From a0866678c47dfd36e3cb1139f206368c226437bc Mon Sep 17 00:00:00 2001
From: Jan Travnicek <Jan.Travnicek@fit.cvut.cz>
Date: Sat, 23 Jul 2016 21:49:34 +0200
Subject: [PATCH] add reversed variants for nonlinear bltpm
---
.../exact/ReversedBadCharacterShiftTable.cpp | 32 +++--
.../exact/ReversedBadCharacterShiftTable.h | 2 +
.../exact/ReversedBoyerMooreHorspool.cpp | 118 ++++++++++++++++++
.../exact/ReversedBoyerMooreHorspool.h | 2 +
tests.aarbology.sh | 2 +
5 files changed, 147 insertions(+), 9 deletions(-)
diff --git a/alib2algo/src/arbology/exact/ReversedBadCharacterShiftTable.cpp b/alib2algo/src/arbology/exact/ReversedBadCharacterShiftTable.cpp
index e8e345eb76..96171faaf2 100644
--- a/alib2algo/src/arbology/exact/ReversedBadCharacterShiftTable.cpp
+++ b/alib2algo/src/arbology/exact/ReversedBadCharacterShiftTable.cpp
@@ -8,7 +8,9 @@
#include "ReversedBadCharacterShiftTable.h"
#include <tree/ranked/PrefixRankedBarPattern.h>
+#include <tree/ranked/PrefixRankedBarNonlinearPattern.h>
#include <tree/ranked/PrefixRankedPattern.h>
+#include <tree/ranked/PrefixRankedNonlinearPattern.h>
namespace arbology {
@@ -19,13 +21,19 @@ std::map < alphabet::RankedSymbol, size_t > ReversedBadCharacterShiftTable::bcs
}
std::map < alphabet::RankedSymbol, size_t > ReversedBadCharacterShiftTable::bcs ( const tree::PrefixRankedBarPattern & pattern ) {
+ return bcs ( tree::PrefixRankedBarNonlinearPattern ( pattern ) );
+}
+
+auto ReversedBadCharacterShiftTablePrefixRankedBarPattern = ReversedBadCharacterShiftTable::RegistratorWrapper < std::map < alphabet::RankedSymbol, size_t >, tree::PrefixRankedBarPattern > ( ReversedBadCharacterShiftTable::bcs );
+
+std::map < alphabet::RankedSymbol, size_t > ReversedBadCharacterShiftTable::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 ( ) ) );
}
@@ -41,7 +49,7 @@ std::map < alphabet::RankedSymbol, size_t > ReversedBadCharacterShiftTable::bcs
// 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 = firstSBarOffset;
@@ -61,7 +69,7 @@ std::map < alphabet::RankedSymbol, size_t > ReversedBadCharacterShiftTable::bcs
// limit the shift by position of symbols within the pattern
for ( unsigned i = pattern.getContent ( ).size ( ) - 1; i >= 1; i-- ) { // first 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 = i;
@@ -72,16 +80,22 @@ std::map < alphabet::RankedSymbol, size_t > ReversedBadCharacterShiftTable::bcs
return bcs;
}
-auto ReversedBadCharacterShiftTablePrefixRankedBarPattern = ReversedBadCharacterShiftTable::RegistratorWrapper < std::map < alphabet::RankedSymbol, size_t >, tree::PrefixRankedBarPattern > ( ReversedBadCharacterShiftTable::bcs );
+auto ReversedBadCharacterShiftTablePrefixRankedBarNonlinearPattern = ReversedBadCharacterShiftTable::RegistratorWrapper < std::map < alphabet::RankedSymbol, size_t >, tree::PrefixRankedBarNonlinearPattern > ( ReversedBadCharacterShiftTable::bcs );
std::map < alphabet::RankedSymbol, size_t > ReversedBadCharacterShiftTable::bcs ( const tree::PrefixRankedPattern & pattern ) {
+ return bcs ( tree::PrefixRankedNonlinearPattern ( pattern ) );
+}
+
+auto ReversedBadCharacterShiftTablePrefixRankedPattern = ReversedBadCharacterShiftTable::RegistratorWrapper < std::map < alphabet::RankedSymbol, size_t >, tree::PrefixRankedPattern > ( ReversedBadCharacterShiftTable::bcs );
+
+std::map < alphabet::RankedSymbol, size_t > ReversedBadCharacterShiftTable::bcs ( const tree::PrefixRankedNonlinearPattern & 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 ( ) ) continue;
+ if ( symbol == pattern.getSubtreeWildcard ( ) || pattern.getNonlinearVariables ( ).count ( symbol ) ) continue;
bcs.insert ( std::make_pair ( symbol, pattern.getContent ( ).size ( ) ) );
}
@@ -91,14 +105,14 @@ std::map < alphabet::RankedSymbol, size_t > ReversedBadCharacterShiftTable::bcs
unsigned firstSOffset = pattern.getContent ( ).size ( ) + 1;
for ( int i = ( int ) pattern.getContent ( ).size ( ) - 1; i >= 0; i-- )
- if ( pattern.getContent ( )[i] == pattern.getSubtreeWildcard ( ) )
+ if ( pattern.getContent ( )[i] == pattern.getSubtreeWildcard ( ) || pattern.getNonlinearVariables ( ).count ( pattern.getContent ( )[i] ) )
firstSOffset = i;
if ( firstSOffset == 0 ) firstSOffset = 1;
// limit the shift by occurrence of the last variable
for ( const alphabet::RankedSymbol & symbol : alphabet ) {
- if ( symbol == pattern.getSubtreeWildcard ( ) ) continue;
+ if ( symbol == pattern.getSubtreeWildcard ( ) || pattern.getNonlinearVariables ( ).count ( symbol ) ) continue;
if ( bcs[symbol] > firstSOffset )
bcs[symbol] = firstSOffset;
@@ -106,7 +120,7 @@ std::map < alphabet::RankedSymbol, size_t > ReversedBadCharacterShiftTable::bcs
// limit the shift by position of symbols within the pattern
for ( unsigned i = pattern.getContent ( ).size ( ) - 1; i >= 1; i-- ) { // first symbol is not concerned
- if ( pattern.getContent ( )[i] == pattern.getSubtreeWildcard ( ) ) continue;
+ if ( pattern.getContent ( )[i] == pattern.getSubtreeWildcard ( ) || pattern.getNonlinearVariables ( ).count ( pattern.getContent ( )[i] ) ) continue;
size_t tmp = i;
if ( bcs[pattern.getContent ( )[i]] > tmp )
@@ -116,7 +130,7 @@ std::map < alphabet::RankedSymbol, size_t > ReversedBadCharacterShiftTable::bcs
return bcs;
}
-auto ReversedBadCharacterShiftTablePrefixRankedPattern = ReversedBadCharacterShiftTable::RegistratorWrapper < std::map < alphabet::RankedSymbol, size_t >, tree::PrefixRankedPattern > ( ReversedBadCharacterShiftTable::bcs );
+auto ReversedBadCharacterShiftTablePrefixRankedNonlinearPattern = ReversedBadCharacterShiftTable::RegistratorWrapper < std::map < alphabet::RankedSymbol, size_t >, tree::PrefixRankedNonlinearPattern > ( ReversedBadCharacterShiftTable::bcs );
} /* namespace exact */
diff --git a/alib2algo/src/arbology/exact/ReversedBadCharacterShiftTable.h b/alib2algo/src/arbology/exact/ReversedBadCharacterShiftTable.h
index 909c4301ca..2699bfe9d8 100644
--- a/alib2algo/src/arbology/exact/ReversedBadCharacterShiftTable.h
+++ b/alib2algo/src/arbology/exact/ReversedBadCharacterShiftTable.h
@@ -33,7 +33,9 @@ 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 );
static std::map < alphabet::RankedSymbol, size_t > bcs ( const tree::PrefixRankedPattern & pattern );
+ static std::map < alphabet::RankedSymbol, size_t > bcs ( const tree::PrefixRankedNonlinearPattern & pattern );
};
diff --git a/alib2algo/src/arbology/exact/ReversedBoyerMooreHorspool.cpp b/alib2algo/src/arbology/exact/ReversedBoyerMooreHorspool.cpp
index c6ddbfb88e..6d79deba94 100644
--- a/alib2algo/src/arbology/exact/ReversedBoyerMooreHorspool.cpp
+++ b/alib2algo/src/arbology/exact/ReversedBoyerMooreHorspool.cpp
@@ -8,12 +8,15 @@
#include "ReversedBoyerMooreHorspool.h"
#include "ReversedBadCharacterShiftTable.h"
#include "SubtreeJumpTable.h"
+#include "ExactSubtreeRepeatsNaive.h"
#include <tree/Tree.h>
#include <tree/ranked/PrefixRankedTree.h>
#include <tree/ranked/PrefixRankedBarTree.h>
#include <tree/ranked/PrefixRankedPattern.h>
#include <tree/ranked/PrefixRankedBarPattern.h>
+#include <tree/ranked/PrefixRankedNonlinearPattern.h>
+#include <tree/ranked/PrefixRankedBarNonlinearPattern.h>
#include <alphabet/RankedSymbol.h>
#include <map>
@@ -75,6 +78,64 @@ std::set < unsigned > ReversedBoyerMooreHorspool::match ( const tree::PrefixRank
auto ReversedBoyerMooreHorspoolPrefixRankedBarTreePrefixRankedBarPattern = ReversedBoyerMooreHorspool::RegistratorWrapper < std::set < unsigned >, tree::PrefixRankedBarTree, tree::PrefixRankedBarPattern > ( ReversedBoyerMooreHorspool::match );
+std::set < unsigned > ReversedBoyerMooreHorspool::match ( const tree::PrefixRankedBarTree & subject, const tree::PrefixRankedBarNonlinearPattern & pattern ) {
+ std::set < unsigned > occ;
+ std::map < alphabet::RankedSymbol, size_t > bcs = ReversedBadCharacterShiftTable::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
+ int i = ( int ) subject.getContent ( ).size ( ) - pattern.getContent ( ).size ( ) + 1;
+
+ // main loop of the algorithm over all possible indexes where the pattern can start
+ while ( i >= 0 ) {
+ // clear the current state of variable to subtree repeat
+ variablesSetting.clear();
+
+ // 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 = offset + 1;
+ j = j + 1;
+ } else if ( ( pattern.getContent ( )[j] == pattern.getSubtreeWildcard ( ) || pattern.getNonlinearVariables ( ).count ( pattern.getContent ( )[j] ) ) && ( ! pattern.getBars ( ).count ( subject.getContent ( )[offset] ) ) ) {
+ // check nonlinear variable
+ if ( pattern.getNonlinearVariables ( ).count ( pattern.getContent ( )[ j ] ) ) {
+ auto setting = variablesSetting.find ( pattern.getContent ( )[ j ] );
+
+ if ( setting != variablesSetting.end ( ) && repeats.getContent ( )[ offset ].getSymbol ( ) != setting->second )
+ break;
+
+ variablesSetting.insert ( std::make_pair ( pattern.getContent ( )[ j ], repeats.getContent( )[ offset ].getSymbol ( ) ) );
+ }
+
+ // match of variable with subtree
+ offset = subjectSubtreeJumpTable[offset];
+ j = j + 2;
+ } else {
+ break;
+ }
+ }
+
+ // match was found
+ if ( j == pattern.getContent ( ).size ( ) ) occ.insert ( i );
+
+ // shift heuristics
+ i -= bcs[subject.getContent ( )[i]];
+ }
+
+ return occ;
+}
+
+auto ReversedBoyerMooreHorspoolPrefixRankedBarTreePrefixRankedBarNonlinearPattern = ReversedBoyerMooreHorspool::RegistratorWrapper < std::set < unsigned >, tree::PrefixRankedBarTree, tree::PrefixRankedBarNonlinearPattern > ( ReversedBoyerMooreHorspool::match );
+
std::set < unsigned > ReversedBoyerMooreHorspool::match ( const tree::PrefixRankedTree & subject, const tree::PrefixRankedTree & pattern ) {
return match ( subject, tree::PrefixRankedPattern ( pattern ) );
}
@@ -123,6 +184,63 @@ std::set < unsigned > ReversedBoyerMooreHorspool::match ( const tree::PrefixRank
auto ReversedBoyerMooreHorspoolPrefixRankedBarTreePrefixRankedPattern = ReversedBoyerMooreHorspool::RegistratorWrapper < std::set < unsigned >, tree::PrefixRankedTree, tree::PrefixRankedPattern > ( ReversedBoyerMooreHorspool::match );
+std::set < unsigned > ReversedBoyerMooreHorspool::match ( const tree::PrefixRankedTree & subject, const tree::PrefixRankedNonlinearPattern & pattern ) {
+ std::set < unsigned > occ;
+ std::map < alphabet::RankedSymbol, size_t > bcs = ReversedBadCharacterShiftTable::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::PrefixRankedTree repeats = ExactSubtreeRepeatsNaive::repeats ( subject );
+
+ // index to the subject
+ int i = ( int ) subject.getContent ( ).size ( ) - pattern.getContent ( ).size ( ) + 1;
+
+ // main loop of the algorithm over all possible indexes where the pattern can start
+ while ( i >= 0 ) {
+ // clear the current state of variable to subtree repeat
+ variablesSetting.clear();
+
+ // 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 = offset + 1;
+ else if ( pattern.getContent ( )[j] == pattern.getSubtreeWildcard ( ) || pattern.getNonlinearVariables ( ).count ( pattern.getContent ( )[ j ] ) ) {
+ // check nonlinear variable
+ if ( pattern.getNonlinearVariables ( ).count ( pattern.getContent ( )[ j ] ) ) {
+ auto setting = variablesSetting.find ( pattern.getContent ( )[ j ] );
+
+ if ( setting != variablesSetting.end ( ) && repeats.getContent ( )[ offset ].getSymbol ( ) != setting->second )
+ break;
+
+ variablesSetting.insert ( std::make_pair ( pattern.getContent ( )[ j ], repeats.getContent( )[ offset ].getSymbol ( ) ) );
+ }
+
+ // match of variable with subtree
+ offset = subjectSubtreeJumpTable[offset];
+ } else
+ break;
+
+ j = j + 1;
+ }
+
+ // match was found
+ if ( j == pattern.getContent ( ).size ( ) ) occ.insert ( i );
+
+ // shift heristics
+ i -= bcs[subject.getContent ( )[i]];
+ }
+
+ return occ;
+}
+
+auto ReversedBoyerMooreHorspoolPrefixRankedBarTreePrefixRankedNonlinearPattern = ReversedBoyerMooreHorspool::RegistratorWrapper < std::set < unsigned >, tree::PrefixRankedTree, tree::PrefixRankedNonlinearPattern > ( ReversedBoyerMooreHorspool::match );
+
} /* namespace exact */
} /* namespace arbology */
diff --git a/alib2algo/src/arbology/exact/ReversedBoyerMooreHorspool.h b/alib2algo/src/arbology/exact/ReversedBoyerMooreHorspool.h
index 9837c35d37..ebde38651c 100644
--- a/alib2algo/src/arbology/exact/ReversedBoyerMooreHorspool.h
+++ b/alib2algo/src/arbology/exact/ReversedBoyerMooreHorspool.h
@@ -30,8 +30,10 @@ 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 );
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 std::set < unsigned > match ( const tree::PrefixRankedTree & subject, const tree::PrefixRankedNonlinearPattern & pattern );
};
diff --git a/tests.aarbology.sh b/tests.aarbology.sh
index 7fa8f9b88a..fee36759d7 100755
--- a/tests.aarbology.sh
+++ b/tests.aarbology.sh
@@ -367,6 +367,8 @@ runTestNonlinearPattern "Exact Pattern Match (NonlinearPattern PrefixRankedBar)"
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"
+runTestNonlinearPattern "Exact Reversed Boyer Moore Horspool (NonlinearPattern PrefixRankedBar)" "./aarbology2 -a reversedBoyerMooreHorspool -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 Reversed Boyer Moore Horspool (NonlinearPattern PrefixRanked)" "./aarbology2 -a reversedBoyerMooreHorspool -s <( ./acast2 -t PrefixRankedTree -i \"\$SUBJECT_FILE\" ) -p <( ./acast2 -t PrefixRankedNonlinearPattern -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"
runTestPattern "Exact Knuth Morris Pratt (Pattern PrefixRanked)" "./aarbology2 -a knuthMorrisPratt -s <( ./acast2 -t PrefixRankedTree -i \"\$SUBJECT_FILE\" ) -p <( ./acast2 -t PrefixRankedPattern -i \"\$PATTERN_FILE\" ) | ./astat2 -p size --set"
runTestPattern "Exact Dead Zone Using Bad Character Shift And Border Array (Pattern PrefixRanked)" "./aarbology2 -a deadZoneUsingBadCharacterShiftAndBorderArray -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"
--
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