org.openscience.nmrshiftdb.util
Class Export

java.lang.Object
  java.lang.Thread
      org.openscience.nmrshiftdb.util.Export

All Implemented Interfaces:

java.lang.Runnable

public class Export
extends java.lang.Thread

This class converts spectra/molecules to various other formats

Author:

shk3

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

java.awt.Color	backColor
private org.openscience.cdk.interfaces.IMolecule	cdkmol
private org.openscience.cdk.interfaces.IMolecule	cdkmolwithh
private boolean	compact
java.lang.String[]	pictures This are the image files used for making pdf
int	selected
private DBSpectrum	spectrum
private boolean	useCSS

Fields inherited from class java.lang.Thread

MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Export(DBMolecule molecule)
Constructor for the Export object

Export(DBMolecule molecule, DBSpectrum spectrum)
Constructor for the Export object

Export(DBSpectrum spectrum)
Constructor for the Export object

Method Summary

java.lang.String	getDocbook(java.lang.String format, java.lang.String formatPic) Gets the spectrum and molecule as docbook
java.lang.String	getHtml(javax.servlet.http.HttpServletRequest request) Gets the molecule/spectrum as a simple html file
java.lang.String	getImage(boolean molecule, java.lang.String format, java.lang.String path, boolean drawNumbers) Gets an image of spectrum or molecule, width/height set to a reasonable value for molecules (Hint: don't use this for spectra).
java.lang.String	getImage(boolean molecule, java.lang.String format, java.lang.String path, int width, int height, boolean drawNumbers, DBAtom[] atoms) Gets an image of spectrum or molecule
java.lang.String	getMolSvg(boolean drawNumbers) Gets the molecule as an svg, with and height set to a reasonable value for the molecule.
java.lang.String	getMolSvg(int width, int height, boolean drawNumbers) Gets the molecule as an svg
java.lang.String	getSpecSvg(DBSpectrum spectrum, int spectrumwidth, int spectrumheight, boolean useCSS, DBAtom[] atoms) Gets a spectrum as svg, given by spectrum
java.lang.String	getSpecSvg(int spectrumwidth, int spectrumheight) Gets the spectrum as svg which was set by the constructor.
java.lang.String	getSpecSvg(int spectrumwidth, int spectrumheight, DBAtom[] atoms) Gets the spectrum as svg which was set by the constructor.
static java.lang.String	getSpecSvg(java.lang.String specfile, java.lang.String spectype, java.lang.String fieldstrength, int spectrumwidth, int spectrumheight, boolean useCSS) Gets a spectrum as svg, given by specfile
java.io.ByteArrayOutputStream	makeZip(java.lang.String[] filenames) Makes a zip file out of several files
void	setCompact(boolean compact)

Methods inherited from class java.lang.Thread

activeCount, checkAccess, countStackFrames, currentThread, destroy, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, resume, run, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, stop, suspend, toString, yield

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

pictures

public java.lang.String[] pictures

This are the image files used for making pdf

backColor

public java.awt.Color backColor

spectrum

private DBSpectrum spectrum

cdkmol

private org.openscience.cdk.interfaces.IMolecule cdkmol

cdkmolwithh

private org.openscience.cdk.interfaces.IMolecule cdkmolwithh

useCSS

private boolean useCSS

selected

public int selected

compact

private boolean compact

Constructor Detail

Export

public Export(DBSpectrum spectrum)
       throws java.lang.Exception

Constructor for the Export object

Parameters:

spectrum - The spectrum to export

Throws:

java.lang.Exception - Database problems

Export

public Export(DBMolecule molecule)
       throws java.lang.Exception

Constructor for the Export object

Parameters:

molecle - The molecule to export

Throws:

java.lang.Exception - Database problems

Export

public Export(DBMolecule molecule,
              DBSpectrum spectrum)
       throws java.lang.Exception

Constructor for the Export object

Parameters:

molecle - The molecule to export

spectrum - The spectrum to export

Throws:

java.lang.Exception - Database problems

Method Detail

setCompact

public void setCompact(boolean compact)

getHtml

public java.lang.String getHtml(javax.servlet.http.HttpServletRequest request)
                         throws java.lang.Exception

Gets the molecule/spectrum as a simple html file

Parameters:

request - The current servlet request.

Returns:

The html value

Throws:

java.lang.Exception - Database problems

getDocbook

public java.lang.String getDocbook(java.lang.String format,
                                   java.lang.String formatPic)
                            throws java.lang.Exception

Gets the spectrum and molecule as docbook

Parameters:

format - rtf=no nested tables, pdf=nested tables

formatPic - Description of Parameter

Returns:

The docbook document

Throws:

java.lang.Exception - Description of Exception

getMolSvg

public java.lang.String getMolSvg(boolean drawNumbers)
                           throws java.lang.Exception

Gets the molecule as an svg, with and height set to a reasonable value for the molecule.

Parameters:

drawnumbers - Should the svg contain atom numbers?

Returns:

The molecule as svg.

Throws:

java.lang.Exception - Description of Exception.

getMolSvg

public java.lang.String getMolSvg(int width,
                                  int height,
                                  boolean drawNumbers)
                           throws java.lang.Exception

Gets the molecule as an svg

Parameters:

width - The width of the svg

height - The height of the svg

drawnumbers - Should the svg contain atom numbers?

Returns:

The molecule as svg

Throws:

java.lang.Exception - Description of Exception

getSpecSvg

public java.lang.String getSpecSvg(int spectrumwidth,
                                   int spectrumheight)
                            throws java.lang.Exception

Gets the spectrum as svg which was set by the constructor.

Parameters:

spectrumwidth - Width of svg

spectrumheight - Height of svg * @return The spectrum as svg

Throws:

java.lang.Exception - Description of Exception

getSpecSvg

public java.lang.String getSpecSvg(int spectrumwidth,
                                   int spectrumheight,
                                   DBAtom[] atoms)
                            throws java.lang.Exception

Gets the spectrum as svg which was set by the constructor.

Parameters:

spectrumwidth - Width of svg

spectrumheight - Height of svg * @return The spectrum as svg

Throws:

java.lang.Exception - Description of Exception

getSpecSvg

public java.lang.String getSpecSvg(DBSpectrum spectrum,
                                   int spectrumwidth,
                                   int spectrumheight,
                                   boolean useCSS,
                                   DBAtom[] atoms)
                            throws java.lang.Exception

Gets a spectrum as svg, given by spectrum

Parameters:

spectrum - The spectrum to export.

spectrumwidth - Width of svg

spectrumheight - Height of svg

useCSS -

Returns:

The spectrum as svg

Throws:

java.lang.Exception - Description of Exception

getSpecSvg

public static java.lang.String getSpecSvg(java.lang.String specfile,
                                          java.lang.String spectype,
                                          java.lang.String fieldstrength,
                                          int spectrumwidth,
                                          int spectrumheight,
                                          boolean useCSS)
                                   throws java.lang.Exception

Gets a spectrum as svg, given by specfile

Parameters:

spectrum - The spectrum to export, a string of type shift,intensity|...

spectype - The type of spectrum, string like 13C, 1H ... ~ @param fieldstrength The fieldstrength

spectrumwidth - Width of svg

spectrumheight - Height of svg

useCSS -

Returns:

The spectrum as svg

Throws:

java.lang.Exception - Description of Exception

getImage

public java.lang.String getImage(boolean molecule,
                                 java.lang.String format,
                                 java.lang.String path,
                                 boolean drawNumbers)
                          throws java.lang.Exception

Gets an image of spectrum or molecule, width/height set to a reasonable value for molecules (Hint: don't use this for spectra).

Parameters:

molecule - true=image of molecule, falso=of spectrum

format - jpeg, tiff or png

path - Where to save the image

drawnumbers - Should the svg contain atom numbers?

Returns:

The path to the image

Throws:

java.lang.Exception - Description of Exception

getImage

public java.lang.String getImage(boolean molecule,
                                 java.lang.String format,
                                 java.lang.String path,
                                 int width,
                                 int height,
                                 boolean drawNumbers,
                                 DBAtom[] atoms)
                          throws java.lang.Exception

Gets an image of spectrum or molecule

Parameters:

molecule - true=image of molecule, falso=of spectrum

format - jpeg, tiff or png

path - Where to save the image

width - The width of the svg

height - The height of the svg

drawnumbers - Should the svg contain atom numbers?

Returns:

The path to the image

Throws:

java.lang.Exception - Description of Exception

makeZip

public java.io.ByteArrayOutputStream makeZip(java.lang.String[] filenames)
                                      throws java.io.IOException

Makes a zip file out of several files

Parameters:

filenames - The files to be zipped

Returns:

The zip file

Throws:

java.io.IOException - Problem reading files