Source code for dasi.constants

r"""
Constants (:mod:`dasi.constants`)
=============================

.. currentmodule:: dasi.constants

This module provides DASi constants.
"""


class Constants:
    """DASi constants."""

    ################
    # INTERNAL TYPES
    ################

    #: an alignment that is generate from an already existing PCR product or fragment
    FRAGMENT = "PRE-MADE DNA FRAGMENT"

    #: an alignment that is to be generated from a PCR product
    PCR_PRODUCT = "PCR_PRODUCT"

    #: PCR product that can be produces from existing primers
    PCR_PRODUCT_WITH_PRIMERS = "PCR_PRODUCT_WITH_PRIMERS"

    #: PCR product with existing left primer
    PCR_PRODUCT_WITH_LEFT_PRIMER = "PCR_PRODUCT_WITH_LEFT_PRIMER"

    #: PCR product with existing right primer
    PCR_PRODUCT_WITH_RIGHT_PRIMER = "PCR_PRODUCT_WITH_RIGHT_PRIMER"

    #: a pcr product that uses no template, but extends two primers
    PRIMER_EXTENSION_PRODUCT_WITH_PRIMERS = "PRIMER_EXTENSION_PRODUCT_WITH_PRIMERS"

    #: a pcr product that uses no template, but extends an existing fwd primer.
    PRIMER_EXTENSION_PRODUCT_WITH_LEFT_PRIMER = (
        "PRIMER_EXTENSION_PRODUCT_WITH_LEFT_PRIMER"
    )

    #: a pcr product that uses no template, but extends an existing rev primer.
    PRIMER_EXTENSION_PRODUCT_WITH_RIGHT_PRIMER = (
        "PRIMER_EXTENSION_PRODUCT_WITH_RIGHT_PRIMER"
    )

    #: explicit definition of a synthesized DNA fragment
    SHARED_SYNTHESIZED_FRAGMENT = "SHARED_SYNTHESIZED_FRAGMENT"

    #: the designed plasmid
    PLASMID = "PLASMID"

    ################
    # EXTERNAL TYPES
    ################
    GAP = "GAP"  #: region that represents a gap that must be synthesized
    OVERLAP = "OVERLAP"  #: region that represents overlapping molecules

    #################
    # MOLECULES TYPES
    #################
    #: A fragment alignment that is shared with other queries for potential reuse
    SHARED_FRAGMENT = "FRAGMENT_SHARED_WITH_OTHER_QUERIES"
    TEMPLATE = "TEMPLATE"  #: A template alignment group. Not an actual molecule.
    MISSING = "__MISSING"  #: missing region
    PRIMER = "PRIMER"  #: a primer binding alignment

    INF = 10.0 ** 6  #: almost infinity

    ############
    # GROUP TAGS
    ############
    PCR_GROUP_TAG = "PCR"
    SHARE_GROUP_TAG = "SHARE"

    ############
    # ALGORITHM
    ############
    ALGORITHM_DEFAULT = "standard optimization"
    ALGORITHM_LIBRARY = "library optimization"