From eaa87ff5cf6198578f25b7be62068c70fc12c19a Mon Sep 17 00:00:00 2001
From: Jan Travnicek <Jan.Travnicek@fit.cvut.cz>
Date: Fri, 12 May 2017 12:30:22 +0200
Subject: [PATCH] organise stringology algorithms
---
.../string/properties/GoodSuffixShiftTable.h | 4 +--
.../exact/ExactFactorAutomaton.cpp | 26 -------------------
...tiNondeterministicSubsequenceAutomaton.cpp | 4 +--
...ultiNondeterministicSubsequenceAutomaton.h | 4 +--
...ctNondeterministicSubsequenceAutomaton.cpp | 4 +--
...xactNondeterministicSubsequenceAutomaton.h | 4 +--
.../ExactSubsequenceAutomaton.cpp | 4 +--
.../ExactSubsequenceAutomaton.h | 4 +--
.../NondeterministicExactFactorAutomaton.cpp | 26 +++++++++++++++++++
.../NondeterministicExactFactorAutomaton.h} | 16 ++++++------
.../ExactMatchingAutomaton.cpp | 4 +--
.../ExactMatchingAutomaton.h | 4 +--
astringology2/src/astringology.cpp | 24 ++++++++---------
13 files changed, 64 insertions(+), 64 deletions(-)
delete mode 100644 alib2algo/src/stringology/exact/ExactFactorAutomaton.cpp
rename alib2algo/src/stringology/{exact => indexing}/ExactMultiNondeterministicSubsequenceAutomaton.cpp (93%)
rename alib2algo/src/stringology/{exact => indexing}/ExactMultiNondeterministicSubsequenceAutomaton.h (97%)
rename alib2algo/src/stringology/{exact => indexing}/ExactNondeterministicSubsequenceAutomaton.cpp (93%)
rename alib2algo/src/stringology/{exact => indexing}/ExactNondeterministicSubsequenceAutomaton.h (97%)
rename alib2algo/src/stringology/{exact => indexing}/ExactSubsequenceAutomaton.cpp (91%)
rename alib2algo/src/stringology/{exact => indexing}/ExactSubsequenceAutomaton.h (97%)
create mode 100644 alib2algo/src/stringology/indexing/NondeterministicExactFactorAutomaton.cpp
rename alib2algo/src/stringology/{exact/ExactFactorAutomaton.h => indexing/NondeterministicExactFactorAutomaton.h} (68%)
rename alib2algo/src/stringology/{exact => matching}/ExactMatchingAutomaton.cpp (92%)
rename alib2algo/src/stringology/{exact => matching}/ExactMatchingAutomaton.h (96%)
diff --git a/alib2algo/src/string/properties/GoodSuffixShiftTable.h b/alib2algo/src/string/properties/GoodSuffixShiftTable.h
index 90fb04c9b6..d190142467 100644
--- a/alib2algo/src/string/properties/GoodSuffixShiftTable.h
+++ b/alib2algo/src/string/properties/GoodSuffixShiftTable.h
@@ -19,7 +19,7 @@
#include <string/properties/BorderArray.h>
#include <automaton/determinize/Determinize.h>
#include <automaton/simplify/EpsilonRemoverIncoming.h>
-#include <stringology/exact/ExactFactorAutomaton.h>
+#include <stringology/indexing/NondeterministicExactFactorAutomaton.h>
namespace string {
@@ -50,7 +50,7 @@ std::vector < size_t > GoodSuffixShiftTable::gss ( const string::LinearString <
std::vector < unsigned > borderArray = string::properties::BorderArray::construct ( reversed );
size_t max = reversed.getContent ( ).size ( ) - borderArray.back ( );
- automaton::DFA < DefaultSymbolType, std::set < unsigned > > factorAutomaton = automaton::determinize::Determinize::determinize ( automaton::simplify::EpsilonRemoverIncoming::remove ( stringology::exact::ExactFactorAutomaton::construct ( reversed ) ) );
+ automaton::DFA < DefaultSymbolType, std::set < unsigned > > factorAutomaton = automaton::determinize::Determinize::determinize ( automaton::simplify::EpsilonRemoverIncoming::remove ( stringology::indexing::NondeterministicExactFactorAutomaton::construct ( reversed ) ) );
std::vector < size_t > result;
diff --git a/alib2algo/src/stringology/exact/ExactFactorAutomaton.cpp b/alib2algo/src/stringology/exact/ExactFactorAutomaton.cpp
deleted file mode 100644
index 0193777efc..0000000000
--- a/alib2algo/src/stringology/exact/ExactFactorAutomaton.cpp
+++ /dev/null
@@ -1,26 +0,0 @@
-/*
- * ExactFactorAutomaton.cpp
- *
- * Created on: 7. 4. 2015
- * Author: Jan Travnicek
- */
-
-#include "ExactFactorAutomaton.h"
-#include <string/LinearString.h>
-#include <string/Epsilon.h>
-
-#include <deque>
-
-namespace stringology {
-
-namespace exact {
-
-automaton::Automaton ExactFactorAutomaton::construct(const string::String& text) {
- return dispatch(text.getData());
-}
-
-auto ExactFactorAutomatonLinearString = ExactFactorAutomaton::RegistratorWrapper<automaton::EpsilonNFA < DefaultSymbolType, DefaultEpsilonType, unsigned >, string::LinearString < > >(ExactFactorAutomaton::construct);
-
-} /* namespace exact */
-
-} /* namespace stringology */
diff --git a/alib2algo/src/stringology/exact/ExactMultiNondeterministicSubsequenceAutomaton.cpp b/alib2algo/src/stringology/indexing/ExactMultiNondeterministicSubsequenceAutomaton.cpp
similarity index 93%
rename from alib2algo/src/stringology/exact/ExactMultiNondeterministicSubsequenceAutomaton.cpp
rename to alib2algo/src/stringology/indexing/ExactMultiNondeterministicSubsequenceAutomaton.cpp
index 4ef32e4c67..6fbfed0d69 100644
--- a/alib2algo/src/stringology/exact/ExactMultiNondeterministicSubsequenceAutomaton.cpp
+++ b/alib2algo/src/stringology/indexing/ExactMultiNondeterministicSubsequenceAutomaton.cpp
@@ -10,12 +10,12 @@
namespace stringology {
-namespace exact {
+namespace indexing {
automaton::Automaton ExactMultiNondeterministicSubsequenceAutomaton::construct ( const std::set < string::String > & texts ) {
return automaton::Automaton ( ExactMultiNondeterministicSubsequenceAutomaton::construct ( common::ContainerConverter < std::set < string::LinearString < > >, std::set < string::String >, string::LinearString < > >::convert ( texts ) ) );
}
-} /* namespace exact */
+} /* namespace indexing */
} /* namespace stringology */
diff --git a/alib2algo/src/stringology/exact/ExactMultiNondeterministicSubsequenceAutomaton.h b/alib2algo/src/stringology/indexing/ExactMultiNondeterministicSubsequenceAutomaton.h
similarity index 97%
rename from alib2algo/src/stringology/exact/ExactMultiNondeterministicSubsequenceAutomaton.h
rename to alib2algo/src/stringology/indexing/ExactMultiNondeterministicSubsequenceAutomaton.h
index cd61e16f2a..e8adc807f2 100644
--- a/alib2algo/src/stringology/exact/ExactMultiNondeterministicSubsequenceAutomaton.h
+++ b/alib2algo/src/stringology/indexing/ExactMultiNondeterministicSubsequenceAutomaton.h
@@ -17,7 +17,7 @@
namespace stringology {
-namespace exact {
+namespace indexing {
class ExactMultiNondeterministicSubsequenceAutomaton {
public:
@@ -59,7 +59,7 @@ automaton::EpsilonNFA < SymbolType, DefaultEpsilonType, std::pair < unsigned, un
return res;
}
-} /* namespace exact */
+} /* namespace indexing */
} /* namespace stringology */
diff --git a/alib2algo/src/stringology/exact/ExactNondeterministicSubsequenceAutomaton.cpp b/alib2algo/src/stringology/indexing/ExactNondeterministicSubsequenceAutomaton.cpp
similarity index 93%
rename from alib2algo/src/stringology/exact/ExactNondeterministicSubsequenceAutomaton.cpp
rename to alib2algo/src/stringology/indexing/ExactNondeterministicSubsequenceAutomaton.cpp
index d479520957..feb46bf22c 100644
--- a/alib2algo/src/stringology/exact/ExactNondeterministicSubsequenceAutomaton.cpp
+++ b/alib2algo/src/stringology/indexing/ExactNondeterministicSubsequenceAutomaton.cpp
@@ -9,7 +9,7 @@
namespace stringology {
-namespace exact {
+namespace indexing {
automaton::Automaton ExactNondeterministicSubsequenceAutomaton::construct(const string::String& text) {
return dispatch(text.getData());
@@ -17,6 +17,6 @@ automaton::Automaton ExactNondeterministicSubsequenceAutomaton::construct(const
auto ExactNondeterministicSubsequenceAutomatonLinearString = ExactNondeterministicSubsequenceAutomaton::RegistratorWrapper < automaton::EpsilonNFA < DefaultSymbolType, DefaultEpsilonType, unsigned >, string::LinearString < > > ( ExactNondeterministicSubsequenceAutomaton::construct );
-} /* namespace exact */
+} /* namespace indexing */
} /* namespace stringology */
diff --git a/alib2algo/src/stringology/exact/ExactNondeterministicSubsequenceAutomaton.h b/alib2algo/src/stringology/indexing/ExactNondeterministicSubsequenceAutomaton.h
similarity index 97%
rename from alib2algo/src/stringology/exact/ExactNondeterministicSubsequenceAutomaton.h
rename to alib2algo/src/stringology/indexing/ExactNondeterministicSubsequenceAutomaton.h
index 952da5cae8..8419b76375 100644
--- a/alib2algo/src/stringology/exact/ExactNondeterministicSubsequenceAutomaton.h
+++ b/alib2algo/src/stringology/indexing/ExactNondeterministicSubsequenceAutomaton.h
@@ -16,7 +16,7 @@
namespace stringology {
-namespace exact {
+namespace indexing {
class ExactNondeterministicSubsequenceAutomaton : public std::SingleDispatch<ExactNondeterministicSubsequenceAutomaton, automaton::Automaton, const string::StringBase & > {
public:
@@ -48,7 +48,7 @@ automaton::EpsilonNFA < SymbolType, DefaultEpsilonType, unsigned > ExactNondeter
return res;
}
-} /* namespace exact */
+} /* namespace indexing */
} /* namespace stringology */
diff --git a/alib2algo/src/stringology/exact/ExactSubsequenceAutomaton.cpp b/alib2algo/src/stringology/indexing/ExactSubsequenceAutomaton.cpp
similarity index 91%
rename from alib2algo/src/stringology/exact/ExactSubsequenceAutomaton.cpp
rename to alib2algo/src/stringology/indexing/ExactSubsequenceAutomaton.cpp
index 46cb28c63c..3da7a3dcd3 100644
--- a/alib2algo/src/stringology/exact/ExactSubsequenceAutomaton.cpp
+++ b/alib2algo/src/stringology/indexing/ExactSubsequenceAutomaton.cpp
@@ -9,7 +9,7 @@
namespace stringology {
-namespace exact {
+namespace indexing {
automaton::Automaton ExactSubsequenceAutomaton::construct(const string::String& text) {
return dispatch(text.getData());
@@ -17,6 +17,6 @@ automaton::Automaton ExactSubsequenceAutomaton::construct(const string::String&
auto ExactSubsequenceAutomatonLinearString = ExactSubsequenceAutomaton::RegistratorWrapper < automaton::DFA < DefaultSymbolType, unsigned >, string::LinearString < > > ( ExactSubsequenceAutomaton::construct );
-} /* namespace exact */
+} /* namespace indexing */
} /* namespace stringology */
diff --git a/alib2algo/src/stringology/exact/ExactSubsequenceAutomaton.h b/alib2algo/src/stringology/indexing/ExactSubsequenceAutomaton.h
similarity index 97%
rename from alib2algo/src/stringology/exact/ExactSubsequenceAutomaton.h
rename to alib2algo/src/stringology/indexing/ExactSubsequenceAutomaton.h
index c7cd07cb05..9e52895cdf 100644
--- a/alib2algo/src/stringology/exact/ExactSubsequenceAutomaton.h
+++ b/alib2algo/src/stringology/indexing/ExactSubsequenceAutomaton.h
@@ -16,7 +16,7 @@
namespace stringology {
-namespace exact {
+namespace indexing {
class ExactSubsequenceAutomaton : public std::SingleDispatch<ExactSubsequenceAutomaton, automaton::Automaton, const string::StringBase & > {
public:
@@ -56,7 +56,7 @@ automaton::DFA < SymbolType, unsigned > ExactSubsequenceAutomaton::construct ( c
return res;
}
-} /* namespace exact */
+} /* namespace indexing */
} /* namespace stringology */
diff --git a/alib2algo/src/stringology/indexing/NondeterministicExactFactorAutomaton.cpp b/alib2algo/src/stringology/indexing/NondeterministicExactFactorAutomaton.cpp
new file mode 100644
index 0000000000..0fa8a91dc2
--- /dev/null
+++ b/alib2algo/src/stringology/indexing/NondeterministicExactFactorAutomaton.cpp
@@ -0,0 +1,26 @@
+/*
+ * NondeterministicExactFactorAutomaton.cpp
+ *
+ * Created on: 7. 4. 2015
+ * Author: Jan Travnicek
+ */
+
+#include "NondeterministicExactFactorAutomaton.h"
+#include <string/LinearString.h>
+#include <string/Epsilon.h>
+
+#include <deque>
+
+namespace stringology {
+
+namespace indexing {
+
+automaton::Automaton NondeterministicExactFactorAutomaton::construct(const string::String& text) {
+ return dispatch(text.getData());
+}
+
+auto ExactFactorAutomatonLinearString = NondeterministicExactFactorAutomaton::RegistratorWrapper<automaton::EpsilonNFA < DefaultSymbolType, DefaultEpsilonType, unsigned >, string::LinearString < > >(NondeterministicExactFactorAutomaton::construct);
+
+} /* namespace indexing */
+
+} /* namespace stringology */
diff --git a/alib2algo/src/stringology/exact/ExactFactorAutomaton.h b/alib2algo/src/stringology/indexing/NondeterministicExactFactorAutomaton.h
similarity index 68%
rename from alib2algo/src/stringology/exact/ExactFactorAutomaton.h
rename to alib2algo/src/stringology/indexing/NondeterministicExactFactorAutomaton.h
index db5c71caef..84930fefb1 100644
--- a/alib2algo/src/stringology/exact/ExactFactorAutomaton.h
+++ b/alib2algo/src/stringology/indexing/NondeterministicExactFactorAutomaton.h
@@ -1,12 +1,12 @@
/*
- * ExactFactorAutomaton.h
+ * NondeterministicExactFactorAutomaton.h
*
* Created on: 7. 4. 2015
* Author: Jan Travnicek
*/
-#ifndef _EXACT_FACTOR_AUTOMATON__H_
-#define _EXACT_FACTOR_AUTOMATON__H_
+#ifndef NONDETERMINISTIC_EXACT_FACTOR_AUTOMATON_H_
+#define NONDETERMINISTIC_EXACT_FACTOR_AUTOMATON_H_
#include <automaton/Automaton.h>
#include <automaton/FSM/EpsilonNFA.h>
@@ -17,9 +17,9 @@
namespace stringology {
-namespace exact {
+namespace indexing {
-class ExactFactorAutomaton : public std::SingleDispatch<ExactFactorAutomaton, automaton::Automaton, const string::StringBase & > {
+class NondeterministicExactFactorAutomaton : public std::SingleDispatch<NondeterministicExactFactorAutomaton, automaton::Automaton, const string::StringBase & > {
public:
/**
* Performs conversion.
@@ -32,7 +32,7 @@ public:
};
template < class SymbolType >
-automaton::EpsilonNFA < SymbolType, DefaultEpsilonType, unsigned > ExactFactorAutomaton::construct(const string::LinearString < SymbolType > & text) {
+automaton::EpsilonNFA < SymbolType, DefaultEpsilonType, unsigned > NondeterministicExactFactorAutomaton::construct(const string::LinearString < SymbolType > & text) {
automaton::EpsilonNFA < SymbolType, DefaultEpsilonType, unsigned > res ( 0 );
res.addFinalState ( 0 );
res.setInputAlphabet(text.getAlphabet());
@@ -47,8 +47,8 @@ automaton::EpsilonNFA < SymbolType, DefaultEpsilonType, unsigned > ExactFactorAu
return res;
}
-} /* namespace exact */
+} /* namespace indexing */
} /* namespace stringology */
-#endif /* _EXACT_FACTOR_AUTOMATON__H_ */
+#endif /* NONDETERMINISTIC_EXACT_FACTOR_AUTOMATON_H_ */
diff --git a/alib2algo/src/stringology/exact/ExactMatchingAutomaton.cpp b/alib2algo/src/stringology/matching/ExactMatchingAutomaton.cpp
similarity index 92%
rename from alib2algo/src/stringology/exact/ExactMatchingAutomaton.cpp
rename to alib2algo/src/stringology/matching/ExactMatchingAutomaton.cpp
index ab84e7dac5..f7114e25c5 100644
--- a/alib2algo/src/stringology/exact/ExactMatchingAutomaton.cpp
+++ b/alib2algo/src/stringology/matching/ExactMatchingAutomaton.cpp
@@ -13,7 +13,7 @@
namespace stringology {
-namespace exact {
+namespace matching {
automaton::Automaton ExactMatchingAutomaton::construct(const string::String& pattern) {
return dispatch(pattern.getData());
@@ -21,6 +21,6 @@ automaton::Automaton ExactMatchingAutomaton::construct(const string::String& pat
auto ExactMatchingAutomatonLinearString = ExactMatchingAutomaton::RegistratorWrapper<automaton::NFA < DefaultSymbolType, unsigned > , string::LinearString < > >(ExactMatchingAutomaton::construct);
-} /* namespace exact */
+} /* namespace matching */
} /* namespace stringology */
diff --git a/alib2algo/src/stringology/exact/ExactMatchingAutomaton.h b/alib2algo/src/stringology/matching/ExactMatchingAutomaton.h
similarity index 96%
rename from alib2algo/src/stringology/exact/ExactMatchingAutomaton.h
rename to alib2algo/src/stringology/matching/ExactMatchingAutomaton.h
index 3df4f87bc0..da23f3913a 100644
--- a/alib2algo/src/stringology/exact/ExactMatchingAutomaton.h
+++ b/alib2algo/src/stringology/matching/ExactMatchingAutomaton.h
@@ -16,7 +16,7 @@
namespace stringology {
-namespace exact {
+namespace matching {
class ExactMatchingAutomaton : public std::SingleDispatch<ExactMatchingAutomaton, automaton::Automaton, const string::StringBase & > {
public:
@@ -47,7 +47,7 @@ automaton::NFA < SymbolType, unsigned > ExactMatchingAutomaton::construct(const
return res;
}
-} /* namespace exact */
+} /* namespace matching */
} /* namespace stringology */
diff --git a/astringology2/src/astringology.cpp b/astringology2/src/astringology.cpp
index 4c770213af..9100d2acfb 100644
--- a/astringology2/src/astringology.cpp
+++ b/astringology2/src/astringology.cpp
@@ -27,11 +27,11 @@
#include <stringology/query/BNDMOccurrences.h>
#include <stringology/exact/BackwardOracleMatching.h>
#include <stringology/exact/BackwardDAWGMatching.h>
-#include <stringology/exact/ExactMatchingAutomaton.h>
-#include <stringology/exact/ExactFactorAutomaton.h>
-#include <stringology/exact/ExactSubsequenceAutomaton.h>
-#include <stringology/exact/ExactNondeterministicSubsequenceAutomaton.h>
-#include <stringology/exact/ExactMultiNondeterministicSubsequenceAutomaton.h>
+#include <stringology/matching/ExactMatchingAutomaton.h>
+#include <stringology/indexing/NondeterministicExactFactorAutomaton.h>
+#include <stringology/indexing/ExactSubsequenceAutomaton.h>
+#include <stringology/indexing/ExactNondeterministicSubsequenceAutomaton.h>
+#include <stringology/indexing/ExactMultiNondeterministicSubsequenceAutomaton.h>
#include <stringology/exact/FactorOracleAutomaton.h>
#include <stringology/exact/SuffixAutomaton.h>
#include <string/properties/BorderArray.h>
@@ -51,7 +51,7 @@ int main ( int argc, char * argv[] ) {
std::vector < std::string > allowed;
allowed.push_back ( "exactMatchingAutomaton" );
- allowed.push_back ( "exactFactorAutomaton" );
+ allowed.push_back ( "exactNondeterministicFactorAutomaton" );
allowed.push_back ( "exactSubsequenceAutomaton" );
allowed.push_back ( "exactNondeterministicSubsequenceAutomaton" );
allowed.push_back ( "exactMultiNondeterministicSubsequenceAutomaton" );
@@ -212,19 +212,19 @@ int main ( int argc, char * argv[] ) {
measurements::end ( );
measurements::start ( "Algorithm", measurements::Type::MAIN );
- automaton::Automaton automaton = stringology::exact::ExactMatchingAutomaton::construct ( pattern );
+ automaton::Automaton automaton = stringology::matching::ExactMatchingAutomaton::construct ( pattern );
measurements::end ( );
measurements::start ( "Output write", measurements::Type::AUXILIARY );
alib::XmlDataFactory::toStdout ( automaton );
- } else if ( algorithm.getValue ( ) == "exactFactorAutomaton" ) {
+ } else if ( algorithm.getValue ( ) == "exactNondeterministicFactorAutomaton" ) {
string::String subject = alib::XmlDataFactory::fromTokens ( std::move ( sax::FromXMLParserHelper::parseInput(true, subjectInput).front ( ) ) );
measurements::end ( );
measurements::start ( "Algorithm", measurements::Type::MAIN );
- automaton::Automaton automaton = stringology::exact::ExactFactorAutomaton::construct ( subject );
+ automaton::Automaton automaton = stringology::indexing::NondeterministicExactFactorAutomaton::construct ( subject );
measurements::end ( );
measurements::start ( "Output write", measurements::Type::AUXILIARY );
@@ -236,7 +236,7 @@ int main ( int argc, char * argv[] ) {
measurements::end ( );
measurements::start ( "Algorithm", measurements::Type::MAIN );
- automaton::Automaton automaton = stringology::exact::ExactSubsequenceAutomaton::construct ( subject );
+ automaton::Automaton automaton = stringology::indexing::ExactSubsequenceAutomaton::construct ( subject );
measurements::end ( );
measurements::start ( "Output write", measurements::Type::AUXILIARY );
@@ -248,7 +248,7 @@ int main ( int argc, char * argv[] ) {
measurements::end ( );
measurements::start ( "Algorithm", measurements::Type::MAIN );
- automaton::Automaton automaton = stringology::exact::ExactNondeterministicSubsequenceAutomaton::construct ( subject );
+ automaton::Automaton automaton = stringology::indexing::ExactNondeterministicSubsequenceAutomaton::construct ( subject );
measurements::end ( );
measurements::start ( "Output write", measurements::Type::AUXILIARY );
@@ -265,7 +265,7 @@ int main ( int argc, char * argv[] ) {
measurements::end ( );
measurements::start ( "Algorithm", measurements::Type::MAIN );
- automaton::Automaton automaton = stringology::exact::ExactMultiNondeterministicSubsequenceAutomaton::construct ( subjects );
+ automaton::Automaton automaton = stringology::indexing::ExactMultiNondeterministicSubsequenceAutomaton::construct ( subjects );
measurements::end ( );
measurements::start ( "Output write", measurements::Type::AUXILIARY );
--
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