From 50534f65359d8d1975f9bb5b0596bb1240137d16 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Tom=C3=A1=C5=A1=20=C4=8Capek?= <tomas@capek.io>
Date: Wed, 18 Apr 2018 16:50:05 +0200
Subject: [PATCH] Implement WildcardLinearString into
HammingSequenceMatchingAutomaton
---
.../HammingSequenceMatchingAutomaton.h | 37 ++++++++++++++-
.../HammingSequenceMatchingAutomatonTest.cpp | 46 +++++++++++++++++++
.../HammingSequenceMatchingAutomatonTest.h | 6 ++-
3 files changed, 86 insertions(+), 3 deletions(-)
diff --git a/alib2algo/src/stringology/matching/HammingSequenceMatchingAutomaton.h b/alib2algo/src/stringology/matching/HammingSequenceMatchingAutomaton.h
index 70a9ae2126..a8eda045f4 100644
--- a/alib2algo/src/stringology/matching/HammingSequenceMatchingAutomaton.h
+++ b/alib2algo/src/stringology/matching/HammingSequenceMatchingAutomaton.h
@@ -10,7 +10,9 @@
#include <automaton/FSM/NFA.h>
#include <stringology/matching/HammingMatchingAutomaton.h>
+#include <automaton/simplify/UnreachableStatesRemover.h>
#include <string/LinearString.h>
+#include <string/WildcardLinearString.h>
namespace stringology {
@@ -20,12 +22,21 @@ namespace matching {
class HammingSequenceMatchingAutomaton {
public:
/**
- * Creates Hamming matching automata for sequence matching.
+ * Creates Hamming matching automata for sequence matching from LinearString.
*
* @return automata for aproximate sequence matching using Hamming method.
*/
template < class SymbolType >
static automaton::NFA < SymbolType, ext::pair<unsigned int, unsigned int> > construct(const string::LinearString < SymbolType > & pattern, unsigned int allowed_errors);
+
+ /**
+ * Creates Hamming matching automata for sequence matching from WildcardLinearString.
+ *
+ * @return automata for aproximate sequence matching using Hamming method.
+ */
+ template < class SymbolType >
+ static automaton::NFA < SymbolType, ext::pair<unsigned int, unsigned int> > construct(const string::WildcardLinearString < SymbolType > & pattern, unsigned int allowed_errors);
+
};
template < class SymbolType >
@@ -47,6 +58,30 @@ automaton::NFA < SymbolType, ext::pair<unsigned int, unsigned int> > HammingSequ
return result;
}
+template < class SymbolType >
+automaton::NFA < SymbolType, ext::pair<unsigned int, unsigned int> > HammingSequenceMatchingAutomaton::construct(const string::WildcardLinearString < SymbolType > & pattern, unsigned int allowed_errors) {
+ automaton::NFA < SymbolType, ext::pair<unsigned int, unsigned int > > result = stringology::matching::HammingMatchingAutomaton::construct_unclean(pattern, allowed_errors);
+
+ SymbolType wildcard = pattern.getWildcardSymbol();
+ ext::set<SymbolType> alphabet_without_wildcard = pattern.getAlphabet();
+ alphabet_without_wildcard.erase(wildcard);
+
+ for (unsigned int j = 0; j<allowed_errors + 1; j++) {
+ for (unsigned int i = j; i<pattern.getContent().size(); i++) {
+ auto current_state = ext::make_pair(i, j);
+
+ if (pattern.getContent()[i] != wildcard) {
+ for (const SymbolType & symbol : alphabet_without_wildcard) {
+ if (symbol != pattern.getContent()[i]) {
+ result.addTransition(current_state, symbol, current_state);
+ }
+ }
+ }
+ }
+ }
+
+ return automaton::simplify::UnreachableStatesRemover::remove(result);
+}
} /* namespace matching */
diff --git a/alib2algo/test-src/stringology/matching/HammingSequenceMatchingAutomatonTest.cpp b/alib2algo/test-src/stringology/matching/HammingSequenceMatchingAutomatonTest.cpp
index 880ffc46a6..2c0ee50416 100644
--- a/alib2algo/test-src/stringology/matching/HammingSequenceMatchingAutomatonTest.cpp
+++ b/alib2algo/test-src/stringology/matching/HammingSequenceMatchingAutomatonTest.cpp
@@ -86,6 +86,52 @@ void HammingSequenceMatchingAutomatonTest::testSimpleConstruction() {
CPPUNIT_ASSERT(resulting_automata == test);
}
+void HammingSequenceMatchingAutomatonTest::testSimpleWildcardConstruction() {
+ ext::set<char> alphabet{'a', 'b', '@'};
+ string::WildcardLinearString <char> input_string(alphabet, ext::vector<char>{'a', '@', 'b'}, '@');
+ auto resulting_automata = stringology::matching::HammingSequenceMatchingAutomaton::construct(input_string, 2);
+
+ typedef ext::pair<unsigned int, unsigned int> State;
+
+ automaton::NFA < char, State > res(ext::make_pair(0,0));
+ res.setInputAlphabet(alphabet);
+
+ State q0 = ext::make_pair(0,0);
+ State q1 = ext::make_pair(1,0);
+ State q2 = ext::make_pair(2,0);
+ State q3 = ext::make_pair(3,0);
+ State q4 = ext::make_pair(1,1);
+ State q5 = ext::make_pair(2,1);
+ State q6 = ext::make_pair(3,1);
+ State q7 = ext::make_pair(3,2);
+
+ res.setStates(ext::set<State> {q0, q1, q2, q3, q4, q5, q6, q7});
+ res.setFinalStates(ext::set<State> {q3, q6, q7});
+
+ res.addTransition(q0, 'a', q0); // initial loops
+ res.addTransition(q0, 'b', q0);
+
+ res.addTransition(q0, 'a', q1); // 3 simple matching automatas (thrid is not connected)
+
+ res.addTransition(q1, 'a', q2);
+ res.addTransition(q1, 'b', q2);
+ res.addTransition(q4, 'a', q5);
+ res.addTransition(q4, 'b', q5);
+
+ res.addTransition(q2, 'b', q3);
+ res.addTransition(q5, 'b', q6);
+
+ res.addTransition(q0, 'b', q4); // error transitions
+
+ res.addTransition(q2, 'a', q6);
+ res.addTransition(q5, 'a', q7);
+
+ res.addTransition(q2, 'a', q2); // loops for sequence matching
+ res.addTransition(q5, 'a', q5);
+
+ CPPUNIT_ASSERT(resulting_automata == res);
+}
+
void HammingSequenceMatchingAutomatonTest::setUp() { }
void HammingSequenceMatchingAutomatonTest::tearDown() { }
diff --git a/alib2algo/test-src/stringology/matching/HammingSequenceMatchingAutomatonTest.h b/alib2algo/test-src/stringology/matching/HammingSequenceMatchingAutomatonTest.h
index 33e9424737..c33a109a6c 100644
--- a/alib2algo/test-src/stringology/matching/HammingSequenceMatchingAutomatonTest.h
+++ b/alib2algo/test-src/stringology/matching/HammingSequenceMatchingAutomatonTest.h
@@ -5,13 +5,15 @@
class HammingSequenceMatchingAutomatonTest : public CppUnit::TestFixture {
CPPUNIT_TEST_SUITE(HammingSequenceMatchingAutomatonTest);
- CPPUNIT_TEST(testSimpleConstruction);
- CPPUNIT_TEST_SUITE_END();
+ CPPUNIT_TEST(testSimpleConstruction);
+ CPPUNIT_TEST(testSimpleWildcardConstruction);
+ CPPUNIT_TEST_SUITE_END();
public:
void setUp ( );
void tearDown ( );
void testSimpleConstruction();
+ void testSimpleWildcardConstruction();
};
#endif //HAMMING_SEQUENCE_MATCHING_AUTOMATA_TEST_H_
--
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