PhylogenyNode.NODE_COUNT does not reset

[Vishal-Joshi]

I am seeing an issue with reading phylogenies with your library. I have multiple files to read phylogenies from sequentially.

Issue is that, once I read the first file, the NODE_COUNT in PhylogenyNode does not reset to 0. That is why, the second file's root does not start with 0 but a count after, where the last file ended. This does not appear to be a correct behavior.

I see that method PhylogenyNode.setNodeCount

synchronized final static void setNodeCount( final long i ) {
       PhylogenyNode.NODE_COUNT = i;
   }

is not accessible from outside the class which prevents me to reset it before I run read phylogenies for second file.

Since NODE_COUNT is a static variable it will live till the class remains loaded by a class loader. Is there a reason why the variable is static? Could we expose this setNodeCount() in PhylogenyNode?

This is the code snipped where I am trying to read multiple files, for your reference.

for (String aFile : files) {
            System.out.println(aFile);

            Phylogeny[] phylogeny = ParserUtils.readPhylogenies(aFile);

           for (Phylogeny p : phylogeny) {
                PhylogenyNode root = p.getRoot();
                System.out.println("Root node: " + root.getName() + " , ID: AN" + root.getId());
                //some more code
            }

        }

Alternatively, if this is not a correct usage for the lib please let me know.