jvx.loader
Class PgXyzLoader

java.lang.Object
  jvx.loader.PgXyzLoader

All Implemented Interfaces:

PgLoaderIf

public final class PgXyzLoader

extends java.lang.Object

implements PgLoaderIf

Loader for XYZ files for molecule configurations. Bonding is automatically computed following the JMOL rules for automatic bonding.

Since:

JavaView 3.54.000

Field Summary

Fields inherited from interface jv.loader.PgLoaderIf

GEOM_DATA_AUTHOR, GEOM_DATA_COLORS, GEOM_DATA_HEADER, GEOM_DATA_INFO, GEOM_DATA_NORMALS, GEOM_DATA_TEXTURE, GEOM_DATA_VECTORS

Constructor Summary

PgXyzLoader()

Method Summary

PgJvxSrc[][]	getAnimations() Retrieve the previously loaded animations.
PvDisplayOption	getDisplayOption() Get display options which some parsers and geometry file formats supply.
PgJvxSrc[]	getGeometries() Retrieve the previously loaded geometries.
PgGeometryIf[]	getSpecializedGeometries() Currently, this method always returns null.
boolean	isAnimation() Determine if currently loaded data is an animation.
boolean	isEnabledOptimization() Determines if the loaded geometry requires some optimization.
boolean	load(java.io.BufferedReader in) Read a geometry file containing a set of geometries or animations.
PgJvxSrc[]	read(java.io.BufferedReader in) Read geometry file in the Brigham Young University's MOVIE.BYU file format.
static PgJvxSrc[]	read(java.lang.String fileName) Read geometry file in the Brigham Young University's MOVIE.BYU file format.
void	setAnimation(boolean flag) Set flag whether current geometry data is an animation.
void	setDisplayOption(PvDisplayOption option) Set the display options to be saved within the geometry file.
void	setGeometryOption(java.util.BitSet option) Set the geometry options which indicate which parts of a geometry shall be saved.
boolean	write(java.io.Writer writer, PgJvxSrc[] geomArr) Write an array of geometries into an output stream writer.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PgXyzLoader

public PgXyzLoader()

Method Detail

isEnabledOptimization

public boolean isEnabledOptimization()

Determines if the loaded geometry requires some optimization. The method in this class prohibits optimization and always returns false.

For example, some file formats do not store a connected mesh but provide individual vertices for each face every time the face is menetioned. In this case, a loader manager may identify equal vertices.

A similar method in the loader manager PgLoader may override the individual settings of each loader.

Specified by:

isEnabledOptimization in interface PgLoaderIf

Returns:

true if loader is enabled for optimization.

Since:

JavaView 2.99.018

See Also:

PgLoader.isEnabledOptimization(), PgLoader.setEnabledOptimization(boolean)

setGeometryOption

public void setGeometryOption(java.util.BitSet option)

Set the geometry options which indicate which parts of a geometry shall be saved. This method must be called before writing the geometry. Note, not all geometry file formats support geometry options.

Specified by:

setGeometryOption in interface PgLoaderIf

Since:

JavaView 2.68.000

getDisplayOption

public PvDisplayOption getDisplayOption()

Get display options which some parsers and geometry file formats supply. This geometry file format does not support loading/saving of display options.

Specified by:

getDisplayOption in interface PgLoaderIf

See Also:

PgLoaderIf.load(BufferedReader)

setDisplayOption

public void setDisplayOption(PvDisplayOption option)

Set the display options to be saved within the geometry file. This method must be called before writing the geometry. This geometry file format does not support loading/saving of display options.

Specified by:

setDisplayOption in interface PgLoaderIf

isAnimation

public boolean isAnimation()

Determine if currently loaded data is an animation.

This method may be called after successful parsing an input stream with the method load(BufferedReader).

Specified by:

isAnimation in interface PgLoaderIf

Returns:

true if loaded data is an animation.

See Also:

load(BufferedReader)

setAnimation

public void setAnimation(boolean flag)

Set flag whether current geometry data is an animation.

Specified by:

setAnimation in interface PgLoaderIf

Parameters:

flag - true if loaded data is an animation.

getAnimations

public PgJvxSrc[][] getAnimations()

Retrieve the previously loaded animations.

This method may be called after successful parsing an input stream with the method load(BufferedReader) and if isAnimation() returns true.

Specified by:

getAnimations in interface PgLoaderIf

Returns:

Double array of JVX geometries.

See Also:

load(BufferedReader)

getGeometries

public PgJvxSrc[] getGeometries()

Retrieve the previously loaded geometries.

This method may be called after successful parsing an input stream with the method load(BufferedReader) and if isAnimation() returns false.

Specified by:

getGeometries in interface PgLoaderIf

Returns:

Array of JVX geometries.

See Also:

load(BufferedReader)

getSpecializedGeometries

public PgGeometryIf[] getSpecializedGeometries()

Currently, this method always returns null.

Return the loaded geometry in a more specialized class. This method allows a loader to return a geometry class which best fits the data found in a geometry file.

The loader manager jv.loader.PgLoader in JavaView will first check if a loader returns specialized geometies, and if not, check for a data supplied in a container class PgJvxSrc.

This method may be called after successful parsing an input stream with the method load(BufferedReader) and if isAnimation() returns false.

Specified by:

getSpecializedGeometries in interface PgLoaderIf

Returns:

Array of geometries whose actual class type may vary between loaders.

Since:

JavaView 2.53

See Also:

getGeometries()

load

public boolean load(java.io.BufferedReader in)

Read a geometry file containing a set of geometries or animations.

After successful parsing retrieve the loaded geometries or animations using the methods getGeometries() respectively getAnimations() depending on the return value of the method isAnimation().

Specified by:

load in interface PgLoaderIf

Parameters:

in - BufferedReader to read textual data from.

Returns:

true if parsing was successfull.

See Also:

getAnimations(), getGeometries(), isAnimation()

read

public static PgJvxSrc[] read(java.lang.String fileName)

Read geometry file in the Brigham Young University's MOVIE.BYU file format.

read

public PgJvxSrc[] read(java.io.BufferedReader in)

Read geometry file in the Brigham Young University's MOVIE.BYU file format.

The returned array of geometry may contain keyframes of an animation. This is checked with the method isAnimation().

Alternatively, one may call load(BuffereredReader) followed by getGeometries() resp. getAnimations() to have a finer control about which information one wants to use from a source. For example, optional display information must be retrieve by a subsequent call getDisplayOption() if available.

Specified by:

read in interface PgLoaderIf

Parameters:

in - BufferedReader to read textual data from.

Returns:

Array of JVX geometries.

See Also:

write(Writer, PgJvxSrc [])

write

public boolean write(java.io.Writer writer,
                     PgJvxSrc[] geomArr)
              throws java.io.IOException

Write an array of geometries into an output stream writer.

Specified by:

write in interface PgLoaderIf

Parameters:

writer - Write all data to this stream

geomArr - Array with geometries to save

Returns:

true on success.

Throws:

java.io.IOException

See Also:

read(BufferedReader)