Style classes for VARNA operations

Two helper class groups can be imported from python varnaapi.param for two VARNA operations, add_annotation and add_bases_style.

Annotation

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 BasicDraw.add_annotation. Four annotation types allowed in VARNA are represented by four objects below.

BaseAnnotation

Bases: _Annotation

Annoation on a base.

Parameters:

Name	Type	Description	Default
text	str	Annotation caption	required
anchor	int	Index of base to annotate	required
color	color	Annotation color	'#000000'
size	int	Font size	12

Source code in src/varnaapi/param.py

class BaseAnnotation(_Annotation):
    """Annoation on a base.

    Args:
        text: Annotation caption
        anchor: Index of base to annotate
        color (color): Annotation color
        size (int): Font size
    """
    def __init__(self, text:str, anchor:int, color="#000000", size=12, **kwargs):
        super().__init__(text, 'B', int(anchor), color, size, **kwargs)

HelixAnnotation

Bases: _Annotation

Same as BaseAnnotation but on an helix. Argument anchor can be index of any base in the helix of interest.

Source code in src/varnaapi/param.py

class HelixAnnotation(_Annotation):
    """Same as [BaseAnnotation][varnaapi.param.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=12, **kwargs):
        super().__init__(text, 'H', int(anchor), color, size, **kwargs)

LoopAnnotation

Bases: _Annotation

Same as BaseAnnotation but on a loop. Argument anchor can be index of any base in the loop of interest.

Source code in src/varnaapi/param.py

class LoopAnnotation(_Annotation):
    """Same as [BaseAnnotation][varnaapi.param.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=12, **kwargs):
        super().__init__(text, 'L', int(anchor), color, size,**kwargs)

StaticAnnotation

Bases: _Annotation

Annotation on a specified position in VARNA drawing. Unlike BaseAnnotation, argument anchor is omitted. However, arguments x and y are needed to specify annotation position.

Danger

It is unrecommended to use static annotation unless you know what you're doing

Parameters:

Name	Type	Description	Default
x	int	x-coordinate of position	required
y	int	y-ccordinate of position	required

Examples:

>>> sa = StaticAnnotation("Hello World", 100, 150, color="#FF0000")

Source code in src/varnaapi/param.py

class StaticAnnotation(_Annotation):
    """Annotation on a specified position in VARNA drawing.
    Unlike [BaseAnnotation][varnaapi.param.BaseAnnotation], argument `anchor` is omitted.
    However, arguments `x` and `y` are needed to specify annotation position.

    Danger:
        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")
    """
    def __init__(self, text, x, y, color="#000000", size=12, **kwargs):
        super().__init__(text, 'P', (int(x), int(y)),  color, size, **kwargs)

BasesStyle

Bases: _DefaultObj

Defines a custom base-style, to be applied later to a set of bases. A BasesStyle style contains colors used for different components of a base. BasesStyle is constructed from given colors for different components.

Error

At least one argument should be given.

Parameters:

Name	Type	Description	Default
fill	color	color of inner part of base	None
outline	color	color of outline of base	None
label	color	base text (name) color	None
number	color	base number color	None

Examples:

>>> style = BasesStyle(fill='#FF0000', outline='#00FF00')

See Also: BasicDraw.add_bases_style

Source code in src/varnaapi/param.py

class BasesStyle(_DefaultObj):
    """Defines a custom base-style, to be applied later to a set of bases.
    A BasesStyle style contains colors used for different components of a base.
    BasesStyle is constructed from given colors for different components.

    Error:
        At least one argument should be given.

    Args:
        fill (color): color of inner part of base
        outline (color): color of outline of base
        label (color): base text (name) color
        number (color): base number color

    Examples:
        >>> style = BasesStyle(fill='#FF0000', outline='#00FF00')

    __See Also:__ [BasicDraw.add_bases_style][varnaapi.BasicDraw.add_bases_style]
    """
    def __init__(self, fill=None, outline=None, label=None, number=None, **kwargs):
        super().__init__(fill=COLOR_DEFAULT['baseInner'], outline=COLOR_DEFAULT['baseOutline'], label=COLOR_DEFAULT['baseName'], number=COLOR_DEFAULT['baseNum'])
        if varnaapi.settings.CONFIG['hackmode']:
            self._update(fill=fill, outline=outline, label=label, number=number, **kwargs)
        else:
            self._update(fill=fill, outline=outline, label=label, number=number)

    def _update(self, **kwargs):
        """Update component _colors.
        Same rule as [\_\_init\_\_][varnaapi.param.BasesStyle.__init__]
        """
        # if fill is None and outline is None and label is None and number is None:
        #     raise Exception("At least one should not be None")
        for par, val in kwargs.items():
            if val is not None:
                self.values[par] = Color(val)

    def _to_cmd(self, **kwargs):
        """Custom command generator for BasesStyle.
        Function takes the default bases color set by user in kwargs
        """
        for par, val in kwargs.items():
            self.default[par] = val
        return ",".join(k+"="+v for k, v in self._get_diff().items() if v is not None)