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

G

GDT - Class in ProGAL.geom3d.superposition

GDT() - Constructor for class ProGAL.geom3d.superposition.GDT

generateAtoms(char) - Method in class ProGAL.proteins.structure.generators.AllAtomAminoAcidGenerator

generateAtoms(char) - Method in interface ProGAL.proteins.structure.generators.AtomGenerator

generateAtoms(char) - Method in class ProGAL.proteins.structure.generators.CABAminoAcidGenerator

generateAtoms(char) - Method in class ProGAL.proteins.structure.generators.HeavyAtomAminoAcidGenerator

generateBonds(AminoAcid[]) - Method in class ProGAL.proteins.structure.generators.AllAtomAminoAcidGenerator

generateBonds(AminoAcid[]) - Method in interface ProGAL.proteins.structure.generators.AtomGenerator

generateBonds(AminoAcid[]) - Method in class ProGAL.proteins.structure.generators.CABAminoAcidGenerator

generateBonds(AminoAcid[]) - Method in class ProGAL.proteins.structure.generators.HeavyAtomAminoAcidGenerator

generatePointsInCube(int) - Static method in class ProGAL.geom3d.PointList

Construct a point-list containing n uniformly distributed random points in the unit cube.

generatePointsInCube(int, double, double, double, double, double, double) - Static method in class ProGAL.geom3d.PointList

generatePointsInCube(int, int) - Static method in class ProGAL.geomNd.PointList

generatePointsOnSphere(int) - Static method in class ProGAL.geom3d.PointList

Construct a point-list of n evenly distributed points (not random) on the unit sphere.

generatePointsOnSphere(int) - Method in class ProGAL.geom3d.volumes.Sphere

TODO: Comment, move up and test

generateRandomPointsOnSphere(int) - Static method in class ProGAL.geom3d.PointList

Construct a point-list of n uniformly distributed random points on the unit sphere.

generateRandomPointsOnSphere(int) - Method in class ProGAL.geom3d.volumes.Sphere

TODO: Comment, move up and test

get(int) - Method in class ProGAL.dataStructures.Set

get(int) - Method in class ProGAL.geomNd.Point

Get the d'th coordinate.

get(int) - Method in class ProGAL.geomNd.Vector

Get the i'th coordinate.

get(int, int) - Method in class ProGAL.math.Matrix

getA() - Method in class ProGAL.geom2d.LineSegment

getA() - Method in class ProGAL.geom3d.LineSegment

Get the first point spanning the segment.

getA() - Method in class ProGAL.geom3d.surface.ParametricParaboloid

getAdjacentEdges() - Method in class ProGAL.geom3d.complex.CVertex

getAdjacentTetrahedra() - Method in class ProGAL.geom3d.complex.CVertex

getAdjacentTetrahedron(int) - Method in class ProGAL.geom3d.complex.CTriangle

getAdjacentTriangles() - Method in class ProGAL.geom3d.complex.CEdge

getAdjacentTriangles() - Method in class ProGAL.geom3d.complex.CVertex

getAllAdjacentTetrahedra() - Method in class ProGAL.geom3d.complex.CVertex

returns all tetrahedra adjacent to the vertex (including big tetrahedra)

getAllBackboneAtoms() - Method in class ProGAL.proteins.chainTree.ChainTree

Collect all backbone atoms using the leaves only.

getAllCavities(ArrayList<CTetrahedron>, int, J3DScene) - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaComplex

getAllCavityPaths(ArrayList<CTetrahedron>, J3DScene) - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaComplex

getAllDeepestCavityTetrahedra(int) - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaComplex

getAllEdges() - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaComplex

getAllPermutations(int) - Static method in class ProGAL.math.Combinatorics

Generates all permutations of integers from 0 (inclusive) to max (exclusive).

getAllSimplices() - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaComplex

getAllTessels() - Method in class ProGAL.geomNd.complex.delaunayComplex.BowyerWatson

Returns all tessels (including tessels with 'big points')

getAllTetrahedra() - Method in class ProGAL.geom3d.complex.delaunayComplex.DelaunayComplex

returns all tetrahedra (including tetrahedra with bigPoint

getAlpha() - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaComplex

getAlpha() - Method in class ProGAL.geom3d.complex.alphaComplex.Node

getAlphaShape(double) - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaFiltration

getAltitude(int) - Method in class ProGAL.geom2d.Triangle

getAnchor() - Method in class ProGAL.geom3d.volumes.OBB

getAngle(Point, Point, Point) - Static method in class ProGAL.geom3d.Point

Get the angle between the line segments p2->p1 and p2->p3.

getAngle(Vector, Vector) - Static method in class ProGAL.geom3d.Vector

Get the angle between vector u and v.

getAngle(Point, Point, Point) - Static method in class ProGAL.geomNd.Point

getAngle(Vector, Vector) - Static method in class ProGAL.geomNd.Vector

Get the angle between vector u and v.

getArea() - Method in class ProGAL.geom2d.LSC

getArea() - Method in class ProGAL.geom3d.Triangle

Return the area of one side of the triangle.

getAToB() - Method in class ProGAL.geom3d.LineSegment

Get the direction of the segment.

getAtom(int, String) - Method in class ProGAL.proteins.belta.PDBFile

getAtom(int, String) - Method in class ProGAL.proteins.PDBFile

getAtom(Point) - Method in class ProGAL.proteins.ProteinComplex

getAtomCoords() - Method in class ProGAL.proteins.PDBFile

Returns all atom-coordinates in the first chain in the first model.

getAtomCoords(String) - Method in class ProGAL.proteins.PDBFile

Returns the coordinates of the specified atom types.

getAtomCoords(int, int) - Method in class ProGAL.proteins.PDBFile

Returns all atom-coordinates of the specified model and chain.

getAtomPosition(int, int) - Method in class ProGAL.proteins.beltaStructure.sheet.SurfaceSheetStructure

Return the specified atom-position.

getAtomRecords() - Method in class ProGAL.proteins.PDBFile

Returns the ATOM-records.

getAtomRecords(String) - Method in class ProGAL.proteins.PDBFile

Returns the ATOM-records.

getAtomRecords(int, int) - Method in class ProGAL.proteins.PDBFile

Returns the ATOM-records of the specified model and chain.

getAtoms() - Method in class ProGAL.proteins.PDBFile.PDBChain

getAtomType(Point) - Method in class ProGAL.proteins.ProteinComplex

getAttached(Simplex) - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaFiltration

getB() - Method in class ProGAL.geom2d.LineSegment

getB() - Method in class ProGAL.geom3d.LineSegment

Get the second point spanning the segment.

getB() - Method in class ProGAL.geom3d.surface.ParametricParaboloid

getBackboneAtom(int, int) - Method in class ProGAL.proteins.chainTree.ChainTree

Return the position of a specific backbone atom.

getBackClip() - Method in class ProGAL.geom3d.viewer.Camera

getBackFog() - Method in class ProGAL.geom3d.viewer.Camera

getBases() - Method in class ProGAL.geom3d.volumes.OBB

getBest() - Method in class ProGAL.proteins.beltaStructure.bnb.BnBSolver

getBetaTopology() - Method in class ProGAL.proteins.belta.PDBFile

getBettiNumbers() - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaFiltration

Get the Betti-numbers of the alpha-filtration.

getBettiPersistence() - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaFiltration

TODO: Comment

getBigAdjacentTetrahedra() - Method in class ProGAL.geom3d.complex.CVertex

returns all big tetrahedra adjacent to the vertex

getBigTetrahedra() - Method in class ProGAL.geom3d.complex.delaunayComplex.DelaunayComplex

returns all big tetrahedra

getBin(double) - Method in class ProGAL.statistics.Histogram

getBisector(Point, Point) - Static method in class ProGAL.geom2d.Point

Creates a bisector between points p and q

getBisector(Point, Point) - Static method in class ProGAL.geom3d.Point

Creates a bisector between points p and q

getC() - Method in class ProGAL.geom3d.surface.ParametricParaboloid

getCACoords() - Method in class ProGAL.proteins.PDBFile

Returns the CA-coordinates of atoms in the first chain in the first model.

getCACoords(int, int) - Method in class ProGAL.proteins.PDBFile

Returns the CA-coordinates of the specified model and chain.

getCamera() - Method in class ProGAL.geom3d.viewer.J3DScene

getCanvas() - Method in class ProGAL.geom2d.viewer.J2DScene

Return the panel that this scene is painted on.

getCanvas() - Method in class ProGAL.geom3d.viewer.J3DScene

Get the canvas that displays the scene.

getCARecords() - Method in class ProGAL.proteins.PDBFile

Returns the ATOM-records of CA-atoms.

getCARecords(int, int) - Method in class ProGAL.proteins.PDBFile

Returns the CA ATOM-records of the specified model and chain.

getCavities() - Method in class ProGAL.proteins.ProteinComplex

getCavity(CTetrahedron, int, J3DScene) - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaComplex

getCavityPath(CTetrahedron, J3DScene) - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaComplex

getCenter() - Method in class ProGAL.geom2d.Circle

getCenter() - Method in class ProGAL.geom2d.Line

getCenter() - Method in class ProGAL.geom2d.LineSegment

getCenter() - Method in class ProGAL.geom2d.LSC

getCenter() - Method in class ProGAL.geom2d.Polygon

getCenter() - Method in interface ProGAL.geom2d.Shape

Get the geometric center of the shape.

getCenter() - Method in class ProGAL.geom2d.Triangle

getCenter() - Method in class ProGAL.geom2d.viewer.TextShape

getCenter() - Method in class ProGAL.geom3d.Circle

Get the center of the circle.

getCenter() - Method in class ProGAL.geom3d.LineSegment

Returns the mid-point of this line-segment.

getCenter() - Method in class ProGAL.geom3d.Plane

Returns the defining point for this plane.

getCenter() - Method in class ProGAL.geom3d.Point

Returns a clone of this point.

getCenter() - Method in interface ProGAL.geom3d.Shape

Get the geometric center of the shape.

getCenter() - Method in class ProGAL.geom3d.surface.ParametricSurface

getCenter() - Method in class ProGAL.geom3d.Triangle

Return the center of the triangle.

getCenter() - Method in class ProGAL.geom3d.viewer.TextShape

getCenter() - Method in class ProGAL.geom3d.volumes.Cone

getCenter() - Method in class ProGAL.geom3d.volumes.Cylinder

getCenter() - Method in class ProGAL.geom3d.volumes.Lens

getCenter() - Method in class ProGAL.geom3d.volumes.LSS

getCenter() - Method in class ProGAL.geom3d.volumes.OBB

getCenter() - Method in class ProGAL.geom3d.volumes.RSS

getCenter() - Method in class ProGAL.geom3d.volumes.Sphere

Get the center

getCenter() - Method in class ProGAL.geom3d.volumes.Tetrahedron

getCenter() - Method in class ProGAL.geomNd.HyperSphere

getCenter() - Method in class ProGAL.proteins.viewer.CoilSurface

getCenter() - Method in class ProGAL.proteins.viewer.HelixSurface

getCenter() - Method in class ProGAL.proteins.viewer.StrandSurface

getCentroid() - Method in class ProGAL.geom2d.PointSet

getCentroid() - Method in class ProGAL.geom3d.PointList

Get the centroid of the points.

getCentroid() - Method in class ProGAL.geomNd.PointList

Get the centroid of the points.

getChain() - Method in class ProGAL.proteins.beltaStructure.bnb.BnBSolver

getChain(int, int) - Method in class ProGAL.proteins.PDBFile

getChains() - Method in class ProGAL.proteins.PDBFile.PDBModel

getCircumCenter(Point, Point, Point) - Static method in class ProGAL.geom3d.Point

getCircumCircle() - Method in class ProGAL.geom2d.Triangle

getCircumCircle() - Method in class ProGAL.geom2d.TriangulationFace

getClickListeners() - Method in class ProGAL.geom3d.viewer.J3DScene

getClosestPoint(Point) - Method in class ProGAL.geom3d.LineSegment

Get the point on the segment closest to a given point q.

getCoils() - Method in class ProGAL.proteins.belta.SecondaryStructure

Return array containing all segments, s, where s.type==SSType.COIL.

getColumn(int) - Method in class ProGAL.math.Matrix

getColumn(int) - Method in class ProGAL.math.Matrix3x3

getCommonTriangle(Tetrahedron) - Method in class ProGAL.geom3d.volumes.Tetrahedron

Return common triangle of 2 tetrahedra

getCommonVertices(CTetrahedron) - Method in class ProGAL.geom3d.complex.CTetrahedron

returns the vertices shared by two tetrahedra.

getCommonVertices(Tessel) - Method in class ProGAL.geomNd.complex.Tessel

getControlPanel() - Method in class ProGAL.geom3d.viewer.Camera

getConvexHull(List<Point>) - Static method in class ProGAL.geom2d.convexHull.DivideAndConquer

getConvexHull(List<Point>) - Static method in class ProGAL.geom2d.convexHull.GrahamScan

getConvexPolygon() - Method in class ProGAL.geom2d.Polygon

returns convex hull of a simple polygon in O(n) time

getCoord(int, int) - Method in class ProGAL.geom3d.PointList

Returns the i'th coordinate of k'th point.

getCoord(int) - Method in class ProGAL.geomNd.Point

Get the d'th coordinate.

getCoord(int, int) - Method in class ProGAL.geomNd.PointList

Returns the i'th coordinate of k'th point.

getCoord(int) - Method in class ProGAL.geomNd.Vector

Get the i'th coordinate.

getCoords() - Method in class ProGAL.geom2d.Vector

getCoords() - Method in class ProGAL.geomNd.Point

Get all coordinates in an array.

getCoords() - Method in class ProGAL.math.Matrix

getCorner(int) - Method in class ProGAL.geom2d.Polygon

getCorner(int) - Method in class ProGAL.geom2d.Triangle

getCorner(int) - Method in class ProGAL.geom2d.TriangulationFace

getCorner(int) - Method in class ProGAL.geom3d.Triangle

Get the specified corner of this triangle

getCorner(int) - Method in class ProGAL.geom3d.volumes.Tetrahedron

Return the specified corner.

getCorners() - Method in class ProGAL.geom2d.TriangulationFace

getCorners() - Method in class ProGAL.geom3d.Rectangle

Return corners of rectangle in counter-clockwise order.

getCorners() - Method in class ProGAL.geom3d.volumes.Tetrahedron

Return all four corners

getCos(int) - Method in class ProGAL.geom2d.Triangle

returns the cosinus of the angle opposite to the vertex with vertex i

getCosAngle() - Method in class ProGAL.geom2d.TriangulationVertex

getCosDihedralAngle(Point, Point, Point, Point) - Static method in class ProGAL.geom3d.Point

getCosDihedralAngle(Vector, Vector, Vector) - Static method in class ProGAL.geom3d.Vector

getCount() - Method in class ProGAL.geom2d.TriangulationFace

getCovariance() - Method in class ProGAL.geom3d.PointList

Get the covariance of the points.

getCovariance() - Method in class ProGAL.geomNd.PointList

Get the covariance of the points.

getCPUTime() - Method in class ProGAL.Benchmark

Returns the threads current CPU-time in ms.

getD() - Method in class ProGAL.math.Matrix.EigenvalueDecomposition

Return the block diagonal eigenvalue matrix.

getDeath() - Method in class ProGAL.geom3d.complex.alphaComplex.Node

getDeepestCavityTetrahedron() - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaComplex

getDefinedResidues(BnBNode) - Method in class ProGAL.proteins.beltaStructure.bnb.BnBSolver

getDegCase() - Method in class ProGAL.geom3d.complex.CVertex

getDegPointA() - Method in class ProGAL.geom3d.complex.CVertex

getDegPointB() - Method in class ProGAL.geom3d.complex.CVertex

getDegPointOpposite() - Method in class ProGAL.geom3d.complex.CVertex

getDepth(Simplex) - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaComplex

Return the depth of simplex from the surface of the alpha complex.

getDiameter() - Method in class ProGAL.geom2d.ConvexPolygon

returns the segment between most distant pair of points.

getDiameter() - Method in class ProGAL.geom3d.PointList

Get the diameter of the point set - trivial O(n^2) algorithm.

getDihedralAngle(Point, Point, Point, Point) - Static method in class ProGAL.geom3d.Point

Get the dihedral angle defined by the 4 non-collinear points p1, p2, p3, p4.

getDihedralAngle(Vector, Vector, Vector) - Static method in class ProGAL.geom3d.Vector

Get the dihedral angle between 3 non-colinear vectors b1, b2, b3.

getDim(Simplex) - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaFiltration

getDim() - Method in class ProGAL.geomNd.complex.delaunayComplex.BowyerWatson

The dimension of the tessellation

getDimension() - Method in class ProGAL.geom3d.LineSegment

Return the 'dimension' of this object.

getDimension() - Method in class ProGAL.geom3d.Point

Return the 'dimension' of this object.

getDimension() - Method in interface ProGAL.geom3d.Simplex

getDimension() - Method in class ProGAL.geom3d.Triangle

Return the 'dimension' of this object.

getDimension() - Method in class ProGAL.geom3d.volumes.Tetrahedron

Return the 'dimension' of this object.

getDimensions() - Method in class ProGAL.geomNd.Point

Return the dimensionality of this point.

getDimensions() - Method in class ProGAL.geomNd.Vector

Get the dimensionality of this vector

getDir() - Method in class ProGAL.geom3d.Line

Returns the direction vector defining this line.

getDirection() - Method in class ProGAL.geom2d.Line

getDisplacement() - Method in class ProGAL.geom3d.surface.ParametricParaboloid

getDistance(Point) - Method in class ProGAL.geom2d.Line

returns the distance of the point q to the line

getDistance(LineSegment) - Method in class ProGAL.geom2d.Point

returns distance of this point to segment s

getDistance(Point) - Method in class ProGAL.geom3d.Line

Gets the orthogonal distance to a point.

getDistance(Point) - Method in class ProGAL.geom3d.LineSegment

Gets the distance from q to the nearest point on this segment.

getDistance(Point) - Method in class ProGAL.geom3d.Plane

Gets perpendicular distance of point to this plane

getDistanceSquared(Point) - Method in class ProGAL.geom3d.Line

Gets the squared orthogonal distance to a point.

getDistribution() - Static method in class ProGAL.proteins.dunbrack.RamachandranDistribution

getDoublePivot() - Method in class ProGAL.math.LUDecomposition

Return pivot permutation vector as a one-dimensional double array

getEdge(int) - Method in class ProGAL.geom3d.complex.CTriangle

getEdges() - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaComplex

getEdges() - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaFiltration

getEdges(double) - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaFiltration

Get a list of edges that are part of the alpha-complex with the specified probe radius.

getEdges() - Method in class ProGAL.geom3d.complex.delaunayComplex.DelaunayComplex

Get the edges in the complex.

getEdges() - Method in interface ProGAL.geom3d.complex.SimplicialComplex

getEdges() - Method in class ProGAL.proteins.ProteinComplex

getEdgeShape(int) - Method in class ProGAL.geom2d.TriangulationFace

getEigenvalueDecomposition() - Method in class ProGAL.math.Matrix

getEigenvectors() - Method in class ProGAL.math.Matrix3x3

Get the eigenvectors of a 3x3 matrix sorted by decreasing eigenvalue.

getElements() - Method in class ProGAL.dataStructures.Set

getEntry() - Method in class ProGAL.dataStructures.DLCyclicList

getEquilateralCircle(Point, Point) - Static method in class ProGAL.geom3d.Circle

Create the equilateral circle of two points.

getEquilateralPoint(Point, Point, Point) - Static method in class ProGAL.geom3d.Point

getExtreme(Vector) - Method in class ProGAL.geom3d.PointList

Get the most extreme point in the direction specified by the vector.

getExtremeBack() - Method in class ProGAL.geom3d.PointList

Get the deepest point (in case of ties the left topmost point is returned).

getExtremeBottom() - Method in class ProGAL.geom3d.PointList

Get the lowest point (in case of ties the bottom rightmost point is returned).

getExtremeFront() - Method in class ProGAL.geom3d.PointList

Get the frontmost point (in case of ties the front rightmost point is returned).

getExtremeIndex(Vector) - Method in class ProGAL.geom3d.PointList

Get the most extreme point in the direction specified by the vector.

getExtremeIndex(int, int, int, boolean) - Method in class ProGAL.geom3d.PointList

Get the index of the extreme point.

getExtremeLeft() - Method in class ProGAL.geom3d.PointList

Get the leftmost point (in case of ties the bottom lefttmost point is returned).

getExtremeRight() - Method in class ProGAL.geom3d.PointList

Get the rightmost point (in case of ties the top rightmost point is returned).

getExtremeTop() - Method in class ProGAL.geom3d.PointList

Get the highest point (in case of ties the left topmost point is returned).

getFace() - Method in class ProGAL.geom2d.TriangulationVertex

getFaces() - Method in class ProGAL.geom2d.TriangulationVertex

getFirst() - Method in class ProGAL.dataStructures.DLCyclicList

getFirst() - Method in class ProGAL.dataStructures.DLList

getFirst() - Method in class ProGAL.dataStructures.Set

getFirstIntersection(Line, Point, Vector, J3DScene) - Method in class ProGAL.geom3d.Circle

returns the smallest rotation angle (direction determined by vector dir) needed to bring point p on this circle to be on the line l as well.

getFirstIntersection(Circle, Point, Vector) - Method in class ProGAL.geom3d.Circle

returns the smallest rotation angle (direction determined by vector dir) needed to bring point p on this circle to be on the circle c as well.

getFocalDistance(int) - Method in class ProGAL.geom3d.volumes.Lens

The distance from a focal point to the equator of the lens

getFrontClip() - Method in class ProGAL.geom3d.viewer.Camera

getFrontFog() - Method in class ProGAL.geom3d.viewer.Camera

getGDT(List<Point>, List<Point>, double) - Static method in class ProGAL.geom3d.superposition.GDT

getGDT(List<Point>, List<Point>, double, int) - Static method in class ProGAL.geom3d.superposition.GDT

getGenerator() - Static method in class ProGAL.math.Randomization

getHeight() - Method in class ProGAL.geom2d.viewer.TextShape

getHelices() - Method in class ProGAL.proteins.belta.SecondaryStructure

Return array containing all segments, s, where s.type==SSType.HELIX.

getHetatmRecords() - Method in class ProGAL.proteins.PDBFile

getHetatmRecords(int, int) - Method in class ProGAL.proteins.PDBFile

Returns the HETATM-records of the specified model and chain.

getHoles() - Method in class ProGAL.proteins.ProteinComplex

getHoles(double) - Method in class ProGAL.proteins.ProteinComplex

getId() - Method in class ProGAL.geom2d.TriangulationFace

getId() - Method in class ProGAL.geom2d.TriangulationVertex

getID(CVertex) - Method in class ProGAL.geom3d.complex.CTetrahedron

getID(Vertex) - Method in class ProGAL.geomNd.complex.Tessel

getImagEigenvalues() - Method in class ProGAL.math.Matrix.EigenvalueDecomposition

Return the imaginary parts of the eigenvalues imag(diag(D)).

getInAlpha(Simplex) - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaFiltration

Return the probe-radius at which the simplex s enters the alpha complex.

getInAlphaComplex() - Method in class ProGAL.geom3d.complex.alphaComplex.EdgeAlphaProperties

getInAlphaComplex() - Method in interface ProGAL.geom3d.complex.alphaComplex.SimplexAlphaProperties

getInAlphaComplex() - Method in class ProGAL.geom3d.complex.alphaComplex.TetrahedronAlphaProperties

getInAlphaComplex() - Method in class ProGAL.geom3d.complex.alphaComplex.TriangleAlphaProperties

getInAlphaComplex() - Method in class ProGAL.geom3d.complex.alphaComplex.VertexAlphaProperties

getIndex(TriangulationVertex) - Method in class ProGAL.geom2d.TriangulationFace

returns the index of the specified vertex in the face

getIndex(TriangulationFace) - Method in class ProGAL.geom2d.TriangulationFace

returns the index of the specified neighbor face

getInradius() - Method in class ProGAL.geom3d.volumes.Tetrahedron

Calculate the radius of the insphere.

getInstance() - Static method in class ProGAL.geom3d.tessellation.BowyerWatson.BigDecimalPredicates

getInstance() - Static method in class ProGAL.geom3d.tessellation.BowyerWatson.ShewchuckPredicates

getInteriorInterval() - Method in class ProGAL.geom3d.complex.alphaComplex.EdgeAlphaProperties

getInteriorInterval() - Method in class ProGAL.geom3d.complex.alphaComplex.TetrahedronAlphaProperties

getInteriorInterval() - Method in class ProGAL.geom3d.complex.alphaComplex.TriangleAlphaProperties

getInteriorInterval() - Method in class ProGAL.geom3d.complex.alphaComplex.VertexAlphaProperties

getIntersection(Line, Line) - Static method in class ProGAL.geom2d.Line

getIntersection(Circle) - Method in class ProGAL.geom3d.Circle

Intersection of 2 circles in the same plane

getIntersection(Line) - Method in class ProGAL.geom3d.Line

Gets the intersection-point of this line with l.

getIntersection(Line) - Method in class ProGAL.geom3d.Plane

Get the intersection of a line with the plane.

getIntersection(LineSegment) - Method in class ProGAL.geom3d.Plane

Get the intersection of a segment with the plane.

getIntersection(Circle) - Method in class ProGAL.geom3d.Plane

Get intersection of a circle with the plane.

getIntersection(Circle, Vector) - Method in class ProGAL.geom3d.Plane

getIntersection(Plane) - Method in class ProGAL.geom3d.Plane

returns the intersection line with another plane

getIntersection(Sphere) - Method in class ProGAL.geom3d.Plane

Get intersection of a sphere with the plane.

getIntersection(Point, Vector) - Method in class ProGAL.geom3d.Triangle

getIntersection(Line) - Method in class ProGAL.geom3d.volumes.Sphere

Gets the secant on the line.

getIntersectionAngle(Circle, Point, Vector, J3DScene) - Method in class ProGAL.geom3d.Plane

getIntersectionAngle(Circle, Point, Vector) - Method in class ProGAL.geom3d.volumes.Sphere

getIntersectionParameter(Line) - Method in class ProGAL.geom3d.Plane

Get the line-parameter of the intersection between a plane and a line.

getIntersections(Circle) - Method in class ProGAL.geom3d.volumes.Sphere

getIntersections(Sphere, Sphere, Sphere) - Static method in class ProGAL.geom3d.volumes.Sphere

Find the two, one or zero points that is at the intersection of the three sphere shells.

getItem(int) - Method in class ProGAL.dataStructures.Heap

returns the i-th object in the binary heap.

getL() - Method in class ProGAL.math.LUDecomposition

Return lower triangular factor

getLast() - Method in class ProGAL.dataStructures.Set

getLastFace() - Method in class ProGAL.geom2d.TriangulationVertex

getLeaves(Node) - Method in class ProGAL.geom3d.complex.alphaComplex.VoidTree

getLeft() - Method in class ProGAL.geom3d.complex.alphaComplex.Interval

getLength() - Method in class ProGAL.geom2d.LineSegment

returns the length of the line segment

getLength() - Method in class ProGAL.geom3d.LineSegment

Get the length of the segment.

getLength() - Method in class ProGAL.geom3d.volumes.Cylinder

getLengthSquared() - Method in class ProGAL.geom3d.LineSegment

Get the squared length of the segment.

getLengthSquared() - Method in class ProGAL.geomNd.Vector

Get the squared length of this vector.

getLocation() - Method in class ProGAL.geom3d.viewer.Camera

getLookingAt() - Method in class ProGAL.geom3d.viewer.Camera

getLoopTransform(SecondaryStructure.SSSegment) - Method in class ProGAL.proteins.beltaStructure.sheet.SurfaceSheetStructure

TODO

getM() - Method in class ProGAL.math.Matrix

getMaxDistance(PointList) - Method in class ProGAL.geom3d.Line

Gets the largest distance from the points to the line.

getMaxDistanceSquared(PointList) - Method in class ProGAL.geom3d.Line

Gets the largest squared distance from the points to the line.

getMidPoint() - Method in class ProGAL.geom3d.LineSegment

Gets the midpoint of the segment.

getMidpoint(Point, Point) - Static method in class ProGAL.geom3d.Point

Creates the midpoint of two points.

getMidpoint(Point, Point) - Static method in class ProGAL.geomNd.Point

Creates the midpoint of two points.

getMinSphere(Circle) - Static method in class ProGAL.geom3d.volumes.Sphere

Get the sphere with the specified circle as equator

getMinSphere(Point, Point) - Static method in class ProGAL.geom3d.volumes.Sphere

Get the smallest sphere through two given points.

getMinSphere(Point, Point, Point) - Static method in class ProGAL.geom3d.volumes.Sphere

Get the smallest sphere through three points.

getMinSphere(Point, Point, Point, Point) - Static method in class ProGAL.geom3d.volumes.Sphere

Constructs the sphere through four points.

getMinSphere(PointList) - Static method in class ProGAL.geom3d.volumes.Sphere

Gets the smallest sphere containing a set of points.

getModels() - Method in class ProGAL.proteins.PDBFile

getN() - Method in class ProGAL.math.Matrix

getNeighbor(int) - Method in class ProGAL.geom2d.TriangulationFace

getNeighboringVertices() - Method in class ProGAL.geom2d.TriangulationVertex

getNeighbour(int) - Method in class ProGAL.geom3d.complex.CTetrahedron

getNeighbour(CVertex) - Method in class ProGAL.geom3d.complex.CTetrahedron

returns neighbour tetrahedron containing specified vertex

getNeighbour(int) - Method in class ProGAL.geomNd.complex.Tessel

getNext() - Method in class ProGAL.dataStructures.DLCyclicList.DLNode

Return next node of the doubly linked list

getNextExtremePoint(Point) - Method in class ProGAL.geom2d.PointSet

returns next extreme point of the point set (counterclockwise)

getNextFace(TriangulationFace) - Method in class ProGAL.geom2d.TriangulationVertex

getNormal() - Method in class ProGAL.geom3d.Circle

getNormal() - Method in class ProGAL.geom3d.Plane

Return the normal defining this plane.

getNormal(double, double) - Method in class ProGAL.geom3d.surface.ParametricSurface

getNormal(Point) - Method in class ProGAL.geom3d.surface.ParametricSurface

getNormal() - Method in class ProGAL.geom3d.Triangle

Return a vector that is normal to this triangle.

getNormal(double, double) - Method in class ProGAL.proteins.beltaStructure.sheet.ParametricSurface

getNormal(Point) - Method in class ProGAL.proteins.beltaStructure.sheet.ParametricSurface

getNormal(double, double) - Method in class ProGAL.proteins.viewer.CoilSurface

getNormal(double, double) - Method in class ProGAL.proteins.viewer.HelixSurface

getNormal(double, double) - Method in class ProGAL.proteins.viewer.StrandSurface

getNormalizedStrandOrder() - Method in class ProGAL.proteins.belta.SheetTopology

Return an array indicating the normalized strand order.

getNormalVector() - Method in class ProGAL.geom3d.Circle

Get the normal of the circle.

getNumberBigPoints() - Method in class ProGAL.geom3d.complex.CTetrahedron

getObject() - Method in class ProGAL.dataStructures.DLCyclicList.DLNode

Returns the object represented by the node

getObjects() - Method in class ProGAL.dataStructures.Heap

getOnCH(Simplex) - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaFiltration

Return true iff the simplex is on the convex hull.

getOnConvexHull() - Method in class ProGAL.geom3d.complex.alphaComplex.EdgeAlphaProperties

getOnConvexHull() - Method in class ProGAL.geom3d.complex.alphaComplex.TriangleAlphaProperties

getOnConvexHull() - Method in class ProGAL.geom3d.complex.alphaComplex.VertexAlphaProperties

getOppFace(TriangulationVertex) - Method in class ProGAL.geom2d.TriangulationFace

returns the face opposite the vertex v in this face, null if such face does not exist

getOppLine(TriangulationVertex) - Method in class ProGAL.geom2d.TriangulationFace

getOppositeTriangles() - Method in class ProGAL.geom3d.complex.CVertex

getOrbit(Point) - Method in class ProGAL.geom2d.TriangulationVertex

getOrthonormal() - Method in class ProGAL.geom3d.Vector

Get a vector (one of many possible) orthonormal to vector v.

getP() - Method in class ProGAL.geom3d.Line

Returns the point defining this line.

getP() - Method in class ProGAL.geom3d.ParametricPlane

getP(double[]) - Method in class ProGAL.geom3d.ParametricPlane

getP1() - Method in class ProGAL.geom3d.Triangle

Get the first corner

getP2() - Method in class ProGAL.geom3d.Triangle

Get the second corner

getP3() - Method in class ProGAL.geom3d.Triangle

Get the third corner

getPairSimplices() - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaFiltration

TODO: Comment

getParallel() - Method in class ProGAL.geom3d.viewer.Camera

getPivot() - Method in class ProGAL.math.LUDecomposition

Return pivot permutation vector

getPlane(CTetrahedron) - Method in class ProGAL.geom3d.complex.CTetrahedron

returns plane through common triangle of this and another tetrahedron.

getPlane() - Method in class ProGAL.geom3d.Rectangle

getPoint(double) - Method in class ProGAL.geom2d.Line

returns the point on the line at distance d from the line-defining point p

getPoint(int) - Method in class ProGAL.geom3d.complex.CEdge

getPoint(int) - Method in class ProGAL.geom3d.complex.CTetrahedron

getPoint(double) - Method in class ProGAL.geom3d.Line

Gets the point on the line defined by the specified parameter.

getPoint(int) - Method in class ProGAL.geom3d.LineSegment

TODO: Comment and test

getPoint() - Method in class ProGAL.geom3d.Plane

Get the point defining this plane.

getPoint(int) - Method in class ProGAL.geom3d.Point

getPoint(int) - Method in interface ProGAL.geom3d.Simplex

TODO: Comment

getPoint(double, double) - Method in class ProGAL.geom3d.surface.ParametricParaboloid

getPoint(Point) - Method in class ProGAL.geom3d.surface.ParametricParaboloid

getPoint(double, double) - Method in class ProGAL.geom3d.surface.ParametricPlane

getPoint(double, double) - Method in class ProGAL.geom3d.surface.ParametricSurface

getPoint(Point) - Method in class ProGAL.geom3d.surface.ParametricSurface

getPoint(int) - Method in class ProGAL.geom3d.Triangle

Get the specified corner-point of this triangle

getPoint(int) - Method in class ProGAL.geom3d.volumes.Tetrahedron

Return the specified corner-point.

getPoint(int) - Method in class ProGAL.geomNd.complex.Tessel

getPoint(double, double) - Method in class ProGAL.proteins.beltaStructure.sheet.ParametricSurface

getPoint(Point) - Method in class ProGAL.proteins.beltaStructure.sheet.ParametricSurface

getPoint(double, double) - Method in class ProGAL.proteins.viewer.CoilSurface

getPoint(double, double) - Method in class ProGAL.proteins.viewer.HelixSurface

getPoint(double, double) - Method in class ProGAL.proteins.viewer.StrandSurface

getPoints() - Method in class ProGAL.geomNd.complex.Tessel

getPolarAngle() - Method in class ProGAL.geom2d.TriangulationVertex

getPolarRadius() - Method in class ProGAL.geom2d.TriangulationVertex

getPos() - Method in class ProGAL.geom2d.viewer.TextShape

getPrev() - Method in class ProGAL.dataStructures.DLCyclicList.DLNode

Returns previous node of the doubly linked list

getPrevFace(TriangulationFace) - Method in class ProGAL.geom2d.TriangulationVertex

getRadius() - Method in class ProGAL.geom2d.Circle

getRadius() - Method in class ProGAL.geom2d.LSC

getRadius() - Method in class ProGAL.geom3d.Circle

Get the radius of the circle.

getRadius() - Method in class ProGAL.geom3d.volumes.Cylinder

getRadius() - Method in class ProGAL.geom3d.volumes.Lens

Radius of the equator of the lens

getRadius() - Method in class ProGAL.geom3d.volumes.Sphere

Get the radius

getRadius() - Method in class ProGAL.geomNd.HyperSphere

getRadiusSquared() - Method in class ProGAL.geom3d.volumes.Sphere

Get the squared radius

getRandomPermutation() - Method in class ProGAL.geom3d.PointList

Returns a new point-list containing all the elements in random order.

getRandomPermutation() - Method in class ProGAL.geomNd.PointList

Returns a new point-list containing all the elements in random order.

getRealEigenvalues() - Method in class ProGAL.math.Matrix.EigenvalueDecomposition

Return the real parts of the eigenvalues real(diag(D)).

getRecords() - Method in class ProGAL.proteins.PDBFile

Returns all records of the specified model and chain.

getRegularInterval() - Method in class ProGAL.geom3d.complex.alphaComplex.EdgeAlphaProperties

getRegularInterval() - Method in class ProGAL.geom3d.complex.alphaComplex.TriangleAlphaProperties

getRegularInterval() - Method in class ProGAL.geom3d.complex.alphaComplex.VertexAlphaProperties

getRemarkRecords() - Method in class ProGAL.proteins.PDBFile

Returns all REMARK records.

getResolution() - Method in class ProGAL.proteins.PDBFile

getRest() - Method in class ProGAL.geom3d.complex.alphaComplex.VoidTree

getRight() - Method in class ProGAL.geom3d.complex.alphaComplex.Interval

getRMSD(List<Point>, List<Point>) - Static method in class ProGAL.geom3d.superposition.FastRMSD

getRMSD(List<Point>, List<Point>) - Static method in class ProGAL.geom3d.superposition.RMSD

getRMSD(List<Point>, List<Point>) - Static method in class ProGAL.geom3d.superposition.Superposition

getRotation() - Method in class ProGAL.geom3d.surface.ParametricParaboloid

getRow(int) - Method in class ProGAL.math.Matrix

getRow(int) - Method in class ProGAL.math.Matrix3x3

getS() - Method in class ProGAL.math.SingularValueDecomposition

Return the diagonal matrix of singular values

getSecondaryStructure() - Method in class ProGAL.proteins.belta.PDBFile

getSegment() - Method in class ProGAL.geom2d.LSC

getSegment() - Method in class ProGAL.geom3d.volumes.Cylinder

getSegmentContainingResidue(int) - Method in class ProGAL.proteins.belta.SecondaryStructure

TODO: Comment and test

getSequence() - Method in class ProGAL.proteins.PDBFile

getSheets() - Method in class ProGAL.proteins.belta.BetaTopology

Construct a list of sheet-topologies from the beta-topology.

getSignedAngle(Point, Point, Point) - Static method in class ProGAL.geom2d.Point

Returns the angle between the points, but if they make a left turn the angle will be negative.

getSimplexType() - Method in class ProGAL.geom3d.complex.alphaComplex.EdgeAlphaProperties

getSimplexType() - Method in interface ProGAL.geom3d.complex.alphaComplex.SimplexAlphaProperties

getSimplexType() - Method in class ProGAL.geom3d.complex.alphaComplex.TetrahedronAlphaProperties

getSimplexType() - Method in class ProGAL.geom3d.complex.alphaComplex.TriangleAlphaProperties

getSimplexType() - Method in class ProGAL.geom3d.complex.alphaComplex.VertexAlphaProperties

getSimplices() - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaComplex

getSimplices() - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaFiltration

getSimplices(double) - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaFiltration

Get a list of simplices that are part of the alpha-complex with the specified probe radius.

getSinAngle() - Method in class ProGAL.geom2d.TriangulationVertex

getSingleCharAAType() - Method in class ProGAL.proteins.PDBFile.AtomRecord

getSingleCharAAType() - Method in class ProGAL.proteins.PDBFile.TerRecord

getSingularInterval() - Method in class ProGAL.geom3d.complex.alphaComplex.EdgeAlphaProperties

getSingularInterval() - Method in class ProGAL.geom3d.complex.alphaComplex.TriangleAlphaProperties

getSingularInterval() - Method in class ProGAL.geom3d.complex.alphaComplex.VertexAlphaProperties

getSingularValues() - Method in class ProGAL.math.SingularValueDecomposition

Return the one-dimensional array of singular values.

getSize() - Method in class ProGAL.dataStructures.DLCyclicList

Returns the number of elements in this cyclic list.

getSize() - Method in class ProGAL.dataStructures.DLList

getSize() - Method in class ProGAL.dataStructures.Heap

getSize() - Method in class ProGAL.dataStructures.Set

getSlope() - Method in class ProGAL.geom2d.Line

getSlope() - Method in class ProGAL.geom2d.Vector

getSphereCenter(int) - Method in class ProGAL.geom3d.volumes.Lens

getSphereRadius(int) - Method in class ProGAL.geom3d.volumes.Lens

getSquaredDistance() - Method in class ProGAL.geom2d.Point

returns squared distance of this point to the origo.

getSquaredDistance(Point) - Method in class ProGAL.geom2d.Point

returns squared distance of this point to point q.

getSquaredDistance(LineSegment) - Method in class ProGAL.geom2d.Point

returns squared distance of this point to segment s

getSquaredDistance(Line) - Method in class ProGAL.geom3d.Line

Gets the minimum squared distance to another line.

getSquaredDistance(Point) - Method in class ProGAL.geom3d.LineSegment

Gets the squared distance from q to the nearest point on this segment.

getSquaredLength() - Method in class ProGAL.geom2d.LineSegment

returns the squared length of the segment

getSquaredLength() - Method in class ProGAL.geom2d.Vector

getSquaredPolarRadius() - Method in class ProGAL.geom2d.TriangulationVertex

getStandardDeviation() - Method in class ProGAL.geom3d.PointList

Get the standard deviation of the point set.

getStandardDeviation() - Method in class ProGAL.geomNd.PointList

Get the standard deviation of the point set.

getSteinerPoint(Point, Point, Point) - Static method in class ProGAL.geom3d.Point

getStrandOrder() - Method in class ProGAL.proteins.belta.SheetTopology

Return an array indicating the strand order.

getStrandOrderString() - Method in class ProGAL.proteins.belta.SheetTopology

String representation of strand order.

getStrandOrientation() - Method in class ProGAL.proteins.belta.SheetTopology

Return an array indicating orientation of strands.

getStrandOrientationString() - Method in class ProGAL.proteins.belta.SheetTopology

String representation of strand orientation.

getStrands() - Method in class ProGAL.proteins.belta.SecondaryStructure

Return array containing all segments, s, where s.type==SSType.STRAND.

getStructures() - Method in interface ProGAL.proteins.beltaStructure.bnb.Branchable

getStructures() - Method in class ProGAL.proteins.beltaStructure.bnb.SegmentStructure

Return the number of structures in this segment.

getStructures() - Method in class ProGAL.proteins.beltaStructure.bnb.SheetStructure

getSubList(int, int) - Method in class ProGAL.geom3d.PointList

Returns a sub-list of elements from (including) from to (not including) to.

getSubList(int, int) - Method in class ProGAL.geomNd.PointList

Returns a sub-list of elements from (including) from to (not including) to.

getSubmatrix(int, int, int, int) - Method in class ProGAL.math.Matrix

getSurface() - Method in class ProGAL.proteins.beltaStructure.sheet.SurfaceSheetStructure

Return a reference to the surface that specifies this sheets structure.

getSurfaceArea() - Method in class ProGAL.geom3d.volumes.Cylinder

getSurfaceArea() - Method in class ProGAL.geom3d.volumes.Sphere

Get the surface area

getSurfaceTriangles(double) - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaFiltration

Returns triangles in one tetrahedron only

getTessels() - Method in class ProGAL.geomNd.complex.delaunayComplex.BowyerWatson

Get the tesselts in the complex.

getTetra() - Method in class ProGAL.geom3d.complex.alphaComplex.Node

getTetrahedra() - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaComplex

getTetrahedra() - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaFiltration

getTetrahedra(double) - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaFiltration

Get a list of tetrahedra that are part of the alpha-complex with the specified probe radius.

getTetrahedra(double, double) - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaFiltration

Get a list of tetrahedra that are part of the alpha-complex with the probe radius in a specified interval.

getTetrahedra() - Method in class ProGAL.geom3d.complex.delaunayComplex.DelaunayComplex

Get the tetrahedra in the complex.

getTetrahedra() - Method in interface ProGAL.geom3d.complex.SimplicialComplex

getTetrahedra() - Method in class ProGAL.geom3d.complex.tessellation.DelaunayTessellation

Get the tetrahedra in the complex.

getTetrahedra() - Method in class ProGAL.proteins.ProteinComplex

getText() - Method in class ProGAL.geom2d.viewer.TextShape

getThirdVertex(TriangulationVertex, TriangulationVertex) - Method in class ProGAL.geom2d.TriangulationFace

returns third vertex of the face

getThirdVertex(TriangulationFace) - Method in class ProGAL.geom2d.TriangulationFace

returns vertex of the face not in this.face

getThreeLetterType(int) - Method in class ProGAL.proteins.belta.PrimaryStructure

getTorsionAngle(int, int) - Method in class ProGAL.proteins.chainTree.ChainTree

Return the torsion angle of the specified residue and bond.

getTranspose() - Method in class ProGAL.math.Matrix

Get the transpose of this matrix

getTranspose() - Method in class ProGAL.math.Matrix3x3

getTriangle() - Method in class ProGAL.geom2d.TriangulationFace

getTriangle(int) - Method in class ProGAL.geom3d.complex.CTetrahedron

getTriangles() - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaComplex

getTriangles() - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaFiltration

getTriangles(double) - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaFiltration

Get a list of triangles that are part of the alpha-complex with the specified probe radius.

getTriangles() - Method in class ProGAL.geom3d.complex.delaunayComplex.DelaunayComplex

Get the triangles in the complex.

getTriangles() - Method in interface ProGAL.geom3d.complex.SimplicialComplex

getTriangles() - Method in class ProGAL.proteins.ProteinComplex

getType() - Method in class ProGAL.geom2d.TriangulationVertex

getType(int) - Method in class ProGAL.proteins.belta.SecondaryStructure

TODO: Comment and test

getTypes() - Method in class ProGAL.proteins.dunbrack.RamachandranDistribution

getU() - Method in class ProGAL.math.LUDecomposition

Return upper triangular factor

getU() - Method in class ProGAL.math.SingularValueDecomposition

Return the left singular vectors

getUnsignedDihedralAngle(Plane) - Method in class ProGAL.geom3d.Plane

Get the unsigned angle between this plane and p.

getUp() - Method in class ProGAL.geom3d.viewer.Camera

getUserTime() - Method in class ProGAL.Benchmark

Returns the threads current user-time in ms.

getV() - Method in class ProGAL.math.Matrix.EigenvalueDecomposition

Return the eigenvector matrix (immutable).

getV() - Method in class ProGAL.math.SingularValueDecomposition

Return the right singular vectors.

getVariance() - Method in class ProGAL.geom3d.PointList

Get the variance of the points.

getVariance() - Method in class ProGAL.geomNd.PointList

Get the variance of the points.

getVertex(int) - Method in class ProGAL.geom3d.complex.delaunayComplex.DelaunayComplex

getVertex(int) - Method in class ProGAL.geomNd.complex.delaunayComplex.BowyerWatson

Get the i'th vertex

getVertex(int) - Method in class ProGAL.geomNd.complex.Tessel

getVertex(Point) - Method in class ProGAL.proteins.ProteinComplex

getVertexHull(CVertex) - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaFiltration

The vertex-hull of v is the set of all tetrahedrons that has v as a corner-point.

getVertexHull(CVertex) - Method in class ProGAL.geom3d.complex.delaunayComplex.DelaunayComplex

The vertex-hull of v is the set of all tetrahedrons that has v as a corner-point

getVertices() - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaFiltration

Get a list of the vertices of the complex.

getVertices() - Method in class ProGAL.geom3d.complex.delaunayComplex.DelaunayComplex

Get the vertices in the complex.

getVertices() - Method in interface ProGAL.geom3d.complex.SimplicialComplex

getVertices() - Method in class ProGAL.geom3d.complex.tessellation.DelaunayTessellation

Get the vertices in the complex.

getVertices() - Method in class ProGAL.geom3d.volumes.OBB

getVertices() - Method in class ProGAL.geomNd.complex.delaunayComplex.BowyerWatson

Get the vertices in the complex.

getViewAngle() - Method in class ProGAL.geom3d.viewer.Camera

getVoids(J3DScene) - Method in class ProGAL.geom3d.complex.alphaComplex.AlphaComplex

getVolume() - Method in class ProGAL.geom3d.volumes.Cone

getVolume() - Method in class ProGAL.geom3d.volumes.Cylinder

getVolume() - Method in class ProGAL.geom3d.volumes.Lens

The volume of the lens

getVolume() - Method in class ProGAL.geom3d.volumes.LSS

getVolume() - Method in class ProGAL.geom3d.volumes.OBB

getVolume() - Method in class ProGAL.geom3d.volumes.RSS

getVolume() - Method in class ProGAL.geom3d.volumes.Sphere

Get the volume

getVolume() - Method in class ProGAL.geom3d.volumes.Tetrahedron

Get the volume of the tetrahedron.

getVolume() - Method in interface ProGAL.geom3d.volumes.Volume

Get the volume.

getWeight() - Method in class ProGAL.geom3d.PointWeighted

getXDir() - Method in class ProGAL.geom3d.volumes.OBB

getYDir() - Method in class ProGAL.geom3d.volumes.OBB

getZDir() - Method in class ProGAL.geom3d.volumes.OBB

GrahamScan - Class in ProGAL.geom2d.convexHull

GrahamScan() - Constructor for class ProGAL.geom2d.convexHull.GrahamScan

GridMap - Class in ProGAL.dataStructures.rangeSearching

GridMap(double, int) - Constructor for class ProGAL.dataStructures.rangeSearching.GridMap

GridMap(double, List<Point>) - Constructor for class ProGAL.dataStructures.rangeSearching.GridMap