/** {@inheritDoc} */
@TestMethod("testGetMIMEType")
public String getMIMEType() {
return null;
}The JavaDoc documentation notes that missing @param and @return values are inherited implicitly since JavaDoc 1.3, but I have never noticed this in Java6. The above explicit markup is confirmed to work.
, which I read with pleasure.
. Don't have time for that.
<b:loop values='data:labels' var='label'>
<b:if cond='data:label.count > 6'>
<span expr:class='"label-size label-size-" + data:label.cssSize'>
<b:if cond='data:blog.url == data:label.url'>
<span expr:dir='data:blog.languageDirection'>
<data:label.name/>
</span>
<b:else/>
<a expr:dir='data:blog.languageDirection'
expr:href='data:label.url'>
<data:label.name/>
</a>
</b:if>
<b:if cond='data:showFreqNumbers'>
<span class='label-count' dir='ltr'>
(<data:label.count/>)
</span>
</b:if>
</span>
</b:if>
</b:loop>
$ ant -f pmd.xmlHowever, when working on a single file, you will likely appreciated running the tests against a single module. This can be done with (for the data module):
$ ant -f pmd.xml -Dpmd.test=custom -Dmodule=data test-moduleThe custom.xml defines the tests we normally run.
$ xpath -e "//violation[@class='DefaultChemObjectBuilder']" \\
reports/pmd/data.xml
// query a service using the OpenTox API 1.1
// See: http://www.opentox.org/dev/apis/api-1.1
var service = "http://apps.ideaconsult.net:8180/ambit2/";
var datasets = opentox.listDataSets(service);
for (set=0; set<datasets.size(); set++) {
var dataset = datasets.get(set);
js.say("Downloading set: " + dataset);
ui.open(
opentox.downloadDataSetAsMDLSDfile(
service, dataset, "/OpenTox/ambit" + dataset + ".sdf"
)
)
}Behind this plugin is again the RDF plugin, as OpenTox uses RDF too, a few simple SPARQL queries was all that needed to be defined. And again, the Bioclipse pluigin code base is pretty small.
System.getProperty("java.version").indexOf("1.6") != -1
you can write:System.getProperty("java.version").contains("1.6")
More efficient use of the LoggingToollogger.debug( "\n" + paths.size() + " paths and " + ac.getAtomCount() + " atoms left." );you can write:
logger.debug( "\n", paths.size(), " paths and ", ac.getAtomCount(), " atoms left." );
List atoms = atomContainer.atoms();
for (int i=0; i<atoms.size(); i++) {
IAtom atom = (IAtom)atoms.get(i);
// .. do something
}you can do:List<IAtom> atoms = atomContainer.atoms();
for (int i=0; i<atoms.size(); i++) {
IAtom atom = atoms.get(i);
// .. do something
}If you do not need the index, use a for-each loopfor (IAtom atom : atomContainer.atoms()) {
// .. do something
}
I'd like to announce first alpha version of OOChemistry. It is an extension for OpenOffice.org which provides cross-platform OLE-like integration of OOo with JChemPaint chemical diagram editor. With OOChemistry you can draw structure, embed into document (text or presentation) and than double click and edit whenever you want on any platform having OpenOffice.org and Java Runtime (Windows, Linux, Mac OS X, other Unix flavours). Remember that it's only alpha and is not recommended for production use (e.g., compatibility with futher versions is not guaranteed).
Known bugs: http://sourceforge.net/tracker/?group_id=273144&atid=1161036, (please, submit if you found other issues!)
More about project, contact info, how to contribute: http://oochemistry.sourceforge.net
Direct link to download: http://sourceforge.net/projects/oochemistry/files/latest
OOChemistry needs your help! Experience in Java, in development of projects dealing with JChemPaint/CDK, or in development of OpenOffice.org extensions will be highly appreciated. Of course, you can help not only in coding, but also in translation of interface and writing docs.
--
Regards,
Konstantin
IMolecule mol = reader.read(new Molecule());The list of patches furthermore contains an update of the PubChem reader to support reading of additional fields, and the support of the CML @ref attribute in CMLReact (doi:10.1021/ci0502698).
26 Egon Willighagen 9 Stefan Kuhn 1 Brian Gilman 1 Mark Rynbeek 1 Miguel Rojas Cherto 1 Gilleain TorranceReviewers
23 Rajarshi Guha 4 Egon Willighagen
<extension point="net.bioclipse.rdf.rdf2bioobjectfactory">
<Factory
instance="net.bioclipse.rdf.ui.RDFToCDKMoleculeFactory"
uri="http://www.bioclipse.net/structuredb/#Molecule" >
</Factory>
</extension>
The API for this factory looks like:public IBioObject rdfToBioObject( Model model, Resource res ); public ImageDescriptor getImageDescriptor();This is very much tied into the Jena data model, so not entirely clean, but has to do for now. The first method converts RDF content into a Bioclipse IBioObject, such as an IMolecule (see this list of currently supported objects). The second method returns an icon, which makes the editor more visually pleasing, and provides a nice way to see when you can double click the RDF node to have it open in an domain specific editor:
