Find record ID from pattern directly (#14)

seqan · Sep 8, 2023 · c897ab5 · c897ab5
1 parent e886796
commit c897ab5
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Showing 3 changed files with 16 additions and 19 deletions.
diff --git a/include/stellar/query_id_map.hpp b/include/stellar/query_id_map.hpp
@@ -11,13 +11,6 @@ namespace stellar
 template <typename TAlphabet, typename TId = CharString>
 struct QueryIDMap
 {
-    size_t recordID(StellarSwiftPattern<TAlphabet> const & pattern) const
-    {
-        StellarQuerySegment<TAlphabet> querySegment
-            = StellarQuerySegment<TAlphabet>::fromPatternMatch(pattern);
-        return recordID(querySegment.underlyingQuery());
-    }
-
     size_t recordID(String<TAlphabet> const & query) const
     {
         String<TAlphabet> const * begin = &queries[0];

diff --git a/include/stellar/stellar_index.hpp b/include/stellar/stellar_index.hpp
@@ -58,6 +58,10 @@ struct StellarIndex
         : StellarIndex{convertImplStringSet(queries), options}
     {}
 
+    StellarIndex(StringSet<TInfixSegment> const & queries, IndexOptions const & options)
+        : StellarIndex{convertSegmentStringSet(queries), options}
+    {}
+
     StellarIndex(std::span<TInfixSegment> const & queries, IndexOptions const & options)
         : StellarIndex{convertImplSpan(queries), options}
     {}
@@ -106,18 +110,24 @@ struct StellarIndex
     }
 
     template <typename TSpec>
-    static StellarQGramStringSet<TAlphabet> convertImplStringSet(StringSet<TSequence, TSpec> const & queries)
+    static TQGramStringSet convertImplStringSet(StringSet<TSequence, TSpec> const & queries)
     {
-        StellarQGramStringSet<TAlphabet> dependentQueries;
+        TQGramStringSet dependentQueries;
         for (TSequence const & query: queries)
             seqan2::appendValue(dependentQueries, seqan2::infix(query, 0, seqan2::length(query)));
 
         return dependentQueries;
     }
 
-    static StellarQGramStringSet<TAlphabet> convertImplSpan(std::span<TInfixSegment> const & queries)
+    static TQGramStringSet convertSegmentStringSet(StringSet<TInfixSegment> const & queries)
+    {
+        TQGramStringSet dependentQueries = queries;
+        return dependentQueries;
+    }
+
+    static TQGramStringSet convertImplSpan(std::span<TInfixSegment> const & queries)
     {
-        StellarQGramStringSet<TAlphabet> dependentQueries;
+        TQGramStringSet dependentQueries;
         for (TInfixSegment const & query: queries)
             seqan2::appendValue(dependentQueries, query);
 

diff --git a/include/stellar/stellar_launcher.hpp b/include/stellar/stellar_launcher.hpp
@@ -69,13 +69,7 @@ struct StellarLauncher
 
         auto getQueryMatches = [&](auto const & pattern) -> QueryMatches<StellarMatch<TSequence const, TId> > &
         {
-            // Note: Index is normally build over all queries [query0, query1, query2, ...],
-            // but in LocalQueryPrefilter case it can just be build over [query0].
-            // We need to translate that position to a "record" ID
-            //!TODO: this shouldn't be necessary
-            // each Stellar instance should be given a set of bin query, all of which should be indexed
-            size_t const queryRecordID = queryIDMap.recordID(pattern);
-            return value(localMatches, queryRecordID);
+            return value(localMatches, pattern.curSeqNo);
         };
 
         auto isPatternDisabled = [&](StellarSwiftPattern<TAlphabet> & pattern) -> bool {
@@ -97,7 +91,7 @@ struct StellarLauncher
                 localOptions.disableThresh,
                 // compactThresh is basically an output-parameter; will be updated in kernel and propagated back
                 // outside of this function, the reason why StellarOptions can't be passed as const to this function.
-                // TODO: We might want to make this tied to the QueryMatches itself, as it should know then to consolidate
+                //!TODO: We might want to make this tied to the QueryMatches itself, as it should know then to consolidate
                 // the matches
                 localOptions.compactThresh,
                 localOptions.numMatches