Package jgromacs.data

Class PointList

  • All Implemented Interfaces:
    java.lang.Cloneable
    public class PointList
extends java.lang.Object
implements java.lang.Cloneable
    Objects of this class represent a list of 3D points

    • Constructor Summary

      Constructors 
      Constructor Description
      PointList()
      Constructs a new PointList object

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void addPoint​(Point3D point)
      Adds a new point to the point list
      void centerPoints()
      Centers the points (around the origin)
      java.lang.Object clone()
      Returns an identical PointList object
      boolean equals​(java.lang.Object other)
      Returns true if the two point lists are identical
      Jama.Matrix getAsMatrix()
      Returns point coordinates in a 3xN matrix
      Point3D getCentroid()
      Returns the centroid of points
      int getNumberOfPoints()
      Returns the number of points in the list
      Point3D getPoint​(int i)
      Returns the point of index i
      java.util.ArrayList<Point3D> getPointsAsArrayList()
      Returns points in an ArrayList
      PointList getSubList​(java.util.ArrayList<java.lang.Integer> indices)
      Returns a subset of points defined by an ArrayList of indices
      int hashCode()
      Returns hash code
      void loadFromMatrix​(Jama.Matrix M)
      Loads point coordinates from a 3xN matrix
      void removePoint​(int i)
      Removes the point of index i from the point list
      void removePoint​(Point3D point)
      Removes the given point from the point list
      void rotate​(Jama.Matrix rotationMatrix)
      Rotates the points by a given 3x3 rotation matrix
      void setPoint​(int i, Point3D point)
      Replaces the point of index i with a given point
      void setPointFromArrayList​(java.util.ArrayList<Point3D> points)
      Loads points from an ArrayList
      java.lang.String toString()
      Returns the String representation of point list
      java.lang.String toStringInfo()
      Returns summary information about the point list
      void translate​(Point3D vector)
      Translates the points by a given vector

      • Methods inherited from class java.lang.Object

        finalize, getClass, notify, notifyAll, wait, wait, wait

    • Constructor Detail

      • PointList

        public PointList()
        Constructs a new PointList object

    • Method Detail

      • getPointsAsArrayList

        public java.util.ArrayList<Point3D> getPointsAsArrayList()
        Returns points in an ArrayList
        Returns:
        Points in an ArrayList

      • setPointFromArrayList

        public void setPointFromArrayList​(java.util.ArrayList<Point3D> points)
        Loads points from an ArrayList
        Parameters:
        points - ArrayList of points

      • addPoint

        public void addPoint​(Point3D point)
        Adds a new point to the point list
        Parameters:
        point - new point

      • getPoint

        public Point3D getPoint​(int i)
        Returns the point of index i
        Parameters:
        i - index
        Returns:
        Point of index i

      • setPoint

        public void setPoint​(int i,
                     Point3D point)
        Replaces the point of index i with a given point
        Parameters:
        i - index
        point - new point

      • removePoint

        public void removePoint​(int i)
        Removes the point of index i from the point list
        Parameters:
        i - index

      • removePoint

        public void removePoint​(Point3D point)
        Removes the given point from the point list
        Parameters:
        point - point to remove

      • getNumberOfPoints

        public int getNumberOfPoints()
        Returns the number of points in the list
        Returns:
        Number of points

      • getSubList

        public PointList getSubList​(java.util.ArrayList<java.lang.Integer> indices)
        Returns a subset of points defined by an ArrayList of indices
        Parameters:
        indices - ArrayList of indices
        Returns:
        subset of points

      • getAsMatrix

        public Jama.Matrix getAsMatrix()
        Returns point coordinates in a 3xN matrix
        Returns:
        coordinate matrix

      • loadFromMatrix

        public void loadFromMatrix​(Jama.Matrix M)
        Loads point coordinates from a 3xN matrix
        Parameters:
        M - coordinate matrix

      • centerPoints

        public void centerPoints()
        Centers the points (around the origin)

      • getCentroid

        public Point3D getCentroid()
        Returns the centroid of points
        Returns:
        centroid point

      • rotate

        public void rotate​(Jama.Matrix rotationMatrix)
        Rotates the points by a given 3x3 rotation matrix
        Parameters:
        rotationMatrix - rotation matrix

      • translate

        public void translate​(Point3D vector)
        Translates the points by a given vector
        Parameters:
        vector - translation vector

      • toString

        public java.lang.String toString()
        Returns the String representation of point list
        Overrides:
        toString in class java.lang.Object
        Returns:
        String representation

      • toStringInfo

        public java.lang.String toStringInfo()
        Returns summary information about the point list
        Returns:
        summary information

      • clone

        public java.lang.Object clone()
        Returns an identical PointList object
        Overrides:
        clone in class java.lang.Object
        Returns:
        clone of the point list

      • equals

        public boolean equals​(java.lang.Object other)
        Returns true if the two point lists are identical
        Overrides:
        equals in class java.lang.Object
        Parameters:
        other - the other point list

      • hashCode

        public int hashCode()
        Returns hash code
        Overrides:
        hashCode in class java.lang.Object