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Rewrote set/getProperty to use atomcontainer.properties to store the …
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…properties.

Solves bug 1195
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@egonw
Arvid Berg authored and egonw committed Mar 25, 2010
1 parent 75736b3 commit 499f63f
Showing 1 changed file with 20 additions and 66 deletions.
86 changes: 20 additions & 66 deletions plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/domain/CDKMolecule.java
View file
Expand Up @@ -15,15 +15,11 @@
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.util.BitSet;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Properties;

import net.bioclipse.cdk.business.Activator;
import net.bioclipse.cdk.business.preferences.PreferenceConstants;
import net.bioclipse.cdk.domain.CDKMoleculeUtils.MolProperty;
import net.bioclipse.core.business.BioclipseException;
import net.bioclipse.core.domain.BioObject;
import net.bioclipse.core.domain.IMolecule;
Expand Down Expand Up @@ -60,10 +56,9 @@ public class CDKMolecule extends BioObject implements ICDKMolecule {
private IAtomContainer atomContainer;

// cached properties
private BitSet cachedFingerprint;
private InChI cachedInchi;

private volatile Map<String,Object> cachedProperties;
private static final String FINGERPRINT_KEY = "net.bioclipse.fingerprint";
private static final String INCHI_KEY = "net.bioclipse.InChI";
private static final String INCHIKEY_KEY = "net.bioclipse.InChI_Key";

private static Preferences prefs;

Expand Down Expand Up @@ -95,7 +90,7 @@ public CDKMolecule( String name,
BitSet fingerprint ) {
this(atomContainer);
this.name = name;
this.cachedFingerprint = fingerprint;
setProperty( FINGERPRINT_KEY, fingerprint );
}


Expand Down Expand Up @@ -200,23 +195,18 @@ public void customize( IAtomContainer molecule,
*/
public BitSet getFingerprint(IMolecule.Property urgency)
throws BioclipseException {
if (urgency == IMolecule.Property.USE_CACHED) return cachedFingerprint;
Object val = getProperty( FINGERPRINT_KEY, urgency );
if(val instanceof BitSet) return (BitSet) val;

if (urgency != IMolecule.Property.USE_CALCULATED) {
if (cachedFingerprint != null) {
return cachedFingerprint;
}
}
Fingerprinter fp=new Fingerprinter();
try {
BitSet fingerprint=fp.getFingerprint(getAtomContainer());
cachedFingerprint=fingerprint;
setProperty( FINGERPRINT_KEY, fingerprint );
return fingerprint;
} catch (Exception e) {
throw new BioclipseException("Could not create fingerprint: "
+ e.getMessage());
}

}

public boolean has3dCoords() throws BioclipseException {
Expand Down Expand Up @@ -265,19 +255,15 @@ public String toString() {

public String getInChI(IMolecule.Property urgency)
throws BioclipseException {
if (urgency == IMolecule.Property.USE_CACHED) {
return cachedInchi == null ? "" : cachedInchi.getValue();
}
Object val = getProperty( INCHI_KEY, urgency );
if(val instanceof InChI) return ((InChI)val).getValue();
if(urgency==Property.USE_CACHED) return "";

if (urgency != IMolecule.Property.USE_CALCULATED) {
if (cachedInchi != null) {
return cachedInchi.getValue();
}
}
IInChIManager inchi = net.bioclipse.inchi.business.Activator.
getDefault().getJavaInChIManager();
try {
cachedInchi = inchi.generate(this);
InChI cachedInchi = inchi.generate(this);
setProperty( INCHI_KEY, cachedInchi );
return cachedInchi.getValue();
} catch (Exception e) {
throw new BioclipseException("Could not create InChI: "
Expand All @@ -287,18 +273,15 @@ public String getInChI(IMolecule.Property urgency)

public String getInChIKey(IMolecule.Property urgency)
throws BioclipseException {
if (urgency == IMolecule.Property.USE_CACHED)
return cachedInchi == null ? "" : cachedInchi.getKey();
Object value = getProperty( INCHI_KEY, urgency );
if(value instanceof InChI) return ((InChI)value).getKey();
if( urgency == Property.USE_CACHED) return "";

if (urgency != IMolecule.Property.USE_CALCULATED) {
if (cachedInchi != null) {
return cachedInchi.getKey();
}
}
IInChIManager inchi = net.bioclipse.inchi.business.Activator.
getDefault().getJavaInChIManager();
try {
cachedInchi = inchi.generate(this);
InChI cachedInchi = inchi.generate(this);
setProperty( INCHI_KEY, cachedInchi );
return cachedInchi.getKey();
} catch (Exception e) {
throw new BioclipseException("Could not create InChIKey: "
Expand All @@ -307,43 +290,14 @@ public String getInChIKey(IMolecule.Property urgency)
}

public Object getProperty(String propertyKey, Property urgency) {
switch (urgency) {
case USE_CALCULATED:
// TODO get calculator for property
case USE_CACHED_OR_CALCULATED:
// TODO if cached use it otherwise calculate
case USE_CACHED:
if(MolProperty.InChI.name().equals( propertyKey ))
return cachedInchi;
if(cachedProperties !=null)
return cachedProperties.get( propertyKey );
}
return null;
return atomContainer.getProperty( propertyKey );
}

public void setProperty(String propertyKey, Object value) {
if(MolProperty.InChI.name().equals( propertyKey ))
cachedInchi = (InChI) value;
else if(MolProperty.Fingerprint.name().equals( propertyKey ))
cachedFingerprint = (BitSet) value;
else {

if(cachedProperties == null)
cachedProperties = Collections.synchronizedMap(
new HashMap<String, Object>() );

cachedProperties.put( propertyKey, value );
}
atomContainer.setProperty( propertyKey, value );
}

void clearProperty( String key ) {
if(MolProperty.InChI.name().equals( key ))
cachedInchi = null;
else if(MolProperty.Fingerprint.name().equals( key ))
cachedFingerprint = null;
else {
if(cachedProperties!= null)
cachedProperties.remove( key );
}
atomContainer.getProperties().remove( key );
}
}

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