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

All Methods Instance Methods Concrete 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

Class Trajectory

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Trajectory

Trajectory

Trajectory

Trajectory

Method Detail

getFrames

getFrameAsPointList

getFrameAsStructure

getNumberOfFrames

getName

setName

getStartTime

setStartTime

getTimeStep

setTimeStep

setStructure

getMeanFrame

getNumberOfAtoms

getNumberOfResidues

getFirstFrameAsPointList

getFirstFrameAsStructure

getLastFrameAsPointList

getLastFrameAsStructure

addFrame

removeFrame

setFrame

convertFrameIndexToTime

convertTimeToFrameIndex

getSubTrajectory

getSubTrajectory

getSubTrajectory

getSubTrajectory

toString

equals

hashCode

clone