Adds standard log4j props.
Adds filters.
Adds query interface and implementation.
Creates the mdk identifier resolver.
First working version.
Adds documentation and todos for various classes.
Adds documentation for more classes.
Merge branch 'feature/documentClasses' into develop
Gets rid of the Retriever interface and replaces the underlying retriever in MultiServiceFilteredRetriever
Changes the order in which the leafs are marked and the pruning is done.
Adds name to the graph and tides up the graph in general. Reduces the number of convenience accessors for elements of the graph. Handles loops when matched leafs are involved. Now leafs and matched leafs are disjoint sets.
Implements intersections and retrieval steps.
Adds the exec class for two protein lists.
Corrects signature of the simplest underlying interaction retriever.
Corrects missing push query invocation.
Merge branch 'feature/mergingDifferentRetrievers' into develop
Corrects the way that the taxon is set.
Avoids concurrent modifications on some collections.
Neglects isoforms… this is probably arguable to do.
Merge branch 'feature/correctionsForFirstRunningVersion' into develop