Doc for annotation

docs/annotation.md

+An `Annotation` object represents a textual annotation added to a VARNA drawing.
+The object stores the text and other informtation needed.
+One can add `Annotation` to drawing using [VARNA.add_annotation](varna.md#varnaapi.VARNA.add_annotation).
+Four annotation types allowed in VARNA are represented by four objects below.
+
+
+::: varnaapi
+    selection:
+		  members: ["BaseAnnotation", "LoopAnnotation", "HelixAnnotation", "StaticAnnotation"]
+

docs/varnaapi.md

 ::: varnaapi
     selection:
-		  filters: ["!^VARNA", "!^_", "__init__"]
+		  filters: ["!^VARNA", "!^_", "__init__", "!Annotation"]

mkdocs.yml

@@ -8,6 +8,7 @@ theme:
 nav:
   - Overview: index.md
   - API: varnaapi.md
+  - Annotation: annotation.md
   - VARNA: varna.md
 
 plugins:
@@ -19,6 +20,8 @@ plugins:
             filters:
               - "!^_"
               - "^__init__$"
+          rendering:
+            show_root_toc_entry: False
       watch:
         - varnaapi.py
 

varnaapi.py

@@ -129,11 +129,13 @@ class BasesStyle:
 
 
 class _Annotation:
+    """Basic Annotation
+    """
     def __init__(self, text, type, color="#000000", size=10):
         self.text = text
         self.type = type
         self.color = color
-        self.size = size
+        self.size = size #: int: font size
 
     def asdict(self):
         return {'text': self.text, 'type': self.type, 'color': self.color,
@@ -160,22 +162,49 @@ class _ObjectAnnotation(_Annotation):
 
 
 class BaseAnnotation(_ObjectAnnotation):
-    def __init__(self, text, anchor, color="#000000", size=10):
+    def __init__(self, text:str, anchor:int, color="#000000", size=10):
+        """Annoation on a base.
+
+        Args:
+            text: Annotation caption
+            anchor: Index of base to annotate
+            color (Hex): Annotation color
+            size (int): Font size
+        """
         super().__init__(text, 'B', color, size)
 
 
 class LoopAnnotation(_ObjectAnnotation):
+    """Same as [BaseAnnotation][varnaapi.BaseAnnotation] but on a loop.
+    Argument `anchor` can be index of any base in the loop of interest.
+    """
     def __init__(self, text, anchor, color="#000000", size=10):
         super().__init__(text, 'L', anchor, color, size)
 
 
 class HelixAnnotation(_ObjectAnnotation):
+    """Same as [BaseAnnotation][varnaapi.BaseAnnotation] but on an helix.
+    Argument `anchor` can be index of any base in the helix of interest.
+    """
     def __init__(self, text, anchor, color="#000000", size=10):
         super().__init__(text, 'H', anchor, color, size)
 
 
 class StaticAnnotation(_Annotation):
     def __init__(self, text, x, y, color="#000000", size=10):
+        """Annotation on a specified position in VARNA drawing.
+        Unlike [BaseAnnotation][varnaapi.BaseAnnotation], argument `anchor` is omitted.
+        However, arguments `x` and `y` are needed to specify annotation position.
+
+        __Note:__ It is unrecommended to use static annotation unless you know what you're doing
+
+        Args:
+            x (int): x-coordinate of position
+            y (int): y-ccordinate of position
+
+        Examples:
+            >>> sa = StaticAnnotation("Hello World", 100, 150, color="#FF0000")
+        """
         super().__init__(text, 'P', color, size)
         self.x = x
         self.y = y
@@ -489,7 +518,10 @@ class VARNA:
             self.bases_styles[style] = self.bases_styles.get(style, set()).union({i+1 for i in bases})
 
 
-    def add_annotation(self, annotation):
+    def add_annotation(self, annotation:_Annotation):
+        """Add an annotation.
+        Argument should be a valid [Annotation](/annotation/) object
+        """
         # Assert is annotation
         if not isinstance(annotation, _Annotation):
             raise Exception("Should be a valid annotation object")