Fix --taxon-list being broken multi-threaded in prefilter and ungappe…

…dprefilter
soedinglab · Apr 2, 2024 · 804bb2a · 804bb2a
1 parent f6c9880
commit 804bb2a
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Showing 3 changed files with 25 additions and 10 deletions.
diff --git a/src/prefiltering/Prefiltering.cpp b/src/prefiltering/Prefiltering.cpp
@@ -226,7 +226,7 @@ Prefiltering::Prefiltering(const std::string &queryDB,
 
 
     if (par.taxonList.length() > 0) {
-        taxonomyHook = new QueryMatcherTaxonomyHook(targetDB, tdbr, par.taxonList);
+        taxonomyHook = new QueryMatcherTaxonomyHook(targetDB, tdbr, par.taxonList, par.threads);
     } else {
         taxonomyHook = NULL;
     }

diff --git a/src/prefiltering/QueryMatcherTaxonomyHook.h b/src/prefiltering/QueryMatcherTaxonomyHook.h
@@ -7,33 +7,47 @@
 #include "DBReader.h"
 #include "TaxonomyExpression.h"
 
+#ifdef OPENMP
+#include <omp.h>
+#endif
+
 class QueryMatcherTaxonomyHook : public QueryMatcherHook {
 public:
-    QueryMatcherTaxonomyHook(std::string targetPath, DBReader<unsigned int>* targetReader, const std::string& expressionString)
-        : targetReader(targetReader), dbFrom(0) {
+    QueryMatcherTaxonomyHook(std::string targetPath, DBReader<unsigned int>* targetReader, const std::string& expressionString, unsigned int threads)
+        : targetReader(targetReader), dbFrom(0), threads(threads) {
         std::string targetName = dbPathWithoutIndex(targetPath);
         taxonomy = NcbiTaxonomy::openTaxonomy(targetName);
         taxonomyMapping = new MappingReader(targetName);
-        expression = new TaxonomyExpression(expressionString, *taxonomy);
+        expression = new TaxonomyExpression*[threads];
+        for (unsigned int i = 0; i < threads; i++) {
+            expression[i] = new TaxonomyExpression(expressionString, *taxonomy);
+        }
     }
 
     ~QueryMatcherTaxonomyHook() {
         delete taxonomy;
         delete taxonomyMapping;
-        delete expression;
+        for (unsigned int i = 0; i < threads; i++) {
+            delete expression[i];
+        }
+        delete[] expression;
     }
 
     void setDbFrom(unsigned int from) {
         dbFrom = from;
     }
 
     size_t afterDiagonalMatchingHook(QueryMatcher& matcher, size_t resultSize) {
+        unsigned int thread_idx = 0;
+#ifdef OPENMP
+        thread_idx = (unsigned int) omp_get_thread_num();
+#endif
         size_t writePos = 0;
         for (size_t i = 0; i < resultSize; i++) {
             unsigned int currId = matcher.foundDiagonals[i].id;
             unsigned int key = targetReader->getDbKey(dbFrom + currId);
             TaxID currTax = taxonomyMapping->lookup(key);
-            if (expression->isAncestor(currTax)) {
+            if (expression[thread_idx]->isAncestor(currTax)) {
                 if (i != writePos) {
                     matcher.foundDiagonals[writePos] = matcher.foundDiagonals[i];
                 }
@@ -63,9 +77,10 @@ class QueryMatcherTaxonomyHook : public QueryMatcherHook {
     NcbiTaxonomy* taxonomy;
     MappingReader* taxonomyMapping;
     DBReader<unsigned int>* targetReader;
-    TaxonomyExpression* expression;
+    TaxonomyExpression** expression;
 
     unsigned int dbFrom;
+    unsigned int threads;
 };
 
 #endif
diff --git a/src/prefiltering/ungappedprefilter.cpp b/src/prefiltering/ungappedprefilter.cpp
@@ -77,8 +77,8 @@ int prefilterInternal(int argc, const char **argv, const Command &command, int m
 
 
     QueryMatcherTaxonomyHook * taxonomyHook = NULL;
-    if(par.PARAM_TAXON_LIST.wasSet){
-        taxonomyHook = new QueryMatcherTaxonomyHook(par.db2, tdbr, par.taxonList);
+    if (par.PARAM_TAXON_LIST.wasSet) {
+        taxonomyHook = new QueryMatcherTaxonomyHook(par.db2, tdbr, par.taxonList, par.threads);
     }
 
     Debug::Progress progress(qdbr->getSize());
@@ -121,7 +121,7 @@ int prefilterInternal(int argc, const char **argv, const Command &command, int m
                 unsigned int targetKey = tdbr->getDbKey(tId);
                 if(taxonomyHook != NULL){
                     TaxID currTax = taxonomyHook->taxonomyMapping->lookup(targetKey);
-                    if (taxonomyHook->expression->isAncestor(currTax) == false) {
+                    if (taxonomyHook->expression[thread_idx]->isAncestor(currTax) == false) {
                         continue;
                     }
                 }