org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app

Class SimilaritySearchTask

java.lang.Object

java.util.concurrent.FutureTask<V>

javafx.concurrent.Task<Integer>

org.pistoiaalliance.helm.HELMSimilarityLibrary.gui.app.SimilaritySearchTask

All Implemented Interfaces:

Runnable, Future<Integer>, RunnableFuture<Integer>, javafx.concurrent.Worker<Integer>, javafx.event.EventTarget

public class SimilaritySearchTask
extends javafx.concurrent.Task<Integer>

SimilaritySearch class to perform the algorithm of calculating the similarity of a query helm notation and a database of more helm notations in the following steps

1. Calculation of the fingerprint of the query notation

2. Calculation of the fingerprints of the notations in database

3. Calculation of tanimoto of the query notation and every other notation

4. Checking for subset in database

5a. Returning the notations with a specified minimum similarity in descending order.

5b. Or returning the notations that the query notation is a subset of.

Author:

bueltel

Property Summary

Properties inherited from class javafx.concurrent.Task

exceptionProperty, messageProperty, onCancelledProperty, onFailedProperty, onRunningProperty, onScheduledProperty, onSucceededProperty, progressProperty, runningProperty, stateProperty, titleProperty, totalWorkProperty, valueProperty, workDoneProperty

Nested Class Summary

Nested classes/interfaces inherited from interface javafx.concurrent.Worker

javafx.concurrent.Worker.State

Field Summary

Fields

Modifier and Type	Field and Description
protected static List<org.helm.notation2.parser.notation.HELM2Notation>	helmList
protected static List<Integer>	idList
static double	MAX_PROGRESS
protected static MyProgressBar	progressbar
protected static List<Map<String,Object>>	resultNotations
protected static List<Double>	tanimotoList

Constructor Summary

Constructors

Constructor and Description
SimilaritySearchTask(org.helm.notation2.parser.notation.HELM2Notation queryNotation, double desiredTanimoto)

Method Summary

Modifier and Type	Method and Description
protected Integer	call()
void	doQuery(org.helm.notation2.parser.notation.HELM2Notation queryNotation, double desiredTanimoto) Method calls the corresponding methods to build moleculeGraphs, find paths, generate fingerprints, calculate tanimoto values, check for subset, store the values in a database and select the desired notations with a specified minimum similarity or subset notations.
protected void	updateProgress(double workDone, double max)

Methods inherited from class javafx.concurrent.Task

addEventFilter, addEventHandler, buildEventDispatchChain, cancel, cancel, cancelled, exceptionProperty, failed, fireEvent, getException, getMessage, getOnCancelled, getOnFailed, getOnRunning, getOnScheduled, getOnSucceeded, getProgress, getState, getTitle, getTotalWork, getValue, getWorkDone, isRunning, messageProperty, onCancelledProperty, onFailedProperty, onRunningProperty, onScheduledProperty, onSucceededProperty, progressProperty, removeEventFilter, removeEventHandler, running, runningProperty, scheduled, setEventHandler, setOnCancelled, setOnFailed, setOnRunning, setOnScheduled, setOnSucceeded, stateProperty, succeeded, titleProperty, totalWorkProperty, updateMessage, updateProgress, updateTitle, updateValue, valueProperty, workDoneProperty

Methods inherited from class java.util.concurrent.FutureTask

done, get, get, isCancelled, isDone, run, runAndReset, set, setException

Methods inherited from class java.lang.Object

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

Field Detail

idList

protected static List<Integer> idList

helmList

protected static List<org.helm.notation2.parser.notation.HELM2Notation> helmList

tanimotoList

protected static List<Double> tanimotoList

resultNotations

protected static List<Map<String,Object>> resultNotations

progressbar

protected static MyProgressBar progressbar

MAX_PROGRESS

public static final double MAX_PROGRESS

See Also:

Constant Field Values

Constructor Detail

SimilaritySearchTask

public SimilaritySearchTask(org.helm.notation2.parser.notation.HELM2Notation queryNotation,
                            double desiredTanimoto)

Method Detail

call

protected Integer call()

Specified by:

call in class javafx.concurrent.Task<Integer>

doQuery

public void doQuery(org.helm.notation2.parser.notation.HELM2Notation queryNotation,
                    double desiredTanimoto)

Method calls the corresponding methods to build moleculeGraphs, find paths, generate fingerprints, calculate tanimoto values, check for subset, store the values in a database and select the desired notations with a specified minimum similarity or subset notations.

Parameters:

queryNotation - the query notation

desiredTanimoto - the desired minimum tanimoto

updateProgress

protected void updateProgress(double workDone,
                              double max)

Overrides:

updateProgress in class javafx.concurrent.Task<Integer>