Uses of Class
edu.sdsc.mbt.Sequence

Packages that use Sequence

edu.sdsc.mbt.viewables	This package provides classes which enable molecular biology data to be represented as visible/renderable viewable objects, plus, this package defines a top-level StructureDocument object to encapsulate the complete state of these objects and properties.
edu.sdsc.sirius.dialogs
edu.sdsc.sirius.io	This package provides classes which enable molecular biology data sets (such as protein structures, sequence data, etc) to be loaded into an MBT application as a Structure object.
edu.sdsc.sirius.viewers
edu.sdsc.sirius.viewers.SequenceViewerImpl
edu.sdsc.sirius.viewers.TreeViewer

Uses of Sequence in edu.sdsc.mbt.viewables

Methods in edu.sdsc.mbt.viewables with parameters of type Sequence

void	StructureDocument.renameSequence(Sequence sequence, java.lang.String name) This method is called when individual sequences from composite entries are renamed in the sequence viewer

Uses of Sequence in edu.sdsc.sirius.dialogs

Methods in edu.sdsc.sirius.dialogs with parameters of type Sequence

static java.lang.String

SequenceRenameDialog.showDialog(javax.swing.JFrame f, Sequence sequence)

Uses of Sequence in edu.sdsc.sirius.io

Methods in edu.sdsc.sirius.io that return Sequence

Sequence	SequenceEntry.getSequence() Returns the Structure object holding the 3D information.
Sequence	SequenceEntry.getSequence(int index)

Methods in edu.sdsc.sirius.io with parameters of type Sequence

void	SequenceEntry.setSequence(Sequence sequence) Sets a Structure object created to represent the 3D structural information
void	SequenceEntry.addSequence(Sequence sequence)
void	SequenceEntry.removeSequence(Sequence sequence)
int	SequenceEntry.getIndexOf(Sequence sequence)

Uses of Sequence in edu.sdsc.sirius.viewers

Methods in edu.sdsc.sirius.viewers with parameters of type Sequence

Entry	SequenceViewer.getEntry(Sequence sequence)
void	SequenceViewer.sequenceRemoved(Sequence sequence)
boolean	SequenceViewer.isStructure(Sequence sequence)
void	SequenceViewer.renameSequence(Sequence sequence, java.lang.String name) This method rename the specified sequence with the provided name.
void	SequenceViewer.movePanel(Sequence sequence, int position)
void	SequenceViewer.setPanelVisibility(Sequence sequence, boolean visible, boolean update)
void	SequenceViewer.removeSequence(Sequence sequence)
void	SequenceViewer.selectCell(Cell cell, Sequence sequence, boolean selected, boolean ctrl) This method speeds up selection, since it narrows down the search for the Cell to the supplied Sequence object
void	SequenceViewer.selectCells(Sequence sequence, java.util.Vector cells)
void	SequenceViewer.replaceResidue(Sequence sequence, int index, java.lang.String replacement) This method is called internally by SequencePanel.
boolean	SequenceViewer.isSelected(Sequence sequence)
void	SequenceViewer.setSelected(Sequence sequence, boolean selected)
void	SequenceViewer.updateSequence(Sequence s, java.lang.String sequence) This method runs through the symbols in the sequence display of the given Sequence object and inserts dashes wherever necessary

Uses of Sequence in edu.sdsc.sirius.viewers.SequenceViewerImpl

Fields in edu.sdsc.sirius.viewers.SequenceViewerImpl declared as Sequence

Sequence

Cell.sequence

Methods in edu.sdsc.sirius.viewers.SequenceViewerImpl that return Sequence

Sequence

SequenceStyles.getSequence() Return a reference to our Sequence object.

Methods in edu.sdsc.sirius.viewers.SequenceViewerImpl with parameters of type Sequence

void	SequenceScalePanel.setSelectedSequence(Sequence s, Cell[] selected) Sets selected sequence that is used as the reference to draw residue numbers.
void	SequencePanel.replaceResidue(Sequence sequence, Cell cell, java.lang.String symbol)
void	SequencePanel.replaceResidue(Sequence currentSequence, int currentIndex, java.lang.String symbol)
void	SequencePanel.editCut(Sequence cSequence, int cIndex)
void	SequencePanel.editCopy(Sequence cSequence, int cIndex)
void	SequencePanel.editPaste(Sequence cSequence, int cIndex)

Constructors in edu.sdsc.sirius.viewers.SequenceViewerImpl with parameters of type Sequence

SequenceStyles(Sequence sequence)
Primary constructor.

Cell(Sequence sequence, int index, java.lang.String symbol, Residue r, int residueId)

Cell(Sequence sequence, int index, java.lang.String symbol, Residue r)

Cell(Sequence sequence, int index, java.lang.String symbol)

Uses of Sequence in edu.sdsc.sirius.viewers.TreeViewer

Methods in edu.sdsc.sirius.viewers.TreeViewer with parameters of type Sequence

void	StructureBrowser.sequenceAdded(Sequence sequence)
void	StructureBrowser.sequenceRemoved(Sequence sequence, boolean update)