org.openscience.nmrshiftdb
Class PredictionTool

java.lang.Object
  org.openscience.nmrshiftdb.PredictionTool

public class PredictionTool
extends java.lang.Object

This class offers a stand-alone prediction based on HOSE codes from NMRShiftDB. Apart from this class, you need a data dump. You can get a jar containing class and dump from any nmrshiftdb server with a URL like http://servername/download/NmrshiftdbServlet/predictor.jar?nmrshiftdbaction=predictor. For an example how to use this class, see the main method. For running this class you need the following additional jars: cdk-core.jar, cdk-extra.jar, JNL.jar. Since the HOSE code table is kept in memory, this class needs a lot of memory depending on the size of the database. We recommand to run the JVM with at least 128 MB memory. Also always set all references to this class to null if you no longer need it in order to have it removed by garbage collection.

Author:

shk3

Nested Class Summary

(package private) class

PredictionTool.ValueBean

Field Summary

private static double[]	confidencelimits
private static java.util.HashMap	mapsmap

Constructor Summary

PredictionTool()
Constructor for the PredictionTool object

Method Summary

static double[]	generalPredict(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtom a, boolean calculated, boolean measured, int ignoreSpectrum, int ignoreSpectrumEnd, java.lang.StringBuffer comment, boolean commentWithMinMax, boolean withRange, org.apache.turbine.util.RunData runData, java.util.Map predictionValuesForApplet, int maxSpheresToUse, boolean cache, java.lang.StringBuffer hoseCodeOut, int spheresMax, boolean fromDB, boolean trueonly) This method does a prediction, either from the database or from the mapsmap initialized in the constructor.
static void	main(java.lang.String[] args) The main program for the PredictionTool class.
double[]	predict(org.openscience.cdk.interfaces.IMolecule mol, org.openscience.cdk.interfaces.IAtom atom) Does a prediction.

Methods inherited from class java.lang.Object

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

Field Detail

confidencelimits

private static double[] confidencelimits

mapsmap

private static java.util.HashMap mapsmap

Constructor Detail

PredictionTool

public PredictionTool()
               throws java.io.IOException

Constructor for the PredictionTool object

Throws:

java.io.IOException - Problems reading the HOSE code file.

Method Detail

main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception

The main program for the PredictionTool class.

Parameters:

args - The file name of the test mdl file.

Throws:

java.lang.Exception - Description of Exception.

generalPredict

public static double[] generalPredict(org.openscience.cdk.interfaces.IAtomContainer mol,
                                      org.openscience.cdk.interfaces.IAtom a,
                                      boolean calculated,
                                      boolean measured,
                                      int ignoreSpectrum,
                                      int ignoreSpectrumEnd,
                                      java.lang.StringBuffer comment,
                                      boolean commentWithMinMax,
                                      boolean withRange,
                                      org.apache.turbine.util.RunData runData,
                                      java.util.Map predictionValuesForApplet,
                                      int maxSpheresToUse,
                                      boolean cache,
                                      java.lang.StringBuffer hoseCodeOut,
                                      int spheresMax,
                                      boolean fromDB,
                                      boolean trueonly)
                               throws java.lang.Exception

This method does a prediction, either from the database or from the mapsmap initialized in the constructor. This should not be used directly when using the stand-alone predictor; use predict() then.

Parameters:

comment - Contains additional text after processing predictRange().

mol - The molecule the atoms comes from.

a - The atom the shift of which to be predicted.

commentWithMinMax - Shall min/max values be included in comments.

ignoreSpectrum - A molecule to be ignored in the prediction (-1=none).

withRange - Is the range to be calculated as well ? (use only when needed for performance reasons).

calculated - Use calculated spectra.

measured - Use measured spectra.

runData - The current runData object.

predictionValuesForApplet - Will become the String to diplay the histogram in the applet, null if not wished.

maxSpheresToUse - Restrict number of spheres to use, to use max spheres set -1.

cache - true=Use HOSE_CODES table, false=do join query.

hoseCodeOut - Contains the used HOSE_CODE.

spheresMax - Default maximum spheres to use.

fromDB - Do prediction from db or mapsmap?

trueonly - Use only spectra review as true

Returns:

An array of doubles. Meaning: 0=lower limit, 1=mean, 2=upper limit calculated via confidence limits, 3=median, 4=used spheres, 5=number of values, 6=standard deviation, 7=min value, 8=max value.

Throws:

java.lang.Exception - Database problems.

predict

public double[] predict(org.openscience.cdk.interfaces.IMolecule mol,
                        org.openscience.cdk.interfaces.IAtom atom)
                 throws java.lang.Exception

Does a prediction.

Parameters:

mol - The molecule.

atom - The atom for which to predict. Typ of spectrum corresponds to element of this atom.

Returns:

An array of doubles. Meaning: 0=lower limit, 1=mean, 2=upper limit calculated via confidence limits, 3=median, 4=used spheres, 5=number of values, 6=standard deviation, 7=min value, 8=max value

Throws:

java.lang.Exception - Description of Exception