Implements randomized testing for stringology::simulations

cf4592ea · Tomáš Čapek · Tomas Capek · 742bb2c9 · cf4592ea · cf4592ea
Commit cf4592ea authored 6 years ago by Tomáš Čapek Committed by Tomas Capek 6 years ago
--- a/astringology2/src/astringology.cpp
+++ b/astringology2/src/astringology.cpp
@@ -31,6 +31,10 @@ int main ( int argc, char * argv[] ) {
 		allowed.push_back ( "deadZoneUsingBadCharacterShift" );
  
 		allowed.push_back ( "exactMatchingAutomaton" );
+		allowed.push_back ( "hammingMatchingAutomaton" );
+		allowed.push_back ( "levenshteinMatchingAutomaton" );
+		allowed.push_back ( "generalizedLevenshteinMatchingAutomaton" );
+
 		allowed.push_back ( "exactNondeterministicFactorAutomaton" );
 		allowed.push_back ( "exactSubsequenceAutomaton" );
 		allowed.push_back ( "exactNondeterministicSubsequenceAutomaton" );
@@ -54,6 +58,13 @@ int main ( int argc, char * argv[] ) {
 		allowed.push_back ( "goodSuffixShiftTable" );
  
 		allowed.push_back ( "hammingMatchDynamicProgramming" );
+		allowed.push_back ( "levenshteinMatchDynamicProgramming" );
+		allowed.push_back ( "generalizedLevenshteinMatchDynamicProgramming" );
+
+		allowed.push_back ( "exactMatchBitParalelism");
+		allowed.push_back ( "hammingMatchBitParalelism" );
+		allowed.push_back ( "levenshteinMatchBitParalelism" );
+		allowed.push_back ( "generalizedLevenshteinMatchBitParalelism");
  
 		TCLAP::ValuesConstraint < std::string > allowedVals ( allowed );
  
@@ -107,7 +118,13 @@ int main ( int argc, char * argv[] ) {
 		  || algorithm.getValue ( ) == "compressedBitParallelIndex"
 		  || algorithm.getValue ( ) == "suffixArray"
 		  || algorithm.getValue ( ) == "suffixAutomaton"
-		  || algorithm.getValue ( ) == "hammingMatchDynamicProgramming" ) {
+		  || algorithm.getValue ( ) == "hammingMatchDynamicProgramming"
+		  || algorithm.getValue ( ) == "levenshteinMatchDynamicProgramming"
+		  || algorithm.getValue ( ) == "generalizedLevenshteinMatchDynamicProgramming"
+			|| algorithm.getValue ( ) == "exactMatchBitParalelism"
+			|| algorithm.getValue ( ) == "hammingMatchBitParalelism"
+			|| algorithm.getValue ( ) == "levenshteinMatchBitParalelism"
+			|| algorithm.getValue ( ) == "generalizedLevenshteinMatchBitParalelism" ) {
 			std::string input;
 			if ( subjectInput.getValue ( ).size ( ) == 0 )
 				input = "-";
@@ -131,13 +148,23 @@ int main ( int argc, char * argv[] ) {
 		  || algorithm.getValue ( ) == "backwardOracleMatching"
 		  || algorithm.getValue ( ) == "backwardDAWGMatching"
 		  || algorithm.getValue ( ) == "exactMatchingAutomaton"
+		  || algorithm.getValue ( ) == "hammingMatchingAutomaton"
+		  || algorithm.getValue ( ) == "levenshteinMatchingAutomaton"
+		  || algorithm.getValue ( ) == "generalizedLevenshteinMatchingAutomaton"
 		  || algorithm.getValue ( ) == "exactFactorOracleAutomaton"
 		  || algorithm.getValue ( ) == "exactNondeterministicSuffixAutomaton"
 		  || algorithm.getValue ( ) == "bndmMatcher"
 		  || algorithm.getValue ( ) == "badCharacterShiftTable"
 		  || algorithm.getValue ( ) == "quickSearchBadCharacterShiftTable"
 		  || algorithm.getValue ( ) == "goodSuffixShiftTable"
-		  || algorithm.getValue ( ) == "hammingMatchDynamicProgramming" ) {
+			|| algorithm.getValue ( ) == "hammingMatchDynamicProgramming"
+		  || algorithm.getValue ( ) == "levenshteinMatchDynamicProgramming"
+		  || algorithm.getValue ( ) == "generalizedLevenshteinMatchDynamicProgramming"
+			|| algorithm.getValue ( ) == "exactMatchBitParalelism"
+			|| algorithm.getValue ( ) == "hammingMatchBitParalelism"
+			|| algorithm.getValue ( ) == "levenshteinMatchBitParalelism"
+			|| algorithm.getValue ( ) == "generalizedLevenshteinMatchBitParalelism" ) {
+
 			std::string input;
 			if ( patternInput.getValue ( ).size ( ) == 0 )
 				input = "-";
@@ -164,7 +191,15 @@ int main ( int argc, char * argv[] ) {
 			parser.parse ( )->run ( environment );
 		}
  
-		if ( algorithm.getValue ( ) == "hammingMatchDynamicProgramming" ) {
+		if ( algorithm.getValue ( ) == "hammingMatchDynamicProgramming"
+				|| algorithm.getValue ( ) == "levenshteinMatchDynamicProgramming"
+				|| algorithm.getValue ( ) == "generalizedLevenshteinMatchDynamicProgramming"
+				|| algorithm.getValue ( ) == "hammingMatchingAutomaton"
+				|| algorithm.getValue ( ) == "levenshteinMatchingAutomaton"
+				|| algorithm.getValue ( ) == "generalizedLevenshteinMatchingAutomaton"
+				|| algorithm.getValue ( ) == "hammingMatchBitParalelism"
+				|| algorithm.getValue ( ) == "levenshteinMatchBitParalelism"
+				|| algorithm.getValue ( ) == "generalizedLevenshteinMatchBitParalelism" ) {
 			unsigned input = distanceInput.getValue ( );
  
 			environment.setVariable ( "distance", input );
@@ -223,6 +258,13 @@ int main ( int argc, char * argv[] ) {
 			cliCommand = "execute stringology::matching::BNDMMatcherConstruction $pattern > $output";
 		} else if ( algorithm.getValue ( ) == "exactMatchingAutomaton" ) {
 			cliCommand = "execute stringology::matching::ExactMatchingAutomaton $pattern > $output";
+		} else if ( algorithm.getValue ( ) == "hammingMatchingAutomaton" ) {
+			cliCommand = "execute stringology::matching::HammingMatchingAutomaton $pattern $distance > $output";
+		} else if ( algorithm.getValue ( ) == "levenshteinMatchingAutomaton" ) {
+			cliCommand = "execute stringology::matching::LevenshteinMatchingAutomaton $pattern $distance > $output";
+		} else if ( algorithm.getValue ( ) == "generalizedLevenshteinMatchingAutomaton" ) {
+			cliCommand = "execute stringology::matching::GeneralizedLevenshteinMatchingAutomaton $pattern $distance > $output";
+
  
 		} else if ( algorithm.getValue ( ) == "borderArray" ) {
 			cliCommand = "execute string::properties::BorderArray $subject > $output";
@@ -234,7 +276,19 @@ int main ( int argc, char * argv[] ) {
 			cliCommand = "execute string::properties::GoodSuffixShiftTable $pattern > $output";
 		} else if ( algorithm.getValue ( ) == "hammingMatchDynamicProgramming" ) {
 			cliCommand = "execute stringology::simulations::HammingDynamicProgramming $subject $pattern $distance > $output";
-		} else {
+		} else if ( algorithm.getValue ( ) == "levenshteinMatchDynamicProgramming" ) {
+			cliCommand = "execute stringology::simulations::LevenshteinDynamicProgramming $subject $pattern $distance > $output";
+		} else if ( algorithm.getValue ( ) == "generalizedLevenshteinMatchDynamicProgramming" ) {
+			cliCommand = "execute stringology::simulations::GeneralizedLevenshteinDynamicProgramming $subject $pattern $distance > $output";
+		} else if ( algorithm.getValue ( ) == "exactMatchBitParalelism" ) {
+			cliCommand = "execute stringology::simulations::ExactBitParalelism $subject $pattern > $output";
+		} else if ( algorithm.getValue ( ) == "hammingMatchBitParalelism" ) {
+			cliCommand = "execute stringology::simulations::HammingBitParalelism $subject $pattern $distance > $output";
+		} else if ( algorithm.getValue ( ) == "levenshteinMatchBitParalelism" ) {
+			cliCommand = "execute stringology::simulations::LevenshteinBitParalelism $subject $pattern $distance > $output";
+		} else if ( algorithm.getValue ( ) == "generalizedLevenshteinMatchBitParalelism" ) {
+			cliCommand = "execute stringology::simulations::GeneralizedLevenshteinBitParalelism $subject $pattern $distance > $output";
+			} else {
 			throw exception::CommonException ( "Invalid algorithm" );
 		}
  

--- a/tests.astringology.sh
+++ b/tests.astringology.sh
@@ -212,6 +212,36 @@ function runTest {
 	clearResults
 }
  
+
+# $1 - aconversions2 sequence
+# $2 - first tested entity
+# $3 - second tested entity
+function runTestAgainst {
+	echo $1
+	echo -ne "\t"
+
+	initResults
+	bgxgrp=""
+
+	# random tests
+	for i in $(seq 1 $TESTCASE_ITERATIONS );
+	do
+		SUBJECT_FILE=$(mktemp)
+		PATTERN_FILE=$(mktemp)
+
+		cat <(generateSubject) > $SUBJECT_FILE
+		cat <(generatePattern) > $PATTERN_FILE
+
+		bgxlimit ${JOBS} runTest2 "$2" "$3" "$SUBJECT_FILE" "$PATTERN_FILE"
+	done
+
+	bgxwait
+
+	outputResults
+	clearResults
+}
+
+
 runTest "DAWG Factors" "./astringology2 -a suffixAutomaton -s \"\$SUBJECT_FILE\" | ./aquery2 -q suffixAutomatonFactors -p \"\$PATTERN_FILE\" | ./astat2 -p size"
 runTest "BNDM Matcher" "./astringology2 -a bndmMatcher -p \"\$PATTERN_FILE\" | ./astringology2 -a bndmOccurrences -p - -s \"\$SUBJECT_FILE\" | ./astat2 -p size"
 runTest "Exact Boyer Moore" "./astringology2 -a boyerMoore -s \"\$SUBJECT_FILE\" -p <(./aaccess2 --string alphabet -o add -i \"\$PATTERN_FILE\" -c <(./aaccess2 --string alphabet -o get -i \"\$SUBJECT_FILE\")) | ./astat2 -p size"
@@ -225,3 +255,15 @@ runTest "Exact Reversed Boyer Moore Horspool" "./astringology2 -a reversedBoyerM
 runTest "Quick Search" "./astringology2 -a quickSearch -s \"\$SUBJECT_FILE\" -p <(./aaccess2 --string alphabet -o add -i \"\$PATTERN_FILE\" -c <(./aaccess2 --string alphabet -o get -i \"\$SUBJECT_FILE\")) | ./astat2 -p size"
 runTest "Exact Matching Automaton" "./arun2 -t occurrences -a <(./astringology2 -a exactMatchingAutomaton -p <(./aaccess2 --string alphabet -o add -i \"\$PATTERN_FILE\" -c <(./aaccess2 --string alphabet -o get -i \"\$SUBJECT_FILE\")) | ./adeterminize2) -i \"\$SUBJECT_FILE\" | ./astat2 -p size"
 runTest "Exact Dead Zone Using Bad Character Shift" "./astringology2 -a deadZoneUsingBadCharacterShift -s \"\$SUBJECT_FILE\" -p <(./aaccess2 --string alphabet -o add -i \"\$PATTERN_FILE\" -c <(./aaccess2 --string alphabet -o get -i \"\$SUBJECT_FILE\")) | ./astat2 -p size"
+
+runTestAgainst "Hamming automaton vs. dynamic programing" "./arun2 -t occurrences -i \"\$SUBJECT_FILE\" -a <(./astringology2 -a hammingMatchingAutomaton -p <(./aaccess2 --string alphabet -o add -i \"\$PATTERN_FILE\" -c <(./aaccess2 --string alphabet -o get -i \"\$SUBJECT_FILE\")) -d 3 | ./adeterminize2) | ./astat2 -p size" "./astringology2 -a hammingMatchDynamicProgramming -p \"\$PATTERN_FILE\" -s \"\$SUBJECT_FILE\" -d 3 | ./astat2 -p size"
+runTestAgainst "Hamming automaton vs. bit paralelism" "./arun2 -t occurrences -i \"\$SUBJECT_FILE\" -a <(./astringology2 -a hammingMatchingAutomaton -p <(./aaccess2 --string alphabet -o add -i \"\$PATTERN_FILE\" -c <(./aaccess2 --string alphabet -o get -i \"\$SUBJECT_FILE\")) -d 3 | ./adeterminize2) | ./astat2 -p size" "./astringology2 -a hammingMatchBitParalelism -p \"\$PATTERN_FILE\" -s \"\$SUBJECT_FILE\" -d 3 | ./astat2 -p size"
+runTestAgainst "Hamming dynamic programming vs. bit paralelism" "./astringology2 -a hammingMatchDynamicProgramming -p \"\$PATTERN_FILE\" -s \"\$SUBJECT_FILE\" -d 3 | ./astat2 -p size" "./astringology2 -a hammingMatchBitParalelism -p \"\$PATTERN_FILE\" -s \"\$SUBJECT_FILE\" -d 3 | ./astat2 -p size"
+
+runTestAgainst "Levenshtein automaton vs. dynamic programing" "./arun2 -t occurrences -i \"\$SUBJECT_FILE\" -a <(./astringology2 -a levenshteinMatchingAutomaton -p <(./aaccess2 --string alphabet -o add -i \"\$PATTERN_FILE\" -c <(./aaccess2 --string alphabet -o get -i \"\$SUBJECT_FILE\")) -d 3 | ./aepsilon2 | ./adeterminize2) | ./astat2 -p size" "./astringology2 -a levenshteinMatchDynamicProgramming -p \"\$PATTERN_FILE\" -s \"\$SUBJECT_FILE\" -d 3 | ./astat2 -p size"
+runTestAgainst "Levenshtein automaton vs. bit paralelism" "./arun2 -t occurrences -i \"\$SUBJECT_FILE\" -a <(./astringology2 -a levenshteinMatchingAutomaton -p <(./aaccess2 --string alphabet -o add -i \"\$PATTERN_FILE\" -c <(./aaccess2 --string alphabet -o get -i \"\$SUBJECT_FILE\")) -d 3 | ./aepsilon2 | ./adeterminize2) | ./astat2 -p size" "./astringology2 -a levenshteinMatchBitParalelism -p \"\$PATTERN_FILE\" -s \"\$SUBJECT_FILE\" -d 3 | ./astat2 -p size"
+runTestAgainst "Levenshtein dynamic programming vs. bit paralelism" "./astringology2 -a levenshteinMatchDynamicProgramming -p \"\$PATTERN_FILE\" -s \"\$SUBJECT_FILE\" -d 3 | ./astat2 -p size" "./astringology2 -a levenshteinMatchBitParalelism -p \"\$PATTERN_FILE\" -s \"\$SUBJECT_FILE\" -d 3 | ./astat2 -p size"
+
+runTestAgainst "Generalized Levenshtein automaton vs. dynamic programing" "./arun2 -t occurrences -i \"\$SUBJECT_FILE\" -a <(./astringology2 -a generalizedLevenshteinMatchingAutomaton -p <(./aaccess2 --string alphabet -o add -i \"\$PATTERN_FILE\" -c <(./aaccess2 --string alphabet -o get -i \"\$SUBJECT_FILE\")) -d 3 | ./aepsilon2 | ./adeterminize2) | ./astat2 -p size" "./astringology2 -a generalizedLevenshteinMatchDynamicProgramming -p \"\$PATTERN_FILE\" -s \"\$SUBJECT_FILE\" -d 3 | ./astat2 -p size"
+runTestAgainst "Generalized Levenshtein automaton vs. bit paralelism" "./arun2 -t occurrences -i \"\$SUBJECT_FILE\" -a <(./astringology2 -a generalizedLevenshteinMatchingAutomaton -p <(./aaccess2 --string alphabet -o add -i \"\$PATTERN_FILE\" -c <(./aaccess2 --string alphabet -o get -i \"\$SUBJECT_FILE\")) -d 3 | ./aepsilon2 | ./adeterminize2) | ./astat2 -p size" "./astringology2 -a generalizedLevenshteinMatchBitParalelism -p \"\$PATTERN_FILE\" -s \"\$SUBJECT_FILE\" -d 3 | ./astat2 -p size"
+runTestAgainst "Generalized Levenshtein dynamic programming vs. bit paralelism" "./astringology2 -a generalizedLevenshteinMatchDynamicProgramming -p \"\$PATTERN_FILE\" -s \"\$SUBJECT_FILE\" -d 3 | ./astat2 -p size" "./astringology2 -a generalizedLevenshteinMatchBitParalelism -p \"\$PATTERN_FILE\" -s \"\$SUBJECT_FILE\" -d 3 | ./astat2 -p size"