Hierarchy For All Packages

Package Hierarchies:

ProGAL, ProGAL.dataStructures, ProGAL.dataStructures.rangeSearching, ProGAL.dataStructures.rangeSearching.rangeTree, ProGAL.dataStructures.viewer, ProGAL.geom2d, ProGAL.geom2d.convexHull, ProGAL.geom2d.delaunay, ProGAL.geom2d.viewer, ProGAL.geom3d, ProGAL.geom3d.complex, ProGAL.geom3d.complex.alphaComplex, ProGAL.geom3d.complex.alphaComplex.tests, ProGAL.geom3d.complex.delaunayComplex, ProGAL.geom3d.complex.delaunayComplex.tests, ProGAL.geom3d.complex.tessellation, ProGAL.geom3d.predicates, ProGAL.geom3d.predicates.tests, ProGAL.geom3d.superposition, ProGAL.geom3d.superposition.tests, ProGAL.geom3d.surface, ProGAL.geom3d.tess, ProGAL.geom3d.tessellation.BowyerWatson, ProGAL.geom3d.tests, ProGAL.geom3d.viewer, ProGAL.geom3d.volumes, ProGAL.geom3d.volumes.tests, ProGAL.geomNd, ProGAL.geomNd.complex, ProGAL.geomNd.complex.delaunayComplex, ProGAL.geomNd.complex.delaunayComplex.tests, ProGAL.geomNd.tests, ProGAL.io, ProGAL.math, ProGAL.math.test, ProGAL.proteins, ProGAL.proteins.belta, ProGAL.proteins.belta.tests, ProGAL.proteins.beltaStructure, ProGAL.proteins.beltaStructure.bnb, ProGAL.proteins.beltaStructure.bnb.lowerBounds, ProGAL.proteins.beltaStructure.loop, ProGAL.proteins.beltaStructure.sheet, ProGAL.proteins.beltaStructure.sheetLoop, ProGAL.proteins.chainTree, ProGAL.proteins.dunbrack, ProGAL.proteins.structure, ProGAL.proteins.structure.generators, ProGAL.proteins.viewer, ProGAL.statistics, ProGAL.statistics.tests

Class Hierarchy

• java.lang.Object
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • java.util.AbstractList<E> (implements java.util.List<E>)
      • java.util.ArrayList<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
        • ProGAL.geomNd.PointList
        • ProGAL.geom3d.PointList
          • ProGAL.geom3d.complex.alphaComplex.EiffelPointList
        • ProGAL.geom2d.Polygon (implements ProGAL.geom2d.Shape)
          • ProGAL.geom2d.ConvexPolygon
  • ProGAL.proteins.structure.generators.AllAtomAminoAcidGenerator (implements ProGAL.proteins.structure.generators.AtomGenerator)
  • ProGAL.AllTests
  • ProGAL.geom3d.complex.alphaComplex.tests.AlphaComplexDebugger
  • ProGAL.geom3d.complex.alphaComplex.AlphaFiltration
    • ProGAL.geom3d.complex.alphaComplex.AlphaComplex (implements ProGAL.geom3d.complex.SimplicialComplex)
      • ProGAL.proteins.ProteinComplex
  • ProGAL.proteins.structure.AminoAcid
  • ProGAL.proteins.structure.AminoAcidChain
    • ProGAL.proteins.beltaStructure.sheetLoop.SheetLoopStructure (implements ProGAL.proteins.beltaStructure.sheetLoop.PartialStructure)
  • ProGAL.geom2d.ApolloniusSolver
  • ProGAL.geomNd.ApolloniusSolver
  • ProGAL.geom3d.ApolloniusSolver
  • ProGAL.dataStructures.rangeSearching.Benchmark
  • ProGAL.Benchmark
  • ProGAL.proteins.belta.BetaTopology
  • ProGAL.proteins.belta.tests.BetaTopologyTest
  • ProGAL.geom3d.complex.alphaComplex.tests.BettiDebugger
  • ProGAL.geom3d.tessellation.BowyerWatson.BigDecimalPredicates
  • ProGAL.dataStructures.viewer.BinaryTreePainter.PNode
  • ProGAL.proteins.beltaStructure.bnb.BnBNode (implements java.lang.Comparable<T>)
  • ProGAL.proteins.beltaStructure.bnb.BnBSolver
  • ProGAL.proteins.beltaStructure.bnb.BnBTreeExplorer
  • ProGAL.geomNd.complex.delaunayComplex.BowyerWatson
  • ProGAL.geomNd.complex.delaunayComplex.tests.BowyerWatsonTest
  • ProGAL.geomNd.complex.delaunayComplex.BWViewer
  • ProGAL.proteins.structure.generators.CABAminoAcidGenerator (implements ProGAL.proteins.structure.generators.AtomGenerator)
  • ProGAL.proteins.beltaStructure.loop.CALoopStructure (implements ProGAL.proteins.beltaStructure.sheetLoop.PartialStructure)
  • ProGAL.proteins.beltaStructure.loop.CALoopStructure.SegmentStructure (implements ProGAL.proteins.beltaStructure.sheetLoop.PartialStructure)
  • ProGAL.geom3d.viewer.Camera (implements java.awt.event.KeyListener, java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.awt.event.MouseWheelListener)
  • ProGAL.proteins.beltaStructure.CanonicalSheet
  • ProGAL.proteins.structure.CBond
  • ProGAL.proteins.chainTree.ChainTree
  • ProGAL.proteins.beltaStructure.ChainTreeLoop
  • ProGAL.geom2d.Circle (implements ProGAL.geom2d.Shape)
  • ProGAL.geom3d.Circle (implements ProGAL.geom3d.Shape)
  • ProGAL.proteins.beltaStructure.bnb.lowerBounds.CN_ClashLowerBound (implements ProGAL.proteins.beltaStructure.bnb.lowerBounds.LowerBound)
  • ProGAL.proteins.beltaStructure.loop.CoilDatabase
  • ProGAL.math.Combinatorics
  • ProGAL.math.test.CombinatoricsTest
  • java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    • java.awt.Container
      • java.awt.Window (implements javax.accessibility.Accessible)
        • java.awt.Frame (implements java.awt.MenuContainer)
          • javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • ProGAL.dataStructures.viewer.BinaryTreePainter
  • ProGAL.geom3d.volumes.Cone (implements ProGAL.geom3d.volumes.Volume)
  • ProGAL.math.Constants
  • ProGAL.geom3d.tessellation.BowyerWatson.Corner
  • ProGAL.geom3d.volumes.Cylinder (implements ProGAL.geom3d.volumes.Volume)
  • ProGAL.geom3d.complex.delaunayComplex.DelaunayComplex (implements ProGAL.geom3d.complex.SimplicialComplex)
    • ProGAL.geom3d.complex.delaunayComplex.RegularComplex (implements ProGAL.geom3d.complex.SimplicialComplex)
  • ProGAL.geom3d.complex.delaunayComplex.DelaunayComplexKinetic
  • ProGAL.geom3d.complex.delaunayComplex.DelaunayComplexRotation
  • ProGAL.geom3d.complex.delaunayComplex.DelaunayComplexRotation_Stavefejl
  • ProGAL.geom3d.complex.delaunayComplex.DelaunayComplexRotation.HeapItemComp (implements ProGAL.dataStructures.SortTool)
  • ProGAL.geom3d.complex.delaunayComplex.tests.DelaunayComplexTest
  • ProGAL.geom3d.complex.tessellation.DelaunayTessellation
  • ProGAL.proteins.beltaStructure.bnb.lowerBounds.Diameter_Clash_LowerBound (implements ProGAL.proteins.beltaStructure.bnb.lowerBounds.LowerBound)
  • ProGAL.dataStructures.DisjointSet
  • ProGAL.geom3d.complex.alphaComplex.DisjointSet
  • ProGAL.dataStructures.DisjointSet.DSNode
  • ProGAL.geom3d.complex.alphaComplex.DisjointSet.Set
  • ProGAL.geom2d.convexHull.DivideAndConquer
  • ProGAL.dataStructures.DLCyclicList<T> (implements java.lang.Iterable<T>)
  • ProGAL.dataStructures.DLCyclicList.DLNode<T>
  • ProGAL.dataStructures.DLList
  • ProGAL.geom2d.delaunay.DTNoBigPoints
  • ProGAL.geom2d.delaunay.DTWithBigPoints
  • ProGAL.geom3d.complex.alphaComplex.EdgeAlphaProperties (implements ProGAL.geom3d.complex.alphaComplex.SimplexAlphaProperties)
  • ProGAL.geom3d.predicates.tests.ExactJavaPredicatesTest
  • ProGAL.geom3d.superposition.FastRMSD
  • java.io.File (implements java.lang.Comparable<T>, java.io.Serializable)
    • ProGAL.proteins.PDBFile
      • ProGAL.proteins.belta.PDBFile
  • ProGAL.math.Functions
  • ProGAL.geom3d.superposition.GDT
  • ProGAL.geom2d.convexHull.GrahamScan
  • ProGAL.dataStructures.rangeSearching.GridMap (implements ProGAL.dataStructures.rangeSearching.RangeSearchDataStructure)
  • ProGAL.dataStructures.Heap
  • ProGAL.proteins.structure.generators.HeavyAtomAminoAcidGenerator (implements ProGAL.proteins.structure.generators.AtomGenerator)
  • ProGAL.statistics.Histogram
  • ProGAL.statistics.tests.HistogramTest
  • ProGAL.geomNd.HyperSphere
  • ProGAL.geom3d.predicates.tests.InexactJavaPredicatesTest
  • ProGAL.geom3d.volumes.InfCylinder
  • ProGAL.geom3d.complex.alphaComplex.Interval
  • ProGAL.io.IOToolbox
  • ProGAL.geom2d.viewer.J2DScene
  • ProGAL.geom3d.viewer.J3DImageFileWriter
  • ProGAL.geom3d.viewer.J3DScene
  • ProGAL.geom2d.delaunay.Kinetic
  • ProGAL.geom3d.volumes.Lens (implements ProGAL.geom3d.volumes.Volume)
  • ProGAL.geom3d.volumes.tests.LensTest
  • ProGAL.geom2d.Line (implements ProGAL.geom2d.Shape)
  • ProGAL.geom3d.Line
  • ProGAL.dataStructures.rangeSearching.LinearRangeSearch (implements ProGAL.dataStructures.rangeSearching.RangeSearchDataStructure)
  • ProGAL.geom2d.LineSegment (implements ProGAL.geom2d.Shape)
  • ProGAL.geom3d.LineSegment (implements ProGAL.geom3d.Simplex)
    • ProGAL.geom3d.complex.CEdge
  • ProGAL.geom3d.tests.LineTest
  • ProGAL.proteins.beltaStructure.loop.LoopStructure (implements ProGAL.proteins.beltaStructure.sheetLoop.PartialStructure)
  • ProGAL.geom2d.LSC (implements ProGAL.geom2d.Shape)
  • ProGAL.geom3d.volumes.LSS (implements ProGAL.geom3d.volumes.Volume)
  • ProGAL.math.LUDecomposition (implements java.io.Serializable)
  • ProGAL.math.Matrix
    • ProGAL.math.Matrix.ImmutableMatrix
    • ProGAL.math.Matrix3x3
  • ProGAL.math.Matrix.EigenvalueDecomposition
  • ProGAL.math.test.MatrixTest
  • ProGAL.geom3d.complex.alphaComplex.Node (implements ProGAL.dataStructures.viewer.InteractiveBinaryTree)
  • ProGAL.geom3d.volumes.OBB (implements ProGAL.geom3d.volumes.Volume)
  • ProGAL.geom3d.tess.OldTESS
  • ProGAL.geom3d.ParametricPlane
  • ProGAL.geom3d.surface.ParametricSurface (implements ProGAL.geom3d.Shape)
    • ProGAL.proteins.viewer.CoilSurface
    • ProGAL.proteins.viewer.HelixSurface
    • ProGAL.geom3d.surface.ParametricParaboloid
    • ProGAL.geom3d.surface.ParametricPlane
    • ProGAL.proteins.viewer.StrandSurface
  • ProGAL.proteins.beltaStructure.sheet.ParametricSurface
  • ProGAL.proteins.PDBFile.AnisouRecord (implements ProGAL.proteins.PDBFile.PDBRecord)
  • ProGAL.proteins.PDBFile.AtomRecord (implements ProGAL.proteins.PDBFile.PDBRecord)
    • ProGAL.proteins.PDBFile.HetatmRecord
  • ProGAL.proteins.PDBFile.EndModelRecord (implements ProGAL.proteins.PDBFile.PDBRecord)
  • ProGAL.proteins.PDBFile.HelixRecord (implements ProGAL.proteins.PDBFile.PDBRecord)
  • ProGAL.proteins.PDBFile.ModelRecord (implements ProGAL.proteins.PDBFile.PDBRecord)
  • ProGAL.proteins.PDBFile.OtherRecord (implements ProGAL.proteins.PDBFile.PDBRecord)
  • ProGAL.proteins.PDBFile.ParentRecord (implements ProGAL.proteins.PDBFile.PDBRecord)
  • ProGAL.proteins.PDBFile.PDBChain
  • ProGAL.proteins.PDBFile.PDBModel
  • ProGAL.proteins.PDBFile.RemarkRecord (implements ProGAL.proteins.PDBFile.PDBRecord)
  • ProGAL.proteins.PDBFile.SheetRecord (implements ProGAL.proteins.PDBFile.PDBRecord)
  • ProGAL.proteins.PDBFile.TerRecord (implements ProGAL.proteins.PDBFile.PDBRecord)
  • ProGAL.proteins.viewer.PDBFileViewer
  • ProGAL.proteins.PDBWebReader
  • ProGAL.geom3d.Plane (implements ProGAL.geom3d.Shape)
  • ProGAL.geom3d.tests.PlaneTest
  • ProGAL.geomNd.Point (implements java.io.Serializable)
    • ProGAL.geom2d.Point
      • ProGAL.geom2d.TriangulationVertex
      • ProGAL.geom2d.delaunay.Vertex
    • ProGAL.geom3d.Point (implements ProGAL.geom3d.Simplex)
      • ProGAL.proteins.structure.Atom
      • ProGAL.geom3d.complex.CVertex
      • ProGAL.geom3d.PointWeighted
    • ProGAL.geomNd.complex.Vertex
  • ProGAL.dataStructures.rangeSearching.rangeTree.PointDimensionComparator (implements java.util.Comparator<T>)
  • ProGAL.geomNd.tests.PointTest
  • ProGAL.geom3d.tests.PointTest
  • ProGAL.math.Polynomial
  • ProGAL.math.test.PolynomialTest
  • ProGAL.geom3d.predicates.Predicates
    • ProGAL.geom3d.predicates.ExactJavaPredicates
    • ProGAL.geom3d.predicates.ExactNativePredicates
    • ProGAL.geom3d.predicates.InexactJavaPredicates
    • ProGAL.geom3d.predicates.InexactRegularJavaPredicates
  • ProGAL.proteins.belta.PrimaryStructure
  • ProGAL.proteins.ProteinComplex.Cavity
  • ProGAL.proteins.ProteinComplex.Hole
  • ProGAL.proteins.dunbrack.RamachandranDistribution
  • ProGAL.math.Randomization
  • ProGAL.dataStructures.rangeSearching.rangeTree.RangeTree (implements ProGAL.dataStructures.rangeSearching.RangeSearchDataStructure)
  • ProGAL.dataStructures.rangeSearching.rangeTree.RangeTreeAssocValue
  • ProGAL.dataStructures.rangeSearching.rangeTree.RangeTreeNode
    • ProGAL.dataStructures.rangeSearching.rangeTree.RangeTreeNode1d
    • ProGAL.dataStructures.rangeSearching.rangeTree.RangeTreeNode2d
    • ProGAL.dataStructures.rangeSearching.rangeTree.RangeTreeNodeNd
  • ProGAL.geom3d.Rectangle
  • ProGAL.geom3d.complex.delaunayComplex.tests.RegularComplexVisualTest
  • ProGAL.geom3d.tessellation.BowyerWatson.RegularTessellation
  • ProGAL.geom3d.superposition.RMSD
  • ProGAL.geom3d.superposition.tests.RMSDTest
  • ProGAL.geom3d.volumes.RSS (implements ProGAL.geom3d.volumes.Volume)
  • ProGAL.proteins.belta.SecondaryStructure
  • ProGAL.proteins.belta.SecondaryStructure.SSSegment
  • ProGAL.proteins.belta.tests.SecondaryStructureTest
  • ProGAL.proteins.beltaStructure.bnb.SegmentStructure (implements ProGAL.proteins.beltaStructure.bnb.Branchable)
  • ProGAL.dataStructures.Set<T> (implements java.lang.Iterable<T>)
    • ProGAL.geom2d.PointSet
  • ProGAL.dataStructures.SetIterator (implements java.util.Iterator<E>)
  • ProGAL.proteins.beltaStructure.sheet.SheetAlignment
  • ProGAL.proteins.beltaStructure.sheetLoop.SheetLoopGUI (implements ProGAL.geom3d.viewer.ClickListener)
  • ProGAL.proteins.beltaStructure.bnb.SheetStructure (implements ProGAL.proteins.beltaStructure.bnb.Branchable)
  • ProGAL.proteins.belta.SheetTopology
  • ProGAL.proteins.belta.SheetTopology.StrandPair
  • ProGAL.proteins.belta.tests.SheetTopologyTest
  • ProGAL.geom3d.tessellation.BowyerWatson.ShewchuckPredicates
  • ProGAL.math.SingularValueDecomposition
  • ProGAL.dataStructures.Sorter
    • ProGAL.dataStructures.SorterQuick
  • ProGAL.dataStructures.SortToolDouble (implements ProGAL.dataStructures.SortTool)
  • ProGAL.dataStructures.SortToolInteger (implements ProGAL.dataStructures.SortTool)
  • ProGAL.dataStructures.SortToolLineSegment2dAroundCommonPoint (implements ProGAL.dataStructures.SortTool)
  • ProGAL.dataStructures.SortToolLineSegment2dByLength (implements ProGAL.dataStructures.SortTool)
  • ProGAL.dataStructures.SortToolPoint2dAroundOrigo (implements ProGAL.dataStructures.SortTool)
  • ProGAL.dataStructures.SortToolPoint2dAroundPoint (implements ProGAL.dataStructures.SortTool)
  • ProGAL.dataStructures.SortToolPoint2dDistance (implements ProGAL.dataStructures.SortTool)
  • ProGAL.dataStructures.SortToolPoint2dXY (implements ProGAL.dataStructures.SortTool)
  • ProGAL.dataStructures.SortToolString (implements ProGAL.dataStructures.SortTool)
  • ProGAL.geom3d.volumes.Sphere (implements ProGAL.geom3d.volumes.Volume)
  • ProGAL.geom3d.superposition.Superposition
  • ProGAL.proteins.beltaStructure.sheet.SurfaceSheetStructure (implements ProGAL.proteins.beltaStructure.sheetLoop.PartialStructure)
  • ProGAL.geom3d.tess.TCorner
  • ProGAL.geom3d.tess.TESS
  • ProGAL.geomNd.complex.Tessel
  • ProGAL.geom3d.tessellation.BowyerWatson.Tet
  • ProGAL.geom3d.volumes.Tetrahedron (implements ProGAL.geom3d.Simplex, ProGAL.geom3d.volumes.Volume)
    • ProGAL.geom3d.complex.CTetrahedron
    • ProGAL.geom3d.tessellation.BowyerWatson.Tetr
  • ProGAL.geom3d.complex.alphaComplex.TetrahedronAlphaProperties (implements ProGAL.geom3d.complex.alphaComplex.SimplexAlphaProperties)
  • ProGAL.geom3d.viewer.TextShape (implements ProGAL.geom3d.Shape)
  • ProGAL.geom2d.viewer.TextShape (implements ProGAL.geom2d.Shape)
  • ProGAL.geom3d.tess.TPoint
  • ProGAL.geom3d.superposition.Transform
  • ProGAL.geom3d.superposition.tests.TransformTest
  • ProGAL.geom2d.Triangle (implements ProGAL.geom2d.Shape)
    • ProGAL.geom2d.delaunay.Triangle
  • ProGAL.geom3d.Triangle (implements ProGAL.geom3d.Simplex)
    • ProGAL.geom3d.complex.CTriangle
  • ProGAL.geom3d.complex.alphaComplex.TriangleAlphaProperties (implements ProGAL.geom3d.complex.alphaComplex.SimplexAlphaProperties)
  • ProGAL.geom3d.tests.TriangleTest
  • ProGAL.geom2d.Triangulation
  • ProGAL.geom2d.TriangulationFace
  • ProGAL.math.Trigonometry
  • ProGAL.geom3d.tess.TSphere
  • ProGAL.geom3d.complex.alphaComplex.UnionFind<E> (implements java.io.Serializable)
  • ProGAL.geomNd.Vector
    • ProGAL.geom2d.Vector
    • ProGAL.geom3d.Vector
      • ProGAL.geom3d.Vector.ImmutableVector3d
  • ProGAL.geom3d.complex.alphaComplex.VertexAlphaProperties (implements ProGAL.geom3d.complex.alphaComplex.SimplexAlphaProperties)
  • ProGAL.geom3d.complex.alphaComplex.VoidTree
  • ProGAL.io.WebIOToolbox

Interface Hierarchy

• ProGAL.proteins.structure.generators.AtomGenerator
• ProGAL.proteins.beltaStructure.bnb.Branchable
• ProGAL.geom3d.viewer.ClickListener
• ProGAL.proteins.beltaStructure.bnb.Constraint
• ProGAL.dataStructures.viewer.InteractiveBinaryTree
• ProGAL.proteins.beltaStructure.bnb.lowerBounds.LowerBound
• ProGAL.proteins.beltaStructure.sheetLoop.PartialStructure
• ProGAL.proteins.PDBFile.PDBRecord
• ProGAL.dataStructures.rangeSearching.RangeSearchDataStructure
• ProGAL.geom2d.Shape
• ProGAL.geom3d.Shape
  • ProGAL.geom3d.Simplex
  • ProGAL.geom3d.volumes.Volume
• ProGAL.geom3d.complex.alphaComplex.SimplexAlphaProperties
• ProGAL.geom3d.complex.SimplicialComplex
• ProGAL.dataStructures.SortTool

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • ProGAL.geom2d.TriangulationVertex.VertexType
    • ProGAL.geom2d.Triangulation.TriangulationAlgorithm
    • ProGAL.geom2d.ConvexPolygon.ConvexHullAlgorithm
    • ProGAL.geom3d.complex.CVertex.DegenerateCase
    • ProGAL.geomNd.complex.Vertex.DegenerateCase
    • ProGAL.geom3d.predicates.Predicates.SphereConfig
    • ProGAL.geom3d.predicates.Predicates.PlaneConfig
    • ProGAL.proteins.belta.SSType