first step to handle discontinuated/split entities

src/bratutils/agreement.py

@@ -266,8 +266,10 @@ def __init__(self, a):
         :type: str
         """
         self.text = None
-        self.start_idx = None
-        self.end_idx = None
+        self.frag = None            # fragment, usually one pair of indexes, but annotation can be
+                                    # composed of several fragments (aka discontinuated annotations)
+        self.start_idx = None       # start index of first fragment
+        self.end_idx = None         # end index of last fragment
         self.tag_name = None
         self.partial_match = None
 
@@ -276,18 +278,23 @@ def __init__(self, a):
         self.border_status = False
         self.border_match = None
 
-        self.text, self.tag_name, self.start_idx, self.end_idx = \
+        self.text, self.tag_name, self.start_idx, self.end_idx, self.frag = \
             self._parse_annotation(a)
 
     @staticmethod
     def _parse_annotation(a):
         items = a.split("\t")
         text = items[2].strip("\n").strip(" ")
         subitems = items[1].split(" ")
-        tag_name = subitems[0]
-        start_idx = int(subitems[1])
-        end_idx = int(subitems[2])
-        return text, tag_name, start_idx, end_idx
+        tag_name = subitems.pop(0)
+        subitems = " ".join(subitems).split(";")
+        frag = []
+        for idx in subitems:
+            start_idx, end_idx = idx.split(" ")
+            frag.append((int(start_idx), int(end_idx)))
+        start_idx = frag[0][0]
+        end_idx = frag[len(frag)-1][1]
+        return text, tag_name, start_idx, end_idx, frag
 
     def reset_markers(self):
         """Resets the comparison marker attributes to default values. The
@@ -370,8 +377,9 @@ def coincides_with(self, parallel_ann):
         :return: True if objects coincide
         :rtype: bool
         """
-        return (self.start_idx == parallel_ann.start_idx and
-                self.end_idx == parallel_ann.end_idx)
+
+        return self.frag == parallel_ann.frag
+
 
     def contains_ann(self, other_ann):
         """Checks if this object's annotation contains another object's
@@ -381,8 +389,15 @@ def contains_ann(self, other_ann):
         :return: True if this annotaion contains the other annotation
         :rtype: bool
         """
-        return (other_ann.start_idx >= self.start_idx and
-                other_ann.end_idx <= self.end_idx)
+        contained_fragments = [False] * len(other_ann.frag)
+        for i in range(len(other_ann.frag)):
+            for j in range(len(self.frag)):
+                if other_ann.frag[i][0] >= self.frag[j][0] and \
+                        other_ann.frag[i][1] <= self.frag[j][1]:
+                    contained_fragments[i] = True
+        # return True if all fragments of other_ann are contained in self
+        return contained_fragments == [True] * len(other_ann.frag)
+
 
     def is_contained_by(self, parallel_ann):
         """Checks if this annotation is contained by a parallel annotation.
@@ -391,8 +406,8 @@ def is_contained_by(self, parallel_ann):
         :return: True if contained in `parallel_ann`
         :rtype: bool
         """
-        return (parallel_ann.start_idx <= self.start_idx and
-                parallel_ann.end_idx >= self.end_idx)
+        return self.contains_ann(parallel_ann)
+
 
     def is_partial_to(self, parallel_ann):
         """Returns `True` if the annotation is a partial match to the parallel
@@ -404,8 +419,9 @@ def is_partial_to(self, parallel_ann):
         :param parallel_ann:
         :return:
         """
-        return (self.start_idx > parallel_ann.start_idx and
-                self.end_idx == parallel_ann.end_idx and
+        # TODO really dive into frag (for now, we check start of first fragment and end of last fragment)
+        return (self.start_idx > parallel_ann.end_idx and
+                self.start_idx == parallel_ann.end_idx and
                 self.tag_name == parallel_ann.tag_name)
 
     def get_same_anns(self, parallel_anns):
@@ -548,15 +564,16 @@ def __eq__(self, ann):
         return (self.text == ann.text and
                 self.start_idx == ann.start_idx and
                 self.end_idx == ann.end_idx and
+                self.frag == ann.frag and
                 self.tag_name == ann.tag_name)
 
     def __str__(self):
-        atts = [self.tag_name, str(self.start_idx), str(self.end_idx),
+        atts = [self.tag_name, str(self.start_idx), str(self.end_idx), str(self.frag),
                 self.text]
         return " ".join(atts)
 
     def __repr__(self):
-        atts = [self.tag_name, str(self.start_idx), str(self.end_idx),
+        atts = [self.tag_name, str(self.start_idx), str(self.end_idx), str(self.frag),
                 self.text]
         return " ".join(atts)
 
@@ -640,13 +657,13 @@ def __init__(self, fp=None, ann_list=None):
         self.basename = ""
         if fp:
             self.basename = os.path.basename(fp)
-            with open(fp) as doc:
+            with open(fp, encoding='utf-8') as doc:
                 for line in doc:
-                    if not line.startswith("#"):
+                    if not line.startswith("#") and not line.startswith("A"):  # ignoring Attributes
                         self.tags.append(Annotation(line))
         elif ann_list:
             for line in ann_list:
-                if not line.startswith("#"):
+                if not line.startswith("#") and not line.startswith("A"):
                     self.tags.append(Annotation(line))
         else:
             self.tags = []