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GUI + refactoring of SignatureDatasetFromSDF
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* Refactored to use IDataset implementation
* Implemented GUI dialog for creating dataset from SDF
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@olas
olas committed Sep 2, 2011
1 parent ab825af commit bb8e938
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Showing 10 changed files with 489 additions and 199 deletions.
7 changes: 6 additions & 1 deletion plugins/net.bioclipse.ds.signatures/META-INF/MANIFEST.MF
View file
Expand Up @@ -26,7 +26,12 @@ Require-Bundle: org.eclipse.ui,
net.bioclipse.ui.business,
org.openscience.cdk.signature,
signatures,
org.openscience.cdk.valencycheck
org.openscience.cdk.valencycheck,
org.openscience.cdk.io,
org.eclipse.core.databinding,
org.eclipse.core.databinding.beans,
org.eclipse.core.databinding.property,
org.eclipse.jface.databinding
Import-Package: org.apache.log4j
Bundle-ActivationPolicy: lazy
Bundle-ClassPath: .
36 changes: 31 additions & 5 deletions plugins/net.bioclipse.ds.signatures/plugin.xml
View file
Expand Up @@ -90,10 +90,10 @@
</menuContribution>

<menuContribution
locationURI="popup:org.eclipse.ui.popup.any?after=additions">
locationURI="popup:net.bioclipse.chemoinformatics.popup.dataset?after=additions">
<command
commandId="net.bioclipse.ds.signatures.handlers.SignaturesDatasetFromSDF"
label="Calculate Signatures Dataset">
label="Signatures Dataset (Dense)">

<visibleWhen>
<iterate operator="and" ifEmpty="false">
Expand All @@ -112,7 +112,28 @@
</iterate>
</visibleWhen>
</command>
<!--command
<command
commandId="net.bioclipse.ds.signatures.handlers.SparseSignaturesDatasetFromSDF"
label="Signatures Dataset (Sparse)">

<visibleWhen>
<iterate operator="and" ifEmpty="false">
<adapt type="org.eclipse.core.resources.IResource">
<or>
<test property="org.eclipse.core.resources.contentTypeId"
value="net.bioclipse.contenttypes.sdf"/>
<test property="org.eclipse.core.resources.contentTypeId"
value="net.bioclipse.contenttypes.sdf0d"/>
<test property="org.eclipse.core.resources.contentTypeId"
value="net.bioclipse.contenttypes.sdf2d"/>
<test property="org.eclipse.core.resources.contentTypeId"
value="net.bioclipse.contenttypes.sdf3d"/>
</or>
</adapt>
</iterate>
</visibleWhen>
</command>
<!--command
commandId="net.bioclipse.ds.signatures.handlers.ChiralSignaturesDatasetFromSDF"
label="Calculate Chiral Signatures Dataset">
Expand Down Expand Up @@ -142,14 +163,19 @@
point="org.eclipse.ui.commands">
<command
id="net.bioclipse.ds.signatures.handlers.SignaturesDatasetFromSDF"
defaultHandler="net.bioclipse.ds.signatures.handlers.SignaturesDatasetFromSDF"
defaultHandler="net.bioclipse.ds.signatures.handlers.DenseSignaturesDatasetFromSDF"
name="signatureDS">
</command>
<command
id="net.bioclipse.ds.signatures.handlers.SparseSignaturesDatasetFromSDF"
defaultHandler="net.bioclipse.ds.signatures.handlers.SparseSignaturesDatasetFromSDF"
name="signatureDS">
</command>
<!--command
id="net.bioclipse.ds.signatures.handlers.ChiralSignaturesDatasetFromSDF"
defaultHandler="net.bioclipse.ds.signatures.handlers.ChiralSignaturesDatasetFromSDF"
name="signatureDS">
</command>
</command-->
</extension>

</plugin>
154 changes: 53 additions & 101 deletions ...signatures/src/net/bioclipse/ds/signatures/handlers/AbstractSignaturesDatasetFromSDF.java
View file
@@ -1,5 +1,5 @@
/* *****************************************************************************
* Copyright (c) 2010 Ola Spjuth
* Copyright (c) 2011 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
Expand All @@ -10,24 +10,19 @@
******************************************************************************/
package net.bioclipse.ds.signatures.handlers;

import java.io.BufferedInputStream;
import java.io.BufferedReader;
import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.lang.reflect.InvocationTargetException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Set;

import org.apache.log4j.Logger;
import org.eclipse.core.commands.AbstractHandler;
import org.eclipse.core.commands.ExecutionEvent;
import org.eclipse.core.commands.ExecutionException;
import org.eclipse.core.resources.IContainer;
import org.eclipse.core.resources.IFile;
import org.eclipse.core.resources.IResource;
import org.eclipse.core.resources.IWorkspace;
import org.eclipse.core.resources.IWorkspaceRoot;
import org.eclipse.core.resources.ResourcesPlugin;
Expand All @@ -42,26 +37,21 @@
import org.eclipse.core.runtime.jobs.Job;
import org.eclipse.jface.viewers.ISelection;
import org.eclipse.jface.viewers.IStructuredSelection;
import org.eclipse.jface.window.Window;
import org.eclipse.ui.handlers.HandlerUtil;
import org.openscience.cdk.interfaces.IAtom;
import org.osgi.framework.AllServiceListener;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.io.iterator.IteratingMDLReader;
import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;

import net.bioclipse.cdk.business.Activator;
import net.bioclipse.cdk.business.ICDKManager;
import net.bioclipse.cdk.domain.ICDKMolecule;
import net.bioclipse.core.business.BioclipseException;
import net.bioclipse.core.domain.IMolecule;
import net.bioclipse.core.util.LogUtils;
import net.bioclipse.ds.signatures.business.ISignaturesManager;
import net.bioclipse.ds.signatures.prop.calc.AtomSignatures;
import net.bioclipse.ui.business.IUIManager;
import net.bioclipse.core.domain.IDataset;

/**
* A handler that can convert SMILES files into SDFiles.
* A SMIELS file is expected to have a header line with property names,
* and data lines should start with a SMILES string, and have
* properties separated by either ',','\t', or ' '. Properties are also
* stored in the SDF, with header names as identifiers.
* An abstract handler to generate signature datasets from SDF
*
* @author ola
*/
Expand All @@ -72,7 +62,7 @@ public abstract class AbstractSignaturesDatasetFromSDF extends AbstractHandler{

@Override
public Object execute(ExecutionEvent event) throws ExecutionException {

ISelection sel=HandlerUtil.getCurrentSelection(event);
if (!(sel instanceof IStructuredSelection))
throw new ExecutionException("Selection is not an SDF file");
Expand All @@ -87,8 +77,34 @@ public Object execute(ExecutionEvent event) throws ExecutionException {

final IFile file = (IFile) obj;

//Select property for response value
//TODO
//Read mol 1 into mem and extract properties
List<String> availableProperties = new ArrayList<String>();
try {
IteratingMDLReader reader = new IteratingMDLReader(file.getContents(), NoNotificationChemObjectBuilder.getInstance());
IMolecule mol = (IMolecule)reader.next();
for (Object p : mol.getProperties().keySet()){
availableProperties.add((String) p);
}

} catch (CoreException e1) {
throw new ExecutionException("Could not parse molecules from input file");
}

SignaturesDatasetParametersDialog dlg = new SignaturesDatasetParametersDialog(
HandlerUtil.getActiveShell(event),
file.getParent(), getFileExtension(),
availableProperties);

//Input dialog regarding height, name, and select property for response value
int ret = dlg.open();
if (ret==Window.CANCEL) return null;
final SignaturesDatasetModel datasetModel = dlg.getDatasetModel();

// System.out.println("height is " + datasetModel.getHeight());
// System.out.println("responseProp is " + datasetModel.getResponseProperty());
// System.out.println("nameProp is " + datasetModel.getNameProperty());
// System.out.println("File is " + datasetModel.getNewFile());


Job job=new Job("Calculating Signatures Dataset"){

Expand All @@ -107,83 +123,18 @@ protected IStatus run(IProgressMonitor monitor) {
net.bioclipse.ds.signatures.Activator.PLUGIN_ID,
"Error reading SDfile: no molecules. ");

List<String> allSignaturesList=new ArrayList<String>();
List<List<Float>> dataset=new ArrayList<List<Float>>();
List<String> names = new ArrayList<String>();

SubProgressMonitor molmonitor = new SubProgressMonitor(monitor, 5);
molmonitor.beginTask("Calculating signatures", mols.size());

int i=0;
//Process the mols
for (IMolecule mol : mols){
AtomSignatures molsigns = generateSignatures(mol);
List<Float> row = new ArrayList<Float>();
dataset.add(row);
i++;
names.add("Compound " + i + ",");

//Loop over all already stored signatures
for (String sign : allSignaturesList){
//Count occurrences
int nohits=Collections.frequency(molsigns.getSignatures(), sign);
row.add((float)nohits);

//remove all occurrences in molsigns - we have now processed this list of signatures
while (molsigns.getSignatures().contains(sign))
molsigns.getSignatures().remove(sign);
}

//process the new signs
List<String> duplicateSigns=new ArrayList<String>();
for (String sign : molsigns.getSignatures()){

//If already processed, just take next
if (duplicateSigns.contains(sign)) continue;

//Count occurrences
int nohits=Collections.frequency(molsigns.getSignatures(), sign);
if (nohits>1) //If duplicates...
duplicateSigns.add(sign);
//Generate the dataset using the signatures manager
IDataset ds = generateDataset(mols, datasetModel.getHeight(), datasetModel.getNameProperty(), datasetModel.getResponseProperty(), monitor);

//Add the new sign to allSignaturesList
row.add((float)nohits);
allSignaturesList.add(sign);
}

//get next molecule
molmonitor.worked(1);
}

molmonitor.done();

//Fill up with zeros to length
for (List<Float> row : dataset){
while (row.size()<allSignaturesList.size())
row.add(new Float(0));
}
System.out.println("File: " + datasetModel.getNewFile());

//debug it out
System.out.println("== ds ==");

StringBuffer buf = new StringBuffer();
buf.append("Compound, " + allSignaturesList.toString() + "\n");
int c=0;
for (List<Float> row : dataset){
buf.append(names.get(c) + " " + row.toString().substring(1,row.toString().length()-1) + "\n");
c++;
}

//Create output file, replace extension with csv
String filename= file.getName();
IPath sdpath = file.getFullPath().removeLastSegments(1);
String apx=getImplSpecificAppendix();
IPath outpath = new Path(sdpath.append(filename).removeFileExtension().toOSString()+apx).addFileExtension("csv");

//Create output file, replace extension with dataset-specific
IContainer folder = file.getParent();
IPath outpath = folder.getFullPath().append(new Path(datasetModel.getNewFile()));
for (int j=1; j<10; j++){
if (j>1)
outpath = new Path(sdpath.append(filename).removeFileExtension().toOSString()+apx+" ("+j+")").addFileExtension("csv");
if (writeFile(outpath, buf.toString().getBytes())){
outpath = new Path(outpath.removeFileExtension().toOSString()+" ("+j+")").addFileExtension(ds.getFileExtension());
if (writeFile(outpath, ds.getFileContents().getBytes())){
break;
}

Expand Down Expand Up @@ -238,11 +189,12 @@ private boolean writeFile(IPath outpath, byte[] bytes) {
job.schedule();

return null;
}
}

protected abstract IDataset generateDataset(List<ICDKMolecule> mols, int height,
String nameProperty, String responseProperty,
IProgressMonitor monitor);

protected abstract String getImplSpecificAppendix();
protected abstract String getFileExtension();

protected abstract AtomSignatures generateSignatures(IMolecule mol)
throws BioclipseException;

}
46 changes: 0 additions & 46 deletions ...s.signatures/src/net/bioclipse/ds/signatures/handlers/ChiralSignaturesDatasetFromSDF.java
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This file was deleted.

41 changes: 41 additions & 0 deletions ...ds.signatures/src/net/bioclipse/ds/signatures/handlers/DenseSignaturesDatasetFromSDF.java
View file
@@ -0,0 +1,41 @@
/* *****************************************************************************
* Copyright (c) 2011 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.signatures.handlers;

import java.util.List;

import org.eclipse.core.runtime.IProgressMonitor;

import net.bioclipse.cdk.domain.ICDKMolecule;
import net.bioclipse.core.domain.IDataset;
import net.bioclipse.ds.signatures.business.ISignaturesManager;

/**
*
* @author ola
*/
public class DenseSignaturesDatasetFromSDF extends AbstractSignaturesDatasetFromSDF{

@Override
protected IDataset generateDataset(List<ICDKMolecule> mols, int height,
String nameProperty, String responseProperty,
IProgressMonitor monitor) {

ISignaturesManager signatures=net.bioclipse.ds.signatures.Activator.getDefault().getJavaSignaturesManager();
return signatures.generateDataset(mols, height, nameProperty, responseProperty, monitor);

}

@Override
protected String getFileExtension() {
return "csv";
}
}

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