A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

M

MAGNIFICATION_MOVE - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences

Constants that define modes of motion: zooming into a structure by changing the angle of view or physically moving the camera (in the latter case, fog interferes with the motion)

MAGNIFICATION_ZOOM - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences

MEDIUM_FONT - Static variable in class edu.sdsc.mbt.viewers.GLViewerImpl.LabelGeometry

MERGE - Static variable in class edu.sdsc.sirius.dialogs.StructureEditDialog

MIN_ATOMS_FOR_FRAGMENTS - Variable in class edu.sdsc.mbt.StructureMap

MIN_WIDTH - Variable in class edu.sdsc.sirius.dialogs.TableImpl.TableViewPanel

MalformedPathException - exception edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.MalformedPathException.

Indicates that a problem has been found in the internal structure of a Path.

MalformedPathException() - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.MalformedPathException

Constructs an IOException with null as its error detail message.

MalformedPathException(String) - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.MalformedPathException

Constructs an IOException with the specified detail message.

Manager - interface edu.sdsc.sirius.util.Manager.

Interface that specifies methods that are implemented by the main application class of the framework that receives data from dialogs and menu events (data loading, dialog handling, etc.) This interface should be used by classes that implement SearchServicePanel interface to pass loaded data to the main application.

MbtRenderable - class edu.sdsc.mbt.viewers.GLViewerImpl.MbtRenderable.

Provides a renderable object which contains all properties needed to regenerate geometry for a visible representation of the data.

MbtRenderable(StructureComponent, StructureStyles, Geometry) - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.MbtRenderable

Construct a Renderable object.

MessageDialog - class edu.sdsc.sirius.dialogs.MessageDialog.

MessageDialog(JFrame, String) - Constructor for class edu.sdsc.sirius.dialogs.MessageDialog

MessageDialog(JFrame, String, String) - Constructor for class edu.sdsc.sirius.dialogs.MessageDialog

MessageDialog(JDialog, String) - Constructor for class edu.sdsc.sirius.dialogs.MessageDialog

MetaData - class edu.sdsc.sirius.io.MetaData.

This class is intended to store various metadata associated with Entries and may be updated in the future.

MetaData() - Constructor for class edu.sdsc.sirius.io.MetaData

Mg - Static variable in class edu.sdsc.mbt.util.Element

Model - class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Model.

Model is a simple bag to hold Chains.

Model() - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Model

Mol2EntryLoader - class edu.sdsc.sirius.io.Mol2EntryLoader.

Mol2EntryLoader() - Constructor for class edu.sdsc.sirius.io.Mol2EntryLoader

MonitorComponent - class edu.sdsc.mbt.MonitorComponent.

MonitorComponent(Atom, Atom, String) - Constructor for class edu.sdsc.mbt.MonitorComponent

MonitorDialog - class edu.sdsc.sirius.monitors.MonitorDialog.

MonitorDialog(JFrame, Manager) - Constructor for class edu.sdsc.sirius.monitors.MonitorDialog

MonitorGeometry - class edu.sdsc.mbt.viewers.GLViewerImpl.MonitorGeometry.

Construct a new object for generating bond geometry using default

MonitorGeometry() - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.MonitorGeometry

Construct a new MonitorGeometry object.

MonitorPanel - class edu.sdsc.sirius.monitors.MonitorPanel.

MonitorPanel(Manager) - Constructor for class edu.sdsc.sirius.monitors.MonitorPanel

MonitorRenderable - class edu.sdsc.mbt.viewers.GLViewerImpl.MonitorRenderable.

Provides a renderable object which contains all properties needed to regenerate geometry for a visible representation of the data.

MonitorRenderable(AnnotationComponent, AnnotationGeometry) - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.MonitorRenderable

Construct a Renderable object.

MotifDialog - class edu.sdsc.sirius.dialogs.MotifDialog.

MotifDialog(JFrame, SequenceViewer, int) - Constructor for class edu.sdsc.sirius.dialogs.MotifDialog

MotionDialog - class edu.sdsc.sirius.dialogs.MotionDialog.

MotionDialog(JFrame, Manager, StructureViewer) - Constructor for class edu.sdsc.sirius.dialogs.MotionDialog

MoveEvent - class edu.sdsc.mbt.viewers.GLViewerImpl.MoveEvent.

GvPickEvent.java
Please complete these missing tags

MoveEvent() - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.MoveEvent

MoveEventListener - interface edu.sdsc.mbt.viewers.GLViewerImpl.MoveEventListener.

GvPickEventListener.java
Please complete these missing tags

MsfEntryLoader - class edu.sdsc.sirius.io.MsfEntryLoader.

This class loads Entries from a file in MSF alignment format.

MsfEntryLoader() - Constructor for class edu.sdsc.sirius.io.MsfEntryLoader

mPageFormat - Variable in class edu.sdsc.sirius.dialogs.DistributionViewer

mPageFormat - Variable in class edu.sdsc.sirius.dialogs.TableImpl.ResultPanel

mPageFormat - Variable in class edu.sdsc.sirius.dialogs.TableImpl.TableViewPanel

mPageFormat - Variable in class edu.sdsc.sirius.viewers.SequenceViewer

m_alignment - Variable in class edu.sdsc.sirius.dialogs.TableImpl.ColumnData

Content alignment.

m_flag - Variable in class edu.sdsc.sirius.dialogs.TableImpl.LineData

m_title - Variable in class edu.sdsc.sirius.dialogs.TableImpl.ColumnData

Column title.

m_width - Variable in class edu.sdsc.sirius.dialogs.TableImpl.ColumnData

Column width in pixels.

magnificationMode - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences

main(String[]) - Static method in class Viewer

main(String[]) - Static method in class edu.sdsc.mbt.image.ImageUtils

Unit testing entry point.

main(String[]) - Static method in class edu.sdsc.mbt.util.Algebra

main(String[]) - Static method in class edu.sdsc.mbt.viewers.GLViewerImpl.BondGeometryUtils

main(String[]) - Static method in class edu.sdsc.mbt.viewers.GLViewerImpl.Interpolator

Unit testing.

main(String[]) - Static method in class edu.sdsc.sirius.dialogs.ElementStylesEditor

This the main application entry point for the example program.

main(String[]) - Static method in class edu.sdsc.sirius.dialogs.MessageDialog

main(String[]) - Static method in class edu.sdsc.sirius.dialogs.PreferencesDialog

main(String[]) - Static method in class edu.sdsc.sirius.io.FileTransfer

Test driver

main(String[]) - Static method in class edu.sdsc.sirius.io.Mol2EntryLoader

main(String[]) - Static method in class edu.sdsc.sirius.util.BrowserControl

main(String[]) - Static method in class edu.sdsc.sirius.util.SplashWindow

matchedSequences - Variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequencePanel

matches(String) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Path

matrix - Variable in class edu.sdsc.mbt.Symmetry

The symmetry matricies expressed as an array of 4x4 3D transforms.

matrix - Static variable in class edu.sdsc.sirius.util.BlastSettings

matrix - Static variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.AlignmentSettings

matrixRotate(double[], double[]) - Static method in class edu.sdsc.mbt.util.Algebra

Rotate the point by the given 16-element rotation matrix.

maxLength() - Method in class edu.sdsc.sirius.util.LimitedLengthDocument

Returns maximum length allowed by this field.

menuFontSize - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences

message - Variable in class edu.sdsc.mbt.util.StatusEvent

The message text.

midpoint(Vec3d, Vec3d) - Static method in class edu.sdsc.mbt.util.Algebra

Compute the midpoint between two points.

minimumLayoutSize(Container) - Method in class edu.sdsc.sirius.util.DialogLayout

minimumLayoutSize(Container) - Method in class edu.sdsc.sirius.util.ExtensionLayout

monitorColor - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences

Color used to display distance monitors in StructureViewer

monitorColor - Variable in class edu.sdsc.sirius.dialogs.PreferencesCache

mouseClicked(MouseEvent) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer

mouseClicked method.

mouseDragged(MouseEvent) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer

Control the camera motion.

mouseEntered(MouseEvent) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer

MouseListener interface - mouseEntered method.

mouseEvent - Variable in class edu.sdsc.mbt.viewers.GLViewerImpl.GvPickEvent

mouseExited(MouseEvent) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer

mouseExited method.

mouseFactor - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences

mouseMoved(MouseEvent) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer

mouseMoved method.

mousePressed(MouseEvent) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer

mousePressed method.

mouseReleased(MouseEvent) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer

mouseReleased method.

movePanel(Sequence, int) - Method in class edu.sdsc.sirius.viewers.SequenceViewer

mul(Quat4f, Quat4f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.util.Quat4f

Sets the value of this quaternion to the quaternion product of quaternions q1 and q2 (this = q1 * q2).

mul(Quat4f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.util.Quat4f

Sets the value of this quaternion to the quaternion product of itself and q1 (this = this * q1).

mulInverse(Quat4f, Quat4f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.util.Quat4f

Multiplies quaternion q1 by the inverse of quaternion q2 and places the value into this quaternion.

mulInverse(Quat4f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.util.Quat4f

Multiplies this quaternion by the inverse of quaternion q1 and places the value into this quaternion.

multiplyMatrices(double[][], double[][]) - Static method in class edu.sdsc.mbt.util.Algebra

multiplySquareMatrices(double[], double[]) - Static method in class edu.sdsc.mbt.util.Algebra

Calculate a product of two matrices and return the result

muscleOutput - Static variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.AlignmentSettings

muscleOutputtree - Static variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.AlignmentSettings