Package schrodinger :: Package application :: Package msv :: Package gui :: Module viewmodel :: Class SequenceAlignmentModel

[frames] | no frames]

Class SequenceAlignmentModel

         object --+                            
                  |                            
  sip.simplewrapper --+                        
                      |                        
            sip.wrapper --+                    
                          |                    
       PyQt4.QtCore.QObject --+                
                              |                
PyQt4.QtCore.QAbstractItemModel --+            
                                  |            
   PyQt4.QtCore.QAbstractTableModel --+        
                                      |        
          Qt.QtCore.QAbstractTableModel --+    
                                          |    
      ui.qt.table_helper.RowBasedTableModel --+
                                              |
                                             SequenceAlignmentModel

A QTable model where each row corresponds to a sequence and each column corresponds to a residue position

Instance Methods

[hide private]

residuesSelected(...)

residueFormatChanged(...)

__init__(self, parent=None, display_mode=<Format.one_letter: 1>, include_gaps=False)
x.__init__(...) initializes x; see help(type(x)) for signature

ResidueFormat

getResidueDisplayMode(self)
Returns: The residue display mode in current use

setResidueDisplayMode(self, mode)

setAlignment(self, alignment)
Set the alignment model to display data from

schrodinger.application.msv.domain.alignment.BaseAlignment

getAlignment(self)
Return the underlying alignment object

int

sequenceCount(self)
Returns: The number of sequences in the alignment

notifyResidueSelection(self, selection)
Takes a list of residues and emits a list of indices corresponding to them.

_disconnectOldModel(self)
Disconnect all signal/slot connections with the old alignment model

columnCount(self, parent=None)

headerData(self, section, orientation, role=0)
Header data for the table.

float

_calculateValueRange(self, values)
Calculate the difference between the maximum and minimum values in a list

_resRole(self, col, res_data)
Return the residue object at the location or an empty string

_residuesAtPosition(self, col, res_data)
Returns an array of indices corresponding to the residues at an index in the underlying alignment

_alignmentMetrics(self, col, res_data, role)
Returns alignment metric value depending on the role given.

_displayData(self, col, res_data)
Return the residue object at the location or an empty string

_seqAlignmentData(self, col, res_data)
Return the underlying alignment object

_textAlignmentData(self, col, res_data)
Make sure that data is center aligned

_seqAnnotationData(self, col, res_data, role)
Return the value for the specified sequence annotation role

_globalAnnotationData(self, col, res_data, role)
Return the value for the specified global annotation role

_seqAnnotationRangeData(self, col, res_data, role)
Return the range for the specified sequence annotation role

_globalAnnotationRangeData(self, col, res_data, role)
Return the range for the specified global annotation role

_consensusData(self, col, res_data, role)
Returns whether the residue in the specified column matches the residue at the corresponding column in the consensus sequence.

_sortByData(self, col, seq, role)
Data used for sorting the table

tuple

annotationTypes(self)
Get the current annotation types

list

strucTitles(self)
Get all structure titles

_alignmentLengthAboutToChange(self, old_length, new_length)
Respond to the alignmentLengthAboutToChange signal by getting ready to insert or remove columns

_alignmentLengthChanged(self, old_length, new_length)
Respond to the alignmentLengthChanged signal by finishing inserting or removing columns

_sequenceResiduesChanged(self, seq, start_col, end_col)
Response to changes within a sequence by updating the appropriate cells

_sequenceNameChanged(self, seq)
Respond to a sequence name changing by updating the appropriate header row

Inherited from ui.qt.table_helper.RowBasedTableModel: af2SettingsGetValue, af2SettingsSetValue, appendRow, appendRowObject, data, flags, formatFloat, loadData, removeRows, removeRowsByIndices, replaceRows, reset, rowCount, setData

Inherited from ui.qt.table_helper.RowBasedTableModel (private): _callDataMethod, _checkEditableCols, _createTableColumnsObject, _getRowFromIndex, _rowObjectData, _setData

Inherited from Qt.QtCore.QAbstractTableModel: setRoleNames, setSupportedDragActions

Inherited from PyQt4.QtCore.QAbstractTableModel: dropMimeData, hasChildren, index, parent

Inherited from PyQt4.QtCore.QAbstractItemModel: beginInsertColumns, beginInsertRows, beginMoveColumns, beginMoveRows, beginRemoveColumns, beginRemoveRows, beginResetModel, buddy, canFetchMore, changePersistentIndex, changePersistentIndexList, columnsAboutToBeInserted, columnsAboutToBeMoved, columnsAboutToBeRemoved, columnsInserted, columnsMoved, columnsRemoved, createIndex, dataChanged, decodeData, encodeData, endInsertColumns, endInsertRows, endMoveColumns, endMoveRows, endRemoveColumns, endRemoveRows, endResetModel, fetchMore, hasIndex, headerDataChanged, insertColumn, insertColumns, insertRow, insertRows, itemData, layoutAboutToBeChanged, layoutChanged, match, mimeData, mimeTypes, modelAboutToBeReset, modelReset, persistentIndexList, removeColumn, removeColumns, removeRow, resetInternalData, revert, roleNames, rowsAboutToBeInserted, rowsAboutToBeMoved, rowsAboutToBeRemoved, rowsInserted, rowsMoved, rowsRemoved, setHeaderData, setItemData, sibling, sort, span, submit, supportedDragActions, supportedDropActions

Inherited from PyQt4.QtCore.QObject: __getattr__, blockSignals, childEvent, children, connect, connectNotify, customEvent, deleteLater, destroyed, disconnect, disconnectNotify, dumpObjectInfo, dumpObjectTree, dynamicPropertyNames, emit, event, eventFilter, findChild, findChildren, inherits, installEventFilter, isWidgetType, killTimer, metaObject, moveToThread, objectName, property, pyqtConfigure, receivers, removeEventFilter, sender, senderSignalIndex, setObjectName, setParent, setProperty, signalsBlocked, startTimer, thread, timerEvent, tr, trUtf8

Inherited from sip.simplewrapper: __new__

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables

[hide private]

Inherited from ui.qt.table_helper.RowBasedTableModel: CHECKABLE_COLS, COLUMN, Column, EDITABLE_COLS, ROW_CLASS, ROW_LIST_OFFSET, SHOW_ROW_NUMBERS, UNEDITABLE_COLS

Inherited from PyQt4.QtCore.QObject: staticMetaObject

Properties

[hide private]

aln
An alias for the table model's _rows attribute

Inherited from object: __class__

Method Details

[hide private]

init(self, parent=None, display_mode=<Format.one_letter: 1>, include_gaps=False)
(Constructor)

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

parent (QtCore.Object) - Parent of the row based table model.
display_mode (ResidueFormat enum) - Display mode of the residues
include_gaps (bool) - Whether or not to include gaps in calculating alignment metrics, such as identity, similarity, etc.

Overrides: object.__init__

getResidueDisplayMode(self)

Returns: ResidueFormat: The residue display mode in current use

setResidueDisplayMode(self, mode)

Parameters:

mode (ResidueFormat) - The display mode for residue text

setAlignment(self, alignment)

Set the alignment model to display data from

Parameters:

alignment (schrodinger.application.msv.domain.alignment .BaseAlignment) - The alignment model

getAlignment(self)

Return the underlying alignment object

Returns: schrodinger.application.msv.domain.alignment.BaseAlignment: The alignment

sequenceCount(self)

Returns: int: The number of sequences in the alignment

notifyResidueSelection(self, selection)

Takes a list of residues and emits a list of indices corresponding to them.

We need this signal in order to convey selection changes from the structure model to the view.

Each proxy in the proxy stack should listen to the residuesSelected signal of its own model and then emit in turn its own residuesSelected signal with the indices appropriately modified

Parameters:

selection (list of schrodinger.application.domain.residue. Residue) - A list of residues to select
residuesSelected (list of QtCore.QModelIndex)

columnCount(self, parent=None)

Overrides: PyQt4.QtCore.QAbstractItemModel.columnCount

headerData(self, section, orientation, role=0)

Header data for the table. Untitled sequences will be given a title of "Sequence #".

See Qt documentation for argument and return value documentation

Overrides: PyQt4.QtCore.QAbstractItemModel.headerData

_calculateValueRange(self, values)

Calculate the difference between the maximum and minimum values in a list

Parameters:

values (list) - The value to calculate the range of

Returns: float

The difference between the max and min values