Release prep for Goldstandard paper #55
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From Hong: > This version supports output the results as a csv file and also output a > version file writeCSVandVersionFiles.
The Ontology folder in v0.1.0-alpha contains the older fish glossaries used for processing fish files before, and it was not used in the SemanticCharaParser experiment for the Goldstandard.
The 4.x release series should have been the one active while this was developed.
Converting from one type to an incompatible one is no longer allowed in Java 1.8. Here, a list of FormalConcept (an interface) instances are not known to the compiler to be instances of Quality at runtime, and so the conversion is disallowed. The fix here is simple - convert to a non-generic list type first, and then back to the desired generics template type.
The code compiles but it may miss resources that need to be packaged.
Although the POM for a Maven-based build of the phenoscapeII subproject is left in place here, the overall gains from it are minimal, for several reasons: - To run the application, both subproject JARs need to be built, and they reuse some of the same dependencies. Building only one through Maven and the other not yields little to no benefit for the overall list of dependencies to store and manage. - To run the application, all the dependency JARs are still needed at runtime. We could instruct Maven to fold each dependency along with the local classes all into a single self-contained JAR, but that would require to build everything through maven to be really effedctive. And it would also require producing platform-specific packages. - Our objective here is not to create a distributable and executable self-contained application, but to have a mechanism to build and run the application reproducibly and platform-independently. Hence, we're going back to simply using the jdk tools to compile and package, and require platform-specific dependencies to be provided by the user.
Also adds a reference to this document into the README.
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