Source code for schrodinger.ui.sequencealignment.align_gui

"""
Alignment settings dialog.

Copyright Schrodinger, LLC. All rights reserved.
"""

# Contributors: Piotr Rotkiewicz

from schrodinger.Qt import QtGui
from schrodinger.Qt import QtWidgets

from . import constants  # noqa: F401

_ALIGNMENT_SETTINGS_DIALOG = None


class AlignmentSettingsDialog(QtWidgets.QDialog):
    """
    This class implements the "Alignment Settings" dialog.
    """

    def __init__(self, parent):

        # Initialize base class.
        QtWidgets.QDialog.__init__(self, parent)
        self.setWindowTitle("Pairwise Alignment Settings")

        #: Custom matrix push button.
        self.button_custom = QtWidgets.QPushButton(self)
        self.button_custom.setText(
            "Create Substitution Matrix from the Alignment")
        self.button_custom.clicked.connect(self.createMatrix)

        self.button_ok = QtWidgets.QPushButton(self)
        self.button_ok.setText("OK")
        self.button_ok.setDefault(True)
        self.button_ok.clicked.connect(self.accept)
        self.layout = QtWidgets.QVBoxLayout(self)
        self.matrix_choice = QtWidgets.QComboBox(self)
        self.matrices = [
            "PAM250", "BLOSUM45", "BLOSUM62", "BLOSUM80", "GONNET", "Custom"
        ]
        for matrix in self.matrices:
            self.matrix_choice.addItem(matrix)
        self.matrix_choice.currentIndexChanged.connect(self.similarityMatrix)
        self.matrix_choice.setCurrentIndex(2)
        self.layout.addWidget(self.matrix_choice)

        #: Gap Opening Penalty
        label = QtWidgets.QLabel("Gap Opening Penalty")
        self.gap_open_input = QtWidgets.QLineEdit()
        self.gap_open_input.setText("-10.0")
        self.gap_open_input.setValidator(
            QtGui.QDoubleValidator(-100.0, 100.0, 1, self.gap_open_input))
        gap_layout = QtWidgets.QHBoxLayout()
        gap_layout.addWidget(label)
        gap_layout.addWidget(self.gap_open_input)
        self.layout.addLayout(gap_layout)

        #: Gap Extension Penalty
        label = QtWidgets.QLabel("Gap Extension Penalty")
        self.gap_extend_input = QtWidgets.QLineEdit()
        self.gap_extend_input.setText("-1.0")
        self.gap_extend_input.setValidator(
            QtGui.QDoubleValidator(-100.0, 100.0, 1, self.gap_extend_input))
        gap_layout = QtWidgets.QHBoxLayout()
        gap_layout.addWidget(label)
        gap_layout.addWidget(self.gap_extend_input)
        self.layout.addLayout(gap_layout)
        self.allow_ssa_gaps = QtWidgets.QCheckBox(
            "Allow gaps in secondary structure elements")
        self.allow_ssa_gaps.setChecked(True)
        self.layout.addWidget(self.allow_ssa_gaps)
        spacer = QtWidgets.QWidget()
        spacer.setSizePolicy(QtWidgets.QSizePolicy.Expanding,
                             QtWidgets.QSizePolicy.Preferred)

        self.button_layout = QtWidgets.QHBoxLayout()
        self.button_layout.addWidget(self.button_custom)
        self.button_layout.addWidget(spacer)
        self.button_layout.addWidget(self.button_ok)
        self.layout.addLayout(self.button_layout)
        self.sizePolicy().setVerticalPolicy(QtWidgets.QSizePolicy.Maximum)
        self.group = None

    def similarityMatrix(self, index):
        global constants
        constants.SIMILARITY_MATRIX = constants.BLOSUM62
        if self.matrices[index] == "BLOSUM80":
            constants.SIMILARITY_MATRIX = constants.BLOSUM80
        elif self.matrices[index] == "BLOSUM45":
            constants.SIMILARITY_MATRIX = constants.BLOSUM45
        elif self.matrices[index] == "GONNET":
            constants.SIMILARITY_MATRIX = constants.GONNET
        elif self.matrices[index] == "PAM250":
            constants.SIMILARITY_MATRIX = constants.PAM250

    def createMatrix(self):
        """
        Creates a new mutation matrix.
        """
        self.group.calculateMatrix()

    def gapPenalties(self):
        """
        Returns alignment gap penalties.
        """
        return (float(self.gap_open_input.text()),
                float(self.gap_extend_input.text()))

    def allowSSGaps(self):
        """
        Returns gaps in SSE status.
        """
        return self.allow_ssa_gaps.isChecked()