missing file added

Author: Dmitry-Antipov

src/tangle.py

@@ -0,0 +1,64 @@
+#!/usr/bin/env python3
+"""
+Tangle class to encapsulate all tangle-related data and reduce function parameters.
+"""
+
+from typing import Optional, Dict, Set, List, Tuple
+import networkx as nx
+from .node_id_mapper import NodeIdMapper
+
+
+class Tangle:
+    """
+    Encapsulates all information about a tangle region in an assembly graph.
+    
+    A tangle represents a complex region in the assembly graph that requires
+    specialized traversal to resolve structural variants or repetitive sequences.
+    
+    Core structural attributes (initialized in __init__):
+        nodes (set): Oriented node IDs within the tangle (includes RC nodes as negatives)
+        nor_nodes (set): Non-oriented/absolute node IDs (nodes without orientation)
+        boundary_nodes (dict): Maps incoming boundary nodes → matching outgoing boundary nodes
+        original_graph (nx.DiGraph): Original GFA graph with node attributes
+        dual_graph (nx.DiGraph): Dual graph where nodes=junctions, edges=original nodes
+        node_id_mapper (NodeIdMapper): Bidirectional mapping between node IDs and string names
+    
+    Solution/derived attributes (added progressively during processing):
+        cleaned_tips (list): Tip nodes removed during pre-processing
+        coverage_dict (dict): Node ID → coverage value mapping
+        median_unique_coverage (float): Estimated coverage for unique nodes
+        coverage_range (tuple/list): [low, high] coverage bounds for unique nodes
+        multiplicities (dict): Node ID → multiplicity value (from MIP solution)
+        multi_graph (nx.MultiDiGraph): Multiplied dual graph after MIP solution
+        detected_coverage (float): Final calculated unique coverage from MIP
+    """
+    
+    def __init__(self, nodes, nor_nodes, boundary_nodes, original_graph, dual_graph, node_id_mapper):
+        """
+        Initialize a Tangle with core structural information.
+        
+        Args:
+            nodes (set): Oriented node IDs within the tangle
+            nor_nodes (set): Non-oriented/absolute node IDs
+            boundary_nodes (dict): Maps incoming → outgoing boundary nodes
+            original_graph (nx.DiGraph): Original GFA graph
+            dual_graph (nx.DiGraph): Dual graph representation
+            node_id_mapper (NodeIdMapper): Node ID to name mapper
+        """
+        # Core structural data
+        self.nodes: Set[int] = nodes
+        self.nor_nodes: Set[int] = nor_nodes
+        self.boundary_nodes: Dict[int, int] = boundary_nodes
+        self.original_graph: nx.DiGraph = original_graph
+        self.dual_graph: nx.DiGraph = dual_graph
+        self.node_id_mapper: NodeIdMapper = node_id_mapper
+        
+        # Solution/derived attributes (to be set later)
+        # These will be populated progressively as the pipeline executes
+        self.cleaned_tips: List[int] = []
+        self.coverage_dict: Dict[int, float] = {}
+        self.median_unique_coverage: Optional[float] = None
+        self.coverage_range: Optional[List[float]] = None
+        self.multiplicities: Dict[int, int] = {}
+        self.multi_graph: Optional[nx.MultiDiGraph] = None
+        self.detected_coverage: Optional[float] = None