domain_layouts.py: Simplify things and do not load big json files jus…

…t to import the module.

This still needs more cleanup, but at least it will not make ete choke
like before!

ete4/smartview/renderer/layouts/domain_layouts.py

@@ -1,3 +1,5 @@
+# TODO: This file needs reviewing. No need to do all this just to get
+# classes LayoutPfamDomains and LayoutSmartDomains.
 import os
 import json
 
@@ -8,103 +10,75 @@
 from ete4.config import ETE_DATA_HOME, update_ete_data
 
 
-pfam2color_file = ETE_DATA_HOME + '/pfam2color.json'
-
-if not os.path.exists(pfam2color_file):
-    url = ('https://github.com/etetoolkit/ete-data/raw/main'
-           '/layouts/pfam2color.json')
-    update_ete_data(pfam2color_file, url)
-
-with open(pfam2color_file) as handle:
-    _pfam2color = json.load(handle)
-
-
-smart2color_file = ETE_DATA_HOME + '/smart2color.json'
-
-if not os.path.exists(smart2color_file):
-    url = ('https://github.com/etetoolkit/ete-data/raw/main'
-           '/layouts/smart2color.json')
-    update_ete_data(smart2color_file, url)
-
-with open(smart2color_file) as handle:
-    _smart2color = json.load(handle)
-
-
 class _LayoutDomains(TreeLayout):
-    def __init__(self, prop, name,
-            column=10, colormap={},
-            min_fsize=4, max_fsize=15,
-            padding_x=5, padding_y=0):
+    def __init__(self, prop, name, column=10, min_fsize=4, max_fsize=15,
+                 padding_x=5, padding_y=0):
         super().__init__(name or "Domains layout")
         self.prop = prop
         self.column = column
         self.aligned_faces = True
-        self.colormap = colormap
         self.min_fsize = min_fsize
         self.max_fsize = max_fsize
         self.padding = Padding(padding_x, padding_y)
 
+        # Load colormap from file if necessary.
+        color_file = ETE_DATA_HOME + f'/{prop}2color.json'
+
+        if not os.path.exists(color_file):
+            url = ('https://github.com/etetoolkit/ete-data/raw/main'
+                   f'/layouts/{prop}2color.json')
+            update_ete_data(color_file, url)
+
+        with open(color_file) as handle:
+            self.colormap = json.load(handle)
+
     def get_doms(self, node):
-        if node.is_leaf:
-            return node.props.get(self.prop, [])
-        else:
-            first_node = next(node.iter_leaves())
-            return first_node.props.get(self.prop, [])
+        leaf = next(node.leaves())  # 1st leaf
+        return leaf.props.get(self.prop, [])
 
     def parse_doms(self, dom_list):
-        doms = []
-        for name, start, end in dom_list:
-            color = self.colormap.get(name, "lightgray")
-            dom = [int(start), int(end), "()",
-                   None, None, color, color,
-                   "arial|20|black|%s" %(name)]
-            doms.append(dom)
-        return doms
+        def translate(dom):
+            name, start, end = dom
+            color = self.colormap.get(name, 'lightgray')
+            return [int(start), int(end), '()', None, None, color, color,
+                    f'arial|20|black|{name}']
+
+        return [translate(dom) for dom in dom_list]
 
     def set_node_style(self, node):
-        dom_list = self.get_doms(node)
-        doms = self.parse_doms(dom_list)
-        fake_seq = '-' * int(node.props.get("len_alg", 0))
+        doms = self.parse_doms(self.get_doms(node))
+        fake_seq = '-' * int(node.props.get('len_alg', 0))
         if doms or fake_seq:
-            seqFace = SeqMotifFace(seq=fake_seq, motifs=doms, width=250,
-                    height=10)
-            node.add_face(seqFace, column=self.column,
-                    position="aligned",
-                    collapsed_only=(not node.is_leaf))
+            seqFace = SeqMotifFace(seq=fake_seq, motifs=doms, width=250, height=10)
+            node.add_face(seqFace, column=self.column, position='aligned',
+                          collapsed_only=(not node.is_leaf))
 
 
-def create_domain_layout(prop, name, colormap, active, column):
-    # branch_right; column 2; color black
+def create_domain_layout(prop, name, active, column):
+    """Add a layout named Layout<name> to the globals, and return it."""
+    # Because this is the wild west, apparently.
     class Layout(_LayoutDomains):
-        def __init__(self,
-                prop=prop,
-                name=name,
-                colormap=colormap,
-                column=column,
-                *args, **kwargs):
-            super().__init__(
-                    prop=prop,
-                    name=name,
-                    colormap=colormap,
-                    column=column,
-                    *args, **kwargs)
+        def __init__(self, prop=prop, name=name, column=column, *args, **kwargs):
+            super().__init__(prop=prop, name=name, column=column, *args, **kwargs)
             self.active = active
 
         def __name__(self):
             return layout_name
+
+    # Let's play with the environment like there's no tomorrow!
     layout_name = "Layout" + cased_name(name)
     Layout.__name__ = layout_name
     globals()[layout_name] = Layout
     return Layout
 
 
 domain_layout_args = [
-        [ "pfam",  "Pfam domains",  _pfam2color,  True  ],
-        [ "smart", "Smart domains", _smart2color, False  ],
-    ]
+    ["pfam", "Pfam domains", True],
+    ["smart", "Smart domains", False],
+]
 
 col0 = 20
-domain_layouts = [ create_domain_layout(*args, i+col0)\
-                 for i, args in enumerate(domain_layout_args) ]
+domain_layouts = [create_domain_layout(*args, i+col0)
+                  for i, args in enumerate(domain_layout_args)]
 
 __all__ = [ *[layout.__name__ for layout in domain_layouts] ]