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Refactor out DS input from ICDKMolecule to IBioObject
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@olas
olas committed Sep 19, 2013
1 parent 84d0219 commit b7ef487
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Showing 21 changed files with 228 additions and 100 deletions.
13 changes: 9 additions & 4 deletions plugins/net.bioclipse.ds.common/src/net/bioclipse/ds/matcher/BaseSDFExactMatcher.java
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Expand Up @@ -16,6 +16,7 @@
import java.util.Map;

import net.bioclipse.cdk.domain.ICDKMolecule;
import net.bioclipse.core.domain.IBioObject;
import net.bioclipse.core.util.LogUtils;
import net.bioclipse.ds.model.DSException;
import net.bioclipse.ds.model.IDSTest;
Expand Down Expand Up @@ -50,10 +51,14 @@ public List<String> getRequiredProperties() {
/**
* InChI implementation for finding exact matches in an SDFModel
*/
protected List<? extends ITestResult> doRunTest(
ICDKMolecule cdkmol,
IProgressMonitor monitor) {
//Store results here
protected List<? extends ITestResult> doRunTest(IBioObject input,
IProgressMonitor monitor) {

if (!(input instanceof ICDKMolecule))
return returnError("Input is not a Molecule", "");
ICDKMolecule cdkmol = (ICDKMolecule) input;

//Store results here
ArrayList<ExternalMoleculeMatch> results=new
ArrayList<ExternalMoleculeMatch>();

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3 changes: 2 additions & 1 deletion plugins/net.bioclipse.ds.common/src/net/bioclipse/ds/matcher/BaseSDFMatcher.java
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Expand Up @@ -28,6 +28,7 @@
import net.bioclipse.cdk.ui.sdfeditor.business.SDFIndexEditorModel;
import net.bioclipse.core.util.FileUtil;
import net.bioclipse.core.util.LogUtils;
import net.bioclipse.ds.model.AbstractDSMolModel;
import net.bioclipse.ds.model.AbstractDSTest;
import net.bioclipse.ds.model.DSException;
import net.bioclipse.ds.model.IDSTest;
Expand All @@ -43,7 +44,7 @@
* @author ola
*
*/
public abstract class BaseSDFMatcher extends AbstractDSTest implements IDSTest{
public abstract class BaseSDFMatcher extends AbstractDSMolModel implements IDSTest{

private static final Logger logger = Logger.getLogger(BaseSDFMatcher.class);

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3 changes: 2 additions & 1 deletion plugins/net.bioclipse.ds.common/src/net/bioclipse/ds/matcher/BaseSignaturesMatcher.java
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Expand Up @@ -28,6 +28,7 @@
import net.bioclipse.core.business.BioclipseException;
import net.bioclipse.core.util.LogUtils;
import net.bioclipse.ds.matcher.model.SignatureFrequenceyResult;
import net.bioclipse.ds.model.AbstractDSMolModel;
import net.bioclipse.ds.model.AbstractDSTest;
import net.bioclipse.ds.model.DSException;
import net.bioclipse.ds.model.IDSTest;
Expand All @@ -40,7 +41,7 @@
* @author Ola Spjuth
*
*/
public abstract class BaseSignaturesMatcher extends AbstractDSTest implements IDSTest{
public abstract class BaseSignaturesMatcher extends AbstractDSMolModel implements IDSTest{

//The logger of the class
private static final Logger logger = Logger.getLogger(BaseSignaturesMatcher.class);
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6 changes: 4 additions & 2 deletions plugins/net.bioclipse.ds.common/src/net/bioclipse/ds/matcher/BogusTest.java
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Expand Up @@ -16,21 +16,23 @@
import org.eclipse.core.runtime.IProgressMonitor;

import net.bioclipse.cdk.domain.ICDKMolecule;
import net.bioclipse.core.domain.IBioObject;
import net.bioclipse.ds.model.AbstractDSMolModel;
import net.bioclipse.ds.model.AbstractDSTest;
import net.bioclipse.ds.model.DSException;
import net.bioclipse.ds.model.IDSTest;
import net.bioclipse.ds.model.ITestResult;


public class BogusTest extends AbstractDSTest implements IDSTest{
public class BogusTest extends AbstractDSMolModel implements IDSTest{

private static final Logger logger = Logger.getLogger(BogusTest.class);

public void initialize( IProgressMonitor monitor ) throws DSException {
}

@Override
protected List<? extends ITestResult> doRunTest( ICDKMolecule cdkmol,
protected List<? extends ITestResult> doRunTest( IBioObject object,
IProgressMonitor monitor ) {

logger.error("This BOGUStest: " + getId() + " should not be called.");
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10 changes: 8 additions & 2 deletions plugins/net.bioclipse.ds.common/src/net/bioclipse/ds/matcher/CSVNearestFP.java
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Expand Up @@ -22,7 +22,9 @@
import net.bioclipse.cdk.business.Activator;
import net.bioclipse.cdk.business.ICDKManager;
import net.bioclipse.cdk.domain.ICDKMolecule;
import net.bioclipse.core.domain.IBioObject;
import net.bioclipse.core.util.LogUtils;
import net.bioclipse.ds.model.AbstractDSMolModel;
import net.bioclipse.ds.model.AbstractDSTest;
import net.bioclipse.ds.model.DSException;
import net.bioclipse.ds.model.IDSTest;
Expand All @@ -34,7 +36,7 @@
* @author Ola Spjuth
*
*/
public class CSVNearestFP extends AbstractDSTest implements IDSTest{
public class CSVNearestFP extends AbstractDSMolModel implements IDSTest{

private static final String TANIMOTO_PARAMETER="distance.tanimoto";
private static final String[] CONTENT_HEADERS = new String[]{"SMILES","TYPE", "VALUE", "TARGET_TYPE",
Expand Down Expand Up @@ -135,8 +137,12 @@ public void initialize(IProgressMonitor monitor) throws DSException {
}

@Override
protected List<? extends ITestResult> doRunTest(ICDKMolecule cdkmol,
protected List<? extends ITestResult> doRunTest(IBioObject input,
IProgressMonitor monitor) {

if (!(input instanceof ICDKMolecule))
return returnError("Input is not a Molecule", "");
ICDKMolecule cdkmol = (ICDKMolecule) input;

//Store results here
ArrayList<ExternalMoleculeMatch> results=new ArrayList<ExternalMoleculeMatch>();
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10 changes: 7 additions & 3 deletions plugins/net.bioclipse.ds.common/src/net/bioclipse/ds/matcher/SDFNearestMatchFP.java
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Expand Up @@ -20,6 +20,7 @@
import net.bioclipse.cdk.business.Activator;
import net.bioclipse.cdk.business.ICDKManager;
import net.bioclipse.cdk.domain.ICDKMolecule;
import net.bioclipse.core.domain.IBioObject;
import net.bioclipse.core.domain.IMolecule;
import net.bioclipse.core.util.LogUtils;
import net.bioclipse.ds.model.DSException;
Expand Down Expand Up @@ -106,9 +107,12 @@ public List<String> getRequiredParameters() {
/**
* FP implementation for finding exact matches in an SDFModel
*/
protected List<? extends ITestResult> doRunTest(
ICDKMolecule cdkmol,
IProgressMonitor monitor) {
protected List<? extends ITestResult> doRunTest(IBioObject input,
IProgressMonitor monitor) {

if (!(input instanceof ICDKMolecule))
return returnError("Input is not a Molecule", "");
ICDKMolecule cdkmol = (ICDKMolecule) input;

// //We divide in 5 parts
// monitor.beginTask(getName(), 5);
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12 changes: 9 additions & 3 deletions plugins/net.bioclipse.ds.common/src/net/bioclipse/ds/matcher/SignatureAlertsMatcher.java
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Expand Up @@ -32,8 +32,10 @@
import org.openscience.cdk.interfaces.IAtomContainer;

import net.bioclipse.cdk.domain.ICDKMolecule;
import net.bioclipse.core.domain.IBioObject;
import net.bioclipse.ds.matcher.model.SignificantSignature;
import net.bioclipse.ds.matcher.model.SignificantSignatureMatch;
import net.bioclipse.ds.model.AbstractDSMolModel;
import net.bioclipse.ds.model.AbstractDSTest;
import net.bioclipse.ds.model.DSException;
import net.bioclipse.ds.model.IDSTest;
Expand All @@ -50,7 +52,7 @@
* @author ola
*
*/
public class SignatureAlertsMatcher extends AbstractDSTest implements IDSTest{
public class SignatureAlertsMatcher extends AbstractDSMolModel implements IDSTest{

private static final Logger logger = Logger.getLogger(SignatureAlertsMatcher.class);

Expand Down Expand Up @@ -200,8 +202,12 @@ else if (line.startsWith("significantSignature")){


@Override
protected List<? extends ITestResult> doRunTest( ICDKMolecule cdkmol,
IProgressMonitor monitor ) {
protected List<? extends ITestResult> doRunTest(IBioObject input,
IProgressMonitor monitor) {

if (!(input instanceof ICDKMolecule))
return returnError("Input is not a Molecule", "");
ICDKMolecule cdkmol = (ICDKMolecule) input;

// //We divide in 6 parts and increment one per height processed
// monitor.beginTask(getName(), 6);
Expand Down
12 changes: 9 additions & 3 deletions plugins/net.bioclipse.ds.common/src/net/bioclipse/ds/matcher/SmartsAlertMatcher.java
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Expand Up @@ -28,7 +28,9 @@
import org.openscience.cdk.smiles.smarts.SMARTSQueryTool;

import net.bioclipse.cdk.domain.ICDKMolecule;
import net.bioclipse.core.domain.IBioObject;
import net.bioclipse.ds.matcher.model.SmartsMatchEntry;
import net.bioclipse.ds.model.AbstractDSMolModel;
import net.bioclipse.ds.model.AbstractDSTest;
import net.bioclipse.ds.model.DSException;
import net.bioclipse.ds.model.IDSTest;
Expand All @@ -48,7 +50,7 @@
* @author ola
*
*/
public class SmartsAlertMatcher extends AbstractDSTest implements IDSTest{
public class SmartsAlertMatcher extends AbstractDSMolModel implements IDSTest{

private static final Logger logger = Logger.getLogger(SmartsAlertMatcher.class);

Expand Down Expand Up @@ -229,8 +231,12 @@ public String toString() {


@Override
protected List<? extends ITestResult> doRunTest( ICDKMolecule cdkmol,
IProgressMonitor monitor ) {
protected List<? extends ITestResult> doRunTest(IBioObject input,
IProgressMonitor monitor) {

if (!(input instanceof ICDKMolecule))
return returnError("Input is not a Molecule", "");
ICDKMolecule cdkmol = (ICDKMolecule) input;

//Store results here
ArrayList<SimpleResult> results=new ArrayList<SimpleResult>();
Expand Down
12 changes: 9 additions & 3 deletions plugins/net.bioclipse.ds.common/src/net/bioclipse/ds/matcher/SmartsMatcher.java
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Expand Up @@ -29,7 +29,9 @@
import org.openscience.cdk.smiles.smarts.SMARTSQueryTool;

import net.bioclipse.cdk.domain.ICDKMolecule;
import net.bioclipse.core.domain.IBioObject;
import net.bioclipse.core.util.LogUtils;
import net.bioclipse.ds.model.AbstractDSMolModel;
import net.bioclipse.ds.model.AbstractDSTest;
import net.bioclipse.ds.model.DSException;
import net.bioclipse.ds.model.IDSTest;
Expand All @@ -45,7 +47,7 @@
* @author ola
*
*/
public class SmartsMatcher extends AbstractDSTest implements IDSTest{
public class SmartsMatcher extends AbstractDSMolModel implements IDSTest{

private static final Logger logger = Logger.getLogger(SmartsMatcher.class);

Expand Down Expand Up @@ -186,8 +188,12 @@ private boolean isValidSmarts( String smarts ) {
}

@Override
protected List<? extends ITestResult> doRunTest( ICDKMolecule cdkmol,
IProgressMonitor monitor ) {
protected List<? extends ITestResult> doRunTest(IBioObject input,
IProgressMonitor monitor) {

if (!(input instanceof ICDKMolecule))
return returnError("Input is not a Molecule", "");
ICDKMolecule cdkmol = (ICDKMolecule) input;

//Task size is number of smarts
// monitor.beginTask(getName(), IProgressMonitor.UNKNOWN);
Expand Down
8 changes: 6 additions & 2 deletions plugins/net.bioclipse.ds.libsvm/src/net/bioclipse/ds/libsvm/PCMSignLibSvmPrediction.java
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Expand Up @@ -11,8 +11,8 @@
import java.util.List;

import libsvm.svm_node;

import net.bioclipse.cdk.domain.ICDKMolecule;
import net.bioclipse.core.domain.IBioObject;
import net.bioclipse.core.util.LogUtils;
import net.bioclipse.ds.model.DSException;
import net.bioclipse.ds.model.ITestResult;
Expand Down Expand Up @@ -103,9 +103,13 @@ public void initialize(IProgressMonitor monitor) throws DSException {
}

@Override
protected List<? extends ITestResult> doRunTest(ICDKMolecule cdkmol,
protected List<? extends ITestResult> doRunTest(IBioObject input,
IProgressMonitor monitor) {

if (!(input instanceof ICDKMolecule))
return returnError("Input is not a Molecule", "");
ICDKMolecule cdkmol = (ICDKMolecule) input;

List<ITestResult> allResults = new ArrayList<ITestResult>();

for (int ix=0; ix<protNames.size();ix++){
Expand Down
11 changes: 8 additions & 3 deletions plugins/net.bioclipse.ds.libsvm/src/net/bioclipse/ds/libsvm/SignaturesLibSVMPrediction.java
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Expand Up @@ -22,12 +22,13 @@
import libsvm.svm;
import libsvm.svm_model;
import libsvm.svm_node;

import net.bioclipse.cdk.domain.ICDKMolecule;
import net.bioclipse.core.business.BioclipseException;
import net.bioclipse.core.domain.IBioObject;
import net.bioclipse.ds.libsvm.model.PredictionModel;
import net.bioclipse.ds.libsvm.model.SignLibsvmModel;
import net.bioclipse.ds.libsvm.model.SignLibsvmUtils;
import net.bioclipse.ds.model.AbstractDSMolModel;
import net.bioclipse.ds.model.AbstractDSTest;
import net.bioclipse.ds.model.DSException;
import net.bioclipse.ds.model.ITestResult;
Expand All @@ -47,7 +48,7 @@
* @author ola
*
*/
public class SignaturesLibSVMPrediction extends AbstractDSTest{
public class SignaturesLibSVMPrediction extends AbstractDSMolModel{


//The logger of the class
Expand Down Expand Up @@ -211,8 +212,12 @@ public void initialize(IProgressMonitor monitor) throws DSException {


@Override
protected List<? extends ITestResult> doRunTest(ICDKMolecule cdkmol,
protected List<? extends ITestResult> doRunTest(IBioObject input,
IProgressMonitor monitor) {

if (!(input instanceof ICDKMolecule))
return returnError("Input is not a Molecule", "");
ICDKMolecule cdkmol = (ICDKMolecule) input;

return predictLibSVM(cdkmol,null,true,monitor);

Expand Down
7 changes: 6 additions & 1 deletion plugins/net.bioclipse.ds.r/src/net/bioclipse/ds/r/DenseCDKRModelMatcher.java
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Expand Up @@ -15,6 +15,7 @@
import net.bioclipse.cdk.domain.ICDKMolecule;
import net.bioclipse.core.business.BioclipseException;
import net.bioclipse.core.domain.DenseDataset;
import net.bioclipse.core.domain.IBioObject;
import net.bioclipse.core.domain.IMolecule;
import net.bioclipse.core.util.LogUtils;
import net.bioclipse.ds.model.DSException;
Expand Down Expand Up @@ -74,9 +75,13 @@ public void initialize(IProgressMonitor monitor) throws DSException {
}

@Override
protected List<? extends ITestResult> doRunTest(ICDKMolecule cdkmol,
protected List<? extends ITestResult> doRunTest(IBioObject input,
IProgressMonitor monitor) {

if (!(input instanceof ICDKMolecule))
return returnError("Input is not a Molecule", "");
ICDKMolecule cdkmol = (ICDKMolecule) input;

//Make room for results
List<ITestResult> results=new ArrayList<ITestResult>();

Expand Down
6 changes: 5 additions & 1 deletion plugins/net.bioclipse.ds.r/src/net/bioclipse/ds/r/DenseSignaturesRModelMatcher.java
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Expand Up @@ -9,6 +9,7 @@

import net.bioclipse.cdk.domain.ICDKMolecule;
import net.bioclipse.core.business.BioclipseException;
import net.bioclipse.core.domain.IBioObject;
import net.bioclipse.ds.matcher.BaseSignaturesMatcher;
import net.bioclipse.ds.matcher.model.SignatureFrequenceyResult;
import net.bioclipse.ds.model.DSException;
Expand All @@ -29,9 +30,12 @@ public abstract class DenseSignaturesRModelMatcher extends SignaturesRModelMatch


@Override
protected List<? extends ITestResult> doRunTest(ICDKMolecule cdkmol,
protected List<? extends ITestResult> doRunTest(IBioObject input,
IProgressMonitor monitor) {

if (!(input instanceof ICDKMolecule))
return returnError("Input is not a Molecule", "");
ICDKMolecule cdkmol = (ICDKMolecule) input;


//Make room for results
Expand Down
3 changes: 2 additions & 1 deletion plugins/net.bioclipse.ds.r/src/net/bioclipse/ds/r/RModelMatcher.java
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Expand Up @@ -19,6 +19,7 @@
import net.bioclipse.core.util.FileUtil;
import net.bioclipse.core.util.LogUtils;
import net.bioclipse.ds.matcher.BaseSignaturesMatcher;
import net.bioclipse.ds.model.AbstractDSMolModel;
import net.bioclipse.ds.model.AbstractDSTest;
import net.bioclipse.ds.model.DSException;
import net.bioclipse.ds.model.IDSTest;
Expand All @@ -36,7 +37,7 @@
* @author ola
*
*/
public abstract class RModelMatcher extends AbstractDSTest implements IDSTest{
public abstract class RModelMatcher extends AbstractDSMolModel implements IDSTest{

private static final String R_DATA_PARAMETER = "rdata";
private static final String R_TRAINED_MODEL = "trainedModel";
Expand Down
3 changes: 2 additions & 1 deletion plugins/net.bioclipse.ds.r/src/net/bioclipse/ds/r/SignaturesRModelMatcher.java
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Expand Up @@ -9,6 +9,7 @@

import net.bioclipse.cdk.domain.ICDKMolecule;
import net.bioclipse.core.business.BioclipseException;
import net.bioclipse.core.domain.IBioObject;
import net.bioclipse.ds.matcher.BaseSignaturesMatcher;
import net.bioclipse.ds.model.DSException;
import net.bioclipse.ds.model.ITestResult;
Expand All @@ -34,7 +35,7 @@ public SignaturesRModelMatcher() {

signaturesMatcher=new BaseSignaturesMatcher() {
@Override
protected List<? extends ITestResult> doRunTest(ICDKMolecule cdkmol, IProgressMonitor monitor) {
protected List<? extends ITestResult> doRunTest(IBioObject input, IProgressMonitor monitor) {
return null;
}
};
Expand Down

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