Recent changes to feature-requests-improvements

Change distances to similarities in Base Matchers

2011-10-07T14:47:00Z

For all base matchers, the distance metric (0 is best, 1 is worst) must be changed to similarities (0 is worst, 1 is best).

Implement correspondence evaluation cache

2011-10-07T14:41:34Z

Some base matchers could cache the evaluations of correspondences.

Refactor cloud deployment code to harmonia-commons or kadmos

2011-05-18T08:18:52Z

It should be evaluated how the cloud deployment implementation can be generalised in order to be available for several population-based alignment algorithms. In particular, the code should then be part of harmonia-commons or kadmos.

Refactor fitness calaculation to harmonia-commons

2011-05-18T08:13:32Z

The fitness calculation should be provided by the harmonia-commons fitness calculator project since it is a shared functionality for this and other alignment algorithms. Fitness calculation means the aggregation of an alignment fitness from the individual correspondences' fitnesses and other global fitnes criteria.

Maven WAR packaging

2011-05-18T07:56:12Z

In order to enable MapPSO to be deployed as a web service, we need a WAR file to be deployed in an application server e.g. Tomcat. Maven must be configured to package such a WAR file.

Switch to KADMOS API

2011-05-18T07:51:04Z

The KADMOS API (https://sourceforge.net/projects/kadmos/) should replace the Alignment API.

Switch to Commons Logging

2011-05-18T07:47:23Z

Apache Commons Logging is the better logging framework for library-like software components like MapPSO. It should be used throughout the project apart from any entry points (which should not exist anyway).

Refactor particle length adjustment

2011-05-02T14:12:10Z

The particle length adjustment procedure is rather obscure and probably buggy. In order to make it easier to test, the single method should be refactored into several that provide the different core functionalities required for length adjustment, i.e. computation of change probability, computation of actual length change, and performing the adding and removal of correspondences. The different methods should be designed for easy testing, and as decoupled as possible from the rest of MapPSO.

Read WordNet dictionary and version from system variables

2010-08-20T09:24:34Z

Before WordNet initialisation, read the dictionary and version parameters from system variables to make it easier to run MapPSO on a distributed environment with different WordNet locations. The parameters coming from params.xml should override the system variables though.

Enable confidence values in alignment

2010-06-13T20:54:36Z

The final alignment should contain confidence values for each correspondence. This means the "strength" value in Cell objects should be used, where
strength = 1 - dist
Setting the strength value in AlignmentParticle immediately after distance computation results in a ConcurrentModificationException using two large ontologies with 4 particles in only 2 iterations.

Exception in thread "0" java.util.ConcurrentModificationException
at java.util.HashMap$HashIterator.nextEntry(HashMap.java:810)
at java.util.HashMap$EntryIterator.next(HashMap.java:851)
at java.util.HashMap$EntryIterator.next(HashMap.java:849)
at de.fzi.mappso.align.impl.AlignmentParticle.proportionalLikelihoodUpdate(AlignmentParticle.java:756)
at de.fzi.mappso.align.impl.AlignmentParticle.updateVelocity(AlignmentParticle.java:724)
at de.fzi.mappso.align.impl.AlignmentParticle.update(AlignmentParticle.java:455)
at de.fzi.mappso.align.impl.AlignmentParticle.step(AlignmentParticle.java:256)
at de.fzi.mappso.align.impl.AlignmentParticle.run(AlignmentParticle.java:230)
at java.lang.Thread.run(Thread.java:636)
Exception in thread "2" java.util.ConcurrentModificationException
at java.util.HashMap$HashIterator.nextEntry(HashMap.java:810)
at java.util.HashMap$EntryIterator.next(HashMap.java:851)
at java.util.HashMap$EntryIterator.next(HashMap.java:849)
at de.fzi.mappso.align.impl.AlignmentParticle.proportionalLikelihoodUpdate(AlignmentParticle.java:756)
at de.fzi.mappso.align.impl.AlignmentParticle.updateVelocity(AlignmentParticle.java:724)
at de.fzi.mappso.align.impl.AlignmentParticle.update(AlignmentParticle.java:455)
at de.fzi.mappso.align.impl.AlignmentParticle.step(AlignmentParticle.java:256)
at de.fzi.mappso.align.impl.AlignmentParticle.run(AlignmentParticle.java:230)
at java.lang.Thread.run(Thread.java:636)
Exception in thread "3" java.util.ConcurrentModificationException
at java.util.HashMap$HashIterator.nextEntry(HashMap.java:810)
at java.util.HashMap$EntryIterator.next(HashMap.java:851)
at java.util.HashMap$EntryIterator.next(HashMap.java:849)
at de.fzi.mappso.align.impl.AlignmentParticle.proportionalLikelihoodUpdate(AlignmentParticle.java:756)
at de.fzi.mappso.align.impl.AlignmentParticle.updateVelocity(AlignmentParticle.java:724)
at de.fzi.mappso.align.impl.AlignmentParticle.update(AlignmentParticle.java:455)
at de.fzi.mappso.align.impl.AlignmentParticle.step(AlignmentParticle.java:256)
at de.fzi.mappso.align.impl.AlignmentParticle.run(AlignmentParticle.java:230)
at java.lang.Thread.run(Thread.java:636)
Exception in thread "1" java.util.ConcurrentModificationException
at java.util.HashMap$HashIterator.nextEntry(HashMap.java:810)
at java.util.HashMap$EntryIterator.next(HashMap.java:851)
at java.util.HashMap$EntryIterator.next(HashMap.java:849)
at de.fzi.mappso.align.impl.AlignmentParticle.proportionalLikelihoodUpdate(AlignmentParticle.java:756)
at de.fzi.mappso.align.impl.AlignmentParticle.updateVelocity(AlignmentParticle.java:724)
at de.fzi.mappso.align.impl.AlignmentParticle.update(AlignmentParticle.java:455)
at de.fzi.mappso.align.impl.AlignmentParticle.step(AlignmentParticle.java:256)
at de.fzi.mappso.align.impl.AlignmentParticle.run(AlignmentParticle.java:230)
at java.lang.Thread.run(Thread.java:636)