Include jgrapht dependency to biojava-structure#352
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A new test for local symmetry
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It was actually a bad idea to replace all the Lists for Sets, when only a single conversion was needed to call the jgrapht connectivity algorithm. I have undone some of the changes so that the tests for local symmetry introduced by @josemduarte pass in the last commit. |
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Include jgrapht dependency to biojava-structure
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As it was discussed in #299, the BioJava implementations and algorithms for Graphs have been replaced by an external library: jgrapht.
The only code replaced is related to the Quaternary Symmetry detection. Tests pass and demos work as before, but @pwrose might want to take a look and check that the changes are conceptually correct.
As a summary, the ComponentFinder was checking if a SubunitGraph had more than one connected component. This is now done by using the ConnectivityInspector from jgrapht, that returns true if the graph is connected (one component) or not (more than one component). The constructor of the SubunitGraph is the same, and also the construction of a SubGraph given a set of vertices.
Merging this closes issue #319.