 #include <tree/ranked/PrefixRankedBarTree.h>
 #include <tree/ranked/PrefixRankedBarPattern.h>
+#include <tree/ranked/PrefixRankedBarNonlinearPattern.h>
 #include <alphabet/RankedSymbol.h>
 #include <map>
@@ -73,6 +75,64 @@ std::set < unsigned > BoyerMooreHorspool::match ( const tree::PrefixRankedBarTre
 auto BoyerMooreHorspoolPrefixRankedBarTreePrefixRankedBarPattern = BoyerMooreHorspool::RegistratorWrapper < std::set < unsigned >, tree::PrefixRankedBarTree, tree::PrefixRankedBarPattern > ( BoyerMooreHorspool::match );
+std::set < unsigned > BoyerMooreHorspool::match ( const tree::PrefixRankedBarTree & subject, const tree::PrefixRankedBarNonlinearPattern & pattern ) {
+	std::set < unsigned > occ;
+	std::map < alphabet::RankedSymbol, size_t > bcs = BadCharacterShiftTable::bcs ( pattern ); //NOTE: the subjects alphabet must be a subset or equal to the pattern
+	std::vector < int > subjectSubtreeJumpTable = SubtreeJumpTable::compute ( subject );
+	std::map < alphabet::RankedSymbol, alphabet::Symbol > variablesSetting;
+
+	tree::PrefixRankedBarTree repeats = ExactSubtreeRepeatsNaive::repeats ( 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 ( ) ) {
+		 // clear the current state of variable to subtree repeat
+		variablesSetting.clear();
+
+		 // index to the pattern
+		unsigned j = pattern.getContent ( ).size ( ) - 1;
+
+		 // offset to the subject
+		unsigned offset = i + j;
+
+		while ( ( j > 0 ) && ( offset > 0 ) ) {
+			if ( subject.getContent ( )[offset] == pattern.getContent ( )[j] ) {
+				 // match of symbol
+				offset = offset - 1;
+				j = j - 1;
+			} else if ( ( pattern.getContent ( )[j] == pattern.getVariablesBar ( ) ) && ( pattern.getBars ( ).count ( subject.getContent ( )[offset] )) ) {
+				 // else match of variable with subtree
+				offset = subjectSubtreeJumpTable[offset];
+
+				 // check nonlinear variable
+				if ( pattern.getNonlinearVariables ( ).count ( pattern.getContent ( )[ j - 1 ] ) ) {
+					auto setting = variablesSetting.find ( pattern.getContent ( )[ j - 1 ] );
+
+					if ( setting != variablesSetting.end ( ) && repeats.getContent ( )[ offset + 1 ].getSymbol ( ) != setting->second )
+						break;
+
+					variablesSetting.insert ( std::make_pair ( pattern.getContent ( )[ j - 1 ], repeats.getContent( )[ offset + 1 ].getSymbol ( ) ) );
+				}
+				j = j - 2;
+			} else {
+				break;
+			}
+		}
+
+		 // match was found
+		if ( j == 0 ) occ.insert ( offset );
+
+		 // shift heuristics
+		i += bcs[subject.getContent ( )[i + pattern.getContent ( ).size ( ) - 1]];
+	}
+
+	return occ;
+}
+
+auto BoyerMooreHorspoolPrefixRankedBarTreePrefixRankedBarNonlinearPattern = BoyerMooreHorspool::RegistratorWrapper < std::set < unsigned >, tree::PrefixRankedBarTree, tree::PrefixRankedBarNonlinearPattern > ( BoyerMooreHorspool::match );
+
 } /* namespace exact */
 } /* namespace arbology */

alib2algo/src/arbology/exact/BoyerMooreHorspool.h

@@ -30,6 +30,7 @@ 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::PrefixRankedBarTree & subject, const tree::PrefixRankedBarNonlinearPattern & pattern );
 };

tests.aarbology.sh

@@ -59,6 +59,10 @@ function log {
 	echo "$5" >> $LOGFILE
 }
+function generateNonlinearPattern {
+	./arand2 -t RNP --nodes $RAND_SIZE_PATTERN --terminals $(( $RANDOM % $RAND_ALPHABET + 1 )) --height $RAND_HEIGHT_PATTERN 2>/dev/null
+}
+
 function generatePattern {
 	./arand2 -t RP --nodes $RAND_SIZE_PATTERN --terminals $(( $RANDOM % $RAND_ALPHABET + 1 )) --height $RAND_HEIGHT_PATTERN 2>/dev/null
 }
@@ -259,6 +263,51 @@ function runTestPattern {
 	clearResults
 }
+# $1 - aconversions2 sequence
+function runTestNonlinearPattern {
+	echo $1
+	echo -ne "\t"
+
+	initResults
+
+	# predefined tests first
+	for SUBJECT_FILE in `ls $TESTS_DIR/aarbology.test*.subject.xml`; do
+		PATTERN_FILE=${SUBJECT_FILE%.subject.xml}.nonlinearPattern.xml
+		if [ -f $PATTERN_FILE ]; then
+			SUBJECT_FILE_COPY=$(mktemp)
+			PATTERN_FILE_COPY=$(mktemp)
+
+			cat $SUBJECT_FILE > $SUBJECT_FILE_COPY
+			cat $PATTERN_FILE > $PATTERN_FILE_COPY
+
+			Occs=`./aarbology2 -a exactPatternMatch -s "$SUBJECT_FILE_COPY" -p "$PATTERN_FILE_COPY" | ./astat2 -p size --set`
+
+			runTest2 "$Occs" "$2" "$SUBJECT_FILE_COPY" "$PATTERN_FILE_COPY"
+		fi
+	done
+
+	echo -n " | "
+
+	# random tests
+	for i in $(seq 1 $TESTCASE_ITERATIONS );
+	do
+		SUBJECT_FILE=$(mktemp)
+		PATTERN_FILE=$(mktemp)
+
+		cat <(generateSubject) > $SUBJECT_FILE
+		cat <(generateNonlinearPattern) > $PATTERN_FILE
+
+		Occs=`./aarbology2 -a exactPatternMatch -s "$SUBJECT_FILE" -p "$PATTERN_FILE" | ./astat2 -p size --set`
+
+		runTest2 "$Occs" "$2" "$SUBJECT_FILE" "$PATTERN_FILE" & (( i%JOBS==0 )) && wait
+	done
+
+	wait
+
+	outputResults
+	clearResults
+}
+
 # $1 - aconversions2 sequence
 function runTestPatternEnds {
 	echo $1
@@ -314,6 +363,8 @@ runTestSubtree "Exact Boyer Moore Horspool (Subtree PrefixRankedBar)" "./aarbolo
 runTestSubtree "Exact Subtree Automaton (Tree)" "./arun2 -t occurrences -a <(./aarbology2 -a exactSubtreeMatchingAutomaton -p \"\$PATTERN_FILE\" | ./adeterminize2) -i \"\$SUBJECT_FILE\" | ./astat2 -p size --set"
 runTestPattern "Exact Boyer Moore Horspool (Pattern PrefixRankedBar)" "./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"
+runTestNonlinearPattern "Exact Pattern Match (NonlinearPattern PrefixRankedBar)" "./aarbology2 -a exactPatternMatch -s <( ./acast2 -t PrefixRankedBarTree -i \"\$SUBJECT_FILE\" ) -p <( ./acast2 -t PrefixRankedBarNonlinearPattern -i <(./alphabetManip2 -o add -i \"\$PATTERN_FILE\" -a <(./alphabetManip2 -o get -i \"\$SUBJECT_FILE\"))) | ./astat2 -p size --set"
+runTestNonlinearPattern "Exact Boyer Moore Horspool (NonlinearPattern PrefixRankedBar)" "./aarbology2 -a boyerMooreHorspool -s <( ./acast2 -t PrefixRankedBarTree -i \"\$SUBJECT_FILE\" ) -p <( ./acast2 -t PrefixRankedBarNonlinearPattern -i <(./alphabetManip2 -o add -i \"\$PATTERN_FILE\" -a <(./alphabetManip2 -o get -i \"\$SUBJECT_FILE\"))) | ./astat2 -p size --set"
 runTestPattern "Exact Reversed Boyer Moore Horspool (Pattern PrefixRankedBar)" "./aarbology2 -a reversedBoyerMooreHorspool -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 Reversed Boyer Moore Horspool (Pattern PrefixRanked)" "./aarbology2 -a reversedBoyerMooreHorspool -s <( ./acast2 -t PrefixRankedTree -i \"\$SUBJECT_FILE\" ) -p <( ./acast2 -t PrefixRankedPattern -i <(./alphabetManip2 -o add -i \"\$PATTERN_FILE\" -a <(./alphabetManip2 -o get -i \"\$SUBJECT_FILE\"))) | ./astat2 -p size --set"
 runTestPattern "Exact Knuth Morris Pratt (Pattern PrefixRankedBar)" "./aarbology2 -a knuthMorrisPratt -s <( ./acast2 -t PrefixRankedBarTree -i \"\$SUBJECT_FILE\" ) -p <( ./acast2 -t PrefixRankedBarPattern -i \"\$PATTERN_FILE\" ) | ./astat2 -p size --set"