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Implemented regression models for NN and exact match.
* Refactored all SDFmodels at the same time.
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158
plugins/net.bioclipse.ds.common/src/net/bioclipse/ds/matcher/BaseSDFExactMatcher.java
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| /* ***************************************************************************** | ||
| * Copyright (c) 2010 Ola Spjuth. | ||
| * All rights reserved. This program and the accompanying materials | ||
| * are made available under the terms of the Eclipse Public License v1.0 | ||
| * which accompanies this distribution, and is available at | ||
| * http://www.eclipse.org/legal/epl-v10.html | ||
| * | ||
| * Contributors: | ||
| * Ola Spjuth - initial API and implementation | ||
| ******************************************************************************/ | ||
| package net.bioclipse.ds.matcher; | ||
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| import java.util.ArrayList; | ||
| import java.util.HashMap; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
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| import net.bioclipse.cdk.domain.ICDKMolecule; | ||
| import net.bioclipse.core.util.LogUtils; | ||
| import net.bioclipse.ds.model.DSException; | ||
| import net.bioclipse.ds.model.IDSTest; | ||
| import net.bioclipse.ds.model.ITestResult; | ||
| import net.bioclipse.ds.model.result.ExternalMoleculeMatch; | ||
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| import org.apache.log4j.Logger; | ||
| import org.eclipse.core.runtime.IProgressMonitor; | ||
| import org.openscience.cdk.CDKConstants; | ||
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| /** | ||
| * Exact match implementation for SDFiles using Signatures | ||
| * | ||
| * @author ola | ||
| * | ||
| */ | ||
| public abstract class BaseSDFExactMatcher extends BaseSDFMatcher implements IDSTest{ | ||
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| private static final Logger logger = Logger.getLogger(BaseSDFExactMatcher.class); | ||
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| /** | ||
| * We require mol sign as property in SDFile | ||
| */ | ||
| @Override | ||
| public List<String> getRequiredProperties() { | ||
| List<String> ret=new ArrayList<String>(); | ||
| ret.add(getPropertyKey()); | ||
| return ret; | ||
| } | ||
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| /** | ||
| * InChI implementation for finding exact matches in an SDFModel | ||
| */ | ||
| protected List<? extends ITestResult> doRunTest( | ||
| ICDKMolecule cdkmol, | ||
| IProgressMonitor monitor) { | ||
| //Store results here | ||
| ArrayList<ExternalMoleculeMatch> results=new | ||
| ArrayList<ExternalMoleculeMatch>(); | ||
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| //Calculate property using subclass implementation | ||
| String calculatedProperty; | ||
| try { | ||
| calculatedProperty = getCalculatedProperty(cdkmol); | ||
| } catch (DSException e) { | ||
| LogUtils.debugTrace(logger, e); | ||
| return returnError("Could not calculate property: " + getPropertyKey(), ""); | ||
| } | ||
| if (calculatedProperty==null || calculatedProperty.length()<=0) | ||
| return returnError("Could not calculate property: " + getPropertyKey(), ""); | ||
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| //Search the entire SDFmodel for the query property | ||
| logger.debug( "Quering for: " + calculatedProperty); | ||
| for (int i=0; i<getSDFmodel().getNumberOfMolecules(); i++){ | ||
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| Object storedPropObject=getSDFmodel().getPropertyFor( i, | ||
| getPropertyKey() ); | ||
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| String storedProp=""; | ||
| try { | ||
| storedProp = processQueryResult(storedPropObject); | ||
| } catch (DSException e) { | ||
| logger.error("Could not process object " + storedPropObject); //Should not happen | ||
| } | ||
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| //Compare signatures | ||
| if (calculatedProperty.equals( storedProp )){ | ||
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| // logger.debug("Found match for mol " + i + ": " + storedProp); | ||
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| ICDKMolecule matchmol = getSDFmodel().getMoleculeAt( i ); | ||
| String molResponse = getSDFmodel().getPropertyFor( i, | ||
| getResponseProperty()); | ||
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| String cdktitle=(String) matchmol.getAtomContainer() | ||
| .getProperty( CDKConstants.TITLE ); | ||
| String molname="Index " + i; | ||
| if (cdktitle!=null) | ||
| molname=cdktitle; | ||
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| ExternalMoleculeMatch match =null; | ||
| if (isClassification){ | ||
| match = | ||
| new ExternalMoleculeMatch(molname, matchmol, | ||
| getConclusion(molResponse)); | ||
| }else{ | ||
| match = | ||
| new ExternalMoleculeMatch(molname + ", value=" + molResponse, matchmol, | ||
| getConclusion(molResponse)); | ||
| } | ||
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| Map<String, Map<String, String>> categories = new HashMap<String, Map<String,String>>(); | ||
| Map<String,String> props = new HashMap<String, String>(); | ||
| props.put("Observed value" , molResponse); | ||
| categories.put("Observations", props); | ||
| match.setProperties(categories); | ||
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| results.add( match ); | ||
| } | ||
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| if (monitor.isCanceled()) | ||
| return returnError( "Cancelled",""); | ||
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| } | ||
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| return results; | ||
| } | ||
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| /** | ||
| * @return the stored property in SDF that we compare with | ||
| */ | ||
| public abstract String getPropertyKey(); | ||
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| /** | ||
| * | ||
| * @param cdkmol Molecule to calculate on | ||
| * @return The calculated property that we compare against all mols in SDF | ||
| * @throws DSException | ||
| */ | ||
| public abstract String getCalculatedProperty(ICDKMolecule cdkmol) throws DSException; | ||
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| /** | ||
| * Optional logic to get from a read property to String | ||
| * used for comparison with calculated property. | ||
| * | ||
| * Subclasses may override, default impl is toString(); | ||
| * | ||
| * @param obj input to process | ||
| * @return String of processed input. | ||
| * @throws DSException if serialization fails. | ||
| */ | ||
| public String processQueryResult(Object obj) throws DSException{ | ||
| return obj.toString(); | ||
| } | ||
| } |
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