Add Accession Lookup find by first word

lib/genesis/taxonomy/accession_lookup.hpp

@@ -33,6 +33,8 @@
 
 #include "genesis/taxonomy/taxonomy.hpp"
 #include "genesis/taxonomy/taxon.hpp"
+#include "genesis/utils/text/char.hpp"
+#include "genesis/utils/text/string.hpp"
 
 #include <stdexcept>
 #include <string>
@@ -115,9 +117,12 @@ class AccessionLookup
      * If not found, either a `nullptr` is returned, or an exception is thrown, depending on
      * @p throw_if_not_found.
      */
-    inline Taxon* get( std::string const& accession, bool throw_if_not_found = false ) const
-    {
-        auto it = map_.find( accession );
+    inline Taxon* get(
+        std::string const& accession,
+        bool also_look_up_first_word = true,
+        bool throw_if_not_found = false
+    ) const {
+        auto const it = find_( accession, also_look_up_first_word );
         if( it == map_.end() ) {
             if( throw_if_not_found ) {
                 throw std::invalid_argument(
@@ -135,17 +140,22 @@ class AccessionLookup
      *
      * Same as get(), but returns the Taxon as a const pointer.
      */
-    inline Taxon const* cget( std::string const& accession, bool throw_if_not_found = false ) const
-    {
-        return get( accession, throw_if_not_found );
+    inline Taxon const* cget(
+        std::string const& accession,
+        bool also_look_up_first_word = true,
+        bool throw_if_not_found = false
+    ) const {
+        return get( accession, also_look_up_first_word, throw_if_not_found );
     }
 
     /**
-     * @brief Check if the map contains a specific key
+     * @brief Check if the map contains a specific key.
      */
-    inline bool contains( std::string const& accession ) const
-    {
-        return map_.find(accession) != map_.end();
+    inline bool contains(
+        std::string const& accession,
+        bool also_look_up_first_word = true
+    ) const {
+        return find_( accession, also_look_up_first_word ) != map_.end();
     }
 
     // -------------------------------------------------------------------------
@@ -251,6 +261,21 @@ class AccessionLookup
         }
     }
 
+    inline ConstIterator find_(
+        std::string const& accession,
+        bool also_look_up_first_word
+    ) const {
+        auto it = map_.find( accession );
+        if( it != map_.end() ) {
+            return it;
+        }
+        if( also_look_up_first_word ) {
+            auto const acc_first = utils::split( accession, "\t " )[0];
+            return map_.find( acc_first );
+        }
+        return map_.end();
+    }
+
     // -------------------------------------------------------------------------
     //     Data Members
     // -------------------------------------------------------------------------

test/src/taxonomy/accession_lookup.cpp

@@ -0,0 +1,64 @@
+/*
+    Genesis - A toolkit for working with phylogenetic data.
+    Copyright (C) 2014-2024 Lucas Czech
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+    Contact:
+    Lucas Czech <[email protected]>
+    University of Copenhagen, Globe Institute, Section for GeoGenetics
+    Oster Voldgade 5-7, 1350 Copenhagen K, Denmark
+*/
+
+/**
+ * @brief
+ *
+ * @file
+ * @ingroup test
+ */
+
+#include "src/common.hpp"
+
+#include "genesis/taxonomy/accession_lookup.hpp"
+#include "genesis/taxonomy/taxon.hpp"
+#include "genesis/taxonomy/taxonomy.hpp"
+#include "genesis/taxonomy/formats/taxonomy_reader.hpp"
+#include "genesis/taxonomy/functions/taxonomy.hpp"
+
+using namespace genesis;
+using namespace genesis::taxonomy;
+
+TEST( Taxonomy, AccessionLookup )
+{
+    // Skip test if no data availabe.
+    NEEDS_TEST_DATA;
+
+    // Read the test taxonomy
+    std::string const infile = environment->data_dir + "taxonomy/tax_slv_ssu_123.1.clean";
+    auto tax = TaxonomyReader().read( utils::from_file( infile ));
+
+    // Get some taxon from the taxonomy
+    auto* taxon = find_taxon_by_name( tax, "Acidilobus" );
+    ASSERT_TRUE( taxon != nullptr );
+
+    // Create a lookup for the taxonomy
+    auto lookup = AccessionLookup();
+    lookup.add( "ABCD.1", taxon );
+
+    // Perform a lookup by full name
+    EXPECT_TRUE( lookup.get( "ABCD.1 Acidilobaceae Acidilobus" ) != nullptr );
+
+    // Perform a lookup by first word
+    EXPECT_TRUE( lookup.get( "ABCD.1" ) != nullptr );
+}