jgromacs.data

Class Trajectory

java.lang.Object

jgromacs.data.Trajectory

All Implemented Interfaces:

java.lang.Cloneable

public class Trajectory
extends java.lang.Object
implements java.lang.Cloneable

Objects of this class represent a single trajectory

Constructor Summary

Constructors

Constructor and Description
Trajectory() Constructs a new Trajectory object
Trajectory(java.lang.String name) Constructs a new Trajectory object of given name
Trajectory(Structure structure) Constructs a new Trajectory object of given structure
Trajectory(Structure[] ensemble) Constructs a new Trajectory object made from an ensemble of structures

Method Summary

Methods

Modifier and Type	Method and Description
void	addFrame(PointList frame) Adds a new frame to the trajectory
java.lang.Object	clone() Returns an identical Trajectory object
double	convertFrameIndexToTime(int frameindex) Converts frame index to simulation time
int	convertTimeToFrameIndex(double time) Converts simulation time to frame index
boolean	equals(java.lang.Object other) Returns true if the two trajectories are identical
PointList	getFirstFrameAsPointList() Returns the initial frame of trajectory as a PointList
Structure	getFirstFrameAsStructure() Returns the initial frame of trajectory as a Structure
PointList	getFrameAsPointList(int i) Returns frame #i of the trajectory as a PointList object
Structure	getFrameAsStructure(int i) Returns frame #i of the trajectory as a Structure object
java.util.ArrayList<PointList>	getFrames() Returns frames of the trajectory as an ArrayList object
PointList	getLastFrameAsPointList() Returns the last frame of trajectory as a PointList
Structure	getLastFrameAsStructure() Returns the last frame of trajectory as a Structure
PointList	getMeanFrame() Returns the mean frame of trajectory
java.lang.String	getName() Returns the name of trajectory
int	getNumberOfAtoms() Returns the number of atoms in the trajectory
int	getNumberOfFrames() Returns the number of frames in the trajectory
int	getNumberOfResidues() Returns the number of residues in the trajectory
double	getStartTime() Returns the start time of trajectory
Trajectory	getSubTrajectory(FrameIndexSet framelist) Returns the subtrajectory defined by the given frame list
Trajectory	getSubTrajectory(IndexSet indices) Returns the subtrajectory defined by the given index set
Trajectory	getSubTrajectory(int startframe, int endframe) Returns the subtrajectory between the given start and end frames
Trajectory	getSubTrajectory(int startframe, int endframe, int frequency) Returns the subtrajectory between the given start and end frames using the given sampling frequency
double	getTimeStep() Returns the time step of trajectory
int	hashCode() Returns hash code
void	removeFrame(int i) Removes frame #i from the trajectory
void	setFrame(int i, PointList frame) Replaces frame #i with a new frame
void	setName(java.lang.String name) Sets the name of trajectory
void	setStartTime(double startTime) Sets the start time of trajectory
void	setStructure(Structure structure) Sets the structure described by the trajectory
void	setTimeStep(double timeStep) Sets the time step of trajectory
java.lang.String	toString() Returns the String representation of trajectory

Methods inherited from class java.lang.Object

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

Constructor Detail

Trajectory

public Trajectory()

Constructs a new Trajectory object

Trajectory

public Trajectory(java.lang.String name)

Constructs a new Trajectory object of given name

Trajectory

public Trajectory(Structure structure)

Constructs a new Trajectory object of given structure

Trajectory

public Trajectory(Structure[] ensemble)

Constructs a new Trajectory object made from an ensemble of structures

Method Detail

getFrames

public java.util.ArrayList<PointList> getFrames()

Returns frames of the trajectory as an ArrayList object

Returns:

frames as an ArrayList

getFrameAsPointList

public PointList getFrameAsPointList(int i)

Returns frame #i of the trajectory as a PointList object

Returns:

frame #i as a PointList

getFrameAsStructure

public Structure getFrameAsStructure(int i)

Returns frame #i of the trajectory as a Structure object

Returns:

frame #i as a Structure

getNumberOfFrames

public int getNumberOfFrames()

Returns the number of frames in the trajectory

Returns:

number of frames

getName

public java.lang.String getName()

Returns the name of trajectory

Returns:

name of trajectory

setName

public void setName(java.lang.String name)

Sets the name of trajectory

Parameters:

name - name of trajectory

getStartTime

public double getStartTime()

Returns the start time of trajectory

Returns:

start time of trajectory

setStartTime

public void setStartTime(double startTime)

Sets the start time of trajectory

Parameters:

startTime - start time of trajectory

getTimeStep

public double getTimeStep()

Returns the time step of trajectory

Returns:

time step of trajectory

setTimeStep

public void setTimeStep(double timeStep)

Sets the time step of trajectory

Parameters:

timeStep - time step of trajectory

setStructure

public void setStructure(Structure structure)

Sets the structure described by the trajectory

Parameters:

structure - structure described by the trajectory

getMeanFrame

public PointList getMeanFrame()

Returns the mean frame of trajectory

Returns:

mean frame

getNumberOfAtoms

public int getNumberOfAtoms()

Returns the number of atoms in the trajectory

Returns:

number of atoms

getNumberOfResidues

public int getNumberOfResidues()

Returns the number of residues in the trajectory

Returns:

number of residues

getFirstFrameAsPointList

public PointList getFirstFrameAsPointList()

Returns the initial frame of trajectory as a PointList

Returns:

initial frame

getFirstFrameAsStructure

public Structure getFirstFrameAsStructure()

Returns the initial frame of trajectory as a Structure

Returns:

initial frame

getLastFrameAsPointList

public PointList getLastFrameAsPointList()

Returns the last frame of trajectory as a PointList

Returns:

last frame

getLastFrameAsStructure

public Structure getLastFrameAsStructure()

Returns the last frame of trajectory as a Structure

Returns:

last frame

addFrame

public void addFrame(PointList frame)

Adds a new frame to the trajectory

Parameters:

frame - new frame

removeFrame

public void removeFrame(int i)

Removes frame #i from the trajectory

setFrame

public void setFrame(int i,
            PointList frame)

Replaces frame #i with a new frame

Parameters:

frame - new frame

convertFrameIndexToTime

public double convertFrameIndexToTime(int frameindex)

Converts frame index to simulation time

Parameters:

frameindex - frame index

Returns:

simulation time

convertTimeToFrameIndex

public int convertTimeToFrameIndex(double time)

Converts simulation time to frame index

Parameters:

time - simulation time

Returns:

frame index

getSubTrajectory

public Trajectory getSubTrajectory(int startframe,
                          int endframe)

Returns the subtrajectory between the given start and end frames

Parameters:

startframe - start frame

endframe - end frame

Returns:

subtrajectory

getSubTrajectory

public Trajectory getSubTrajectory(int startframe,
                          int endframe,
                          int frequency)

Returns the subtrajectory between the given start and end frames using the given sampling frequency

Parameters:

startframe - start frame

endframe - end frame

frequency - sampling frequency

Returns:

subtrajectory

getSubTrajectory

public Trajectory getSubTrajectory(IndexSet indices)

Returns the subtrajectory defined by the given index set

Parameters:

indices - index set of subtrajectory

Returns:

subtrajectory

getSubTrajectory

public Trajectory getSubTrajectory(FrameIndexSet framelist)

Returns the subtrajectory defined by the given frame list

Parameters:

framelist - frame list

Returns:

subtrajectory

toString

public java.lang.String toString()

Returns the String representation of trajectory

Overrides:

toString in class java.lang.Object

Returns:

String representation

equals

public boolean equals(java.lang.Object other)

Returns true if the two trajectories are identical

Overrides:

equals in class java.lang.Object

Parameters:

other - the other trajectory

hashCode

public int hashCode()

Returns hash code

Overrides:

hashCode in class java.lang.Object

clone

public java.lang.Object clone()

Returns an identical Trajectory object

Overrides:

clone in class java.lang.Object

Returns:

clone of the trajectory