From 564d79f72cbe816963baec2b987e45d974d473cf Mon Sep 17 00:00:00 2001
From: Joshua Klein <mobiusklein@gmail.com>
Date: Fri, 1 Dec 2023 09:05:44 -0500
Subject: [PATCH] Use `__getitem__` instead of `by_id`, always available

---
 pyteomics/proforma.py | 46 ++++++++++++++++++++++++++++++++++---------
 1 file changed, 37 insertions(+), 9 deletions(-)

diff --git a/pyteomics/proforma.py b/pyteomics/proforma.py
index 1d493808..5ff5bc9c 100644
--- a/pyteomics/proforma.py
+++ b/pyteomics/proforma.py
@@ -102,6 +102,14 @@ class TagTypeEnum(Enum):
     group_placeholder = 999
 
 
+class ModificationTagStyle(Enum):
+    Unset = 0
+    ShortId = 1
+    LongId = 2
+    ShortName = 3
+    LongName = 4
+
+
 _sentinel = object()
 
 
@@ -354,7 +362,7 @@ def resolve(self, name=None, id=None, **kwargs):
             if not defn:
                 raise KeyError(name)
         elif id is not None:
-            defn = self.database.by_id(id)
+            defn = self.database[id]
             if not defn:
                 raise KeyError(id)
         else:
@@ -365,7 +373,8 @@ def resolve(self, name=None, id=None, **kwargs):
                 'name': defn['title'],
                 'id': defn['record_id'],
                 'mass': defn['mono_mass'],
-                'provider': self.name
+                'provider': self.name,
+                "source": self
             }
         else:
             name = defn.ex_code_name
@@ -376,7 +385,8 @@ def resolve(self, name=None, id=None, **kwargs):
                 "name": name,
                 "id": defn.id,
                 "mass": defn.monoisotopic_mass,
-                "provider": self.name
+                "provider": self.name,
+                "source": self
             }
 
 
@@ -420,7 +430,8 @@ def resolve(self, name=None, id=None, **kwargs):
             'composition': composition,
             'name': defn.name,
             'id': defn.id,
-            'provider': self.name
+            'provider': self.name,
+            "source": self
         }
 
 
@@ -453,7 +464,8 @@ def resolve(self, name=None, id=None, **kwargs):
             'composition': composition,
             'name': defn.name,
             'id': defn.id,
-            'provider': self.name
+            'provider': self.name,
+            "source": self
         }
 
 # TODO: Implement resolve walking up the graph to get the mass. Can't really
@@ -565,7 +577,8 @@ def resolve(self, name=None, id=None, **kwargs):
             "provider": self.name,
             "composition": composition,
             "monosaccharides": monosaccharides,
-            "mass": self.get_mass_from_term(term, raw_mass)
+            "mass": self.get_mass_from_term(term, raw_mass),
+            "source": self
         }
         return rec
 
@@ -631,12 +644,15 @@ class ModificationBase(TagBase):
     '''
 
     _tag_type = None
-    __slots__ = ('_definition', )
+    __slots__ = ('_definition', 'style')
 
-    def __init__(self, value, extra=None, group_id=None):
+    def __init__(self, value, extra=None, group_id=None, style=None):
+        if style is None:
+            style = ModificationTagStyle.Unset
         super(ModificationBase, self).__init__(
             self._tag_type, value, extra, group_id)
         self._definition = None
+        self.style = style
 
     def __eq__(self, other):
         if isinstance(other, ModificationToken):
@@ -720,7 +736,19 @@ def _populate_from_definition(self, definition):
         self._definition = definition
 
     def _format_main(self):
-        return "{self.prefix_name}:{self.value}".format(self=self)
+        if self.style == ModificationTagStyle.Unset or self.style is None:
+            return "{self.prefix_name}:{self.value}".format(self=self)
+        elif self.style == ModificationTagStyle.LongId:
+            return "{self.prefix_name}:{self.id}".format(self=self)
+        elif self.style == ModificationTagStyle.ShortId:
+            return "{self.short_prefix}:{self.id}".format(self=self)
+        elif self.style == ModificationTagStyle.LongName:
+            return "{self.prefix_name}:{self.name}".format(self=self)
+        elif self.style == ModificationTagStyle.ShortName:
+            return "{self.short_prefix}:{self.name}".format(self=self)
+        else:
+            warnings.warn("Unknown formatting style {!r}".format(self.style))
+            return "{self.prefix_name}:{self.value}".format(self=self)
 
     def resolve(self):
         '''Find the term and return it's properties