From a0ca81d5673f1e72074042684a80ac179b55d2e7 Mon Sep 17 00:00:00 2001
From: Harun Mustafa <bilgisayaradami@gmail.com>
Date: Fri, 11 Oct 2024 18:38:41 +0200
Subject: [PATCH] renamed AnnotatedSequenceGraph::get_labels to
 get_stored_labels

---
 metagraph/src/graph/annotated_dbg.cpp             | 2 +-
 metagraph/src/graph/annotated_dbg.hpp             | 7 +++++--
 metagraph/tests/annotation/test_annotated_dbg.cpp | 4 ++--
 3 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/metagraph/src/graph/annotated_dbg.cpp b/metagraph/src/graph/annotated_dbg.cpp
index 787da9850f..9efbdd3bfe 100644
--- a/metagraph/src/graph/annotated_dbg.cpp
+++ b/metagraph/src/graph/annotated_dbg.cpp
@@ -334,7 +334,7 @@ AnnotatedDBG::get_labels(const std::vector<std::pair<row_index, size_t>> &index_
 }
 
 std::vector<Label>
-AnnotatedSequenceGraph::get_labels(node_index index) const {
+AnnotatedSequenceGraph::get_stored_labels(node_index index) const {
     assert(check_compatibility());
     assert(index != SequenceGraph::npos);
 
diff --git a/metagraph/src/graph/annotated_dbg.hpp b/metagraph/src/graph/annotated_dbg.hpp
index 927a7b3cc2..2d67cba27f 100644
--- a/metagraph/src/graph/annotated_dbg.hpp
+++ b/metagraph/src/graph/annotated_dbg.hpp
@@ -28,7 +28,10 @@ class AnnotatedSequenceGraph {
 
     virtual ~AnnotatedSequenceGraph() {}
 
-    virtual std::vector<Label> get_labels(node_index index) const;
+    // Return the labels explicitly stored at this node. Some annotation schemes
+    // may not store labels at all nodes
+    // (e.g., canonical-mode graphs only annotate canonical k-mers)
+    virtual std::vector<Label> get_stored_labels(node_index index) const;
 
     // thread-safe, can be called from multiple threads concurrently
     virtual void annotate_sequence(std::string_view sequence,
@@ -72,7 +75,7 @@ class AnnotatedDBG : public AnnotatedSequenceGraph {
                  std::unique_ptr<Annotator>&& annotation,
                  bool force_fast = false);
 
-    using AnnotatedSequenceGraph::get_labels;
+    using AnnotatedSequenceGraph::get_stored_labels;
 
     const DeBruijnGraph& get_graph() const { return dbg_; }
 
diff --git a/metagraph/tests/annotation/test_annotated_dbg.cpp b/metagraph/tests/annotation/test_annotated_dbg.cpp
index 6aa80ebfa6..5e864d6413 100644
--- a/metagraph/tests/annotation/test_annotated_dbg.cpp
+++ b/metagraph/tests/annotation/test_annotated_dbg.cpp
@@ -32,7 +32,7 @@ void check_labels(const AnnotatedDBG &anno_graph,
     call_annotated_nodes_offsets(graph, sequence, [&](auto index, int64_t) {
         ASSERT_NE(SequenceGraph::npos, index);
         indices.insert(index);
-        auto cur_labels = anno_graph.get_labels(index);
+        auto cur_labels = anno_graph.get_stored_labels(index);
         EXPECT_EQ(labels_present.size(), cur_labels.size());
         EXPECT_EQ(convert_to_set(labels_present), convert_to_set(cur_labels));
 
@@ -46,7 +46,7 @@ void check_labels(const AnnotatedDBG &anno_graph,
                       convert_to_set(cur_labels));
 
             for (DeBruijnGraph::node_index node = contig_id + 1; node <= last_node; ++node) {
-                EXPECT_TRUE(anno_graph.get_labels(node).empty());
+                EXPECT_TRUE(anno_graph.get_stored_labels(node).empty());
             }
         }
     });