Glue code

[averagehat]

@crashfrog

final static int DEFAULT_NUM_ROWS = 100;

        final SeqrController controller = new SeqrController(solrServer);
        //pass on to appropriate subcommand

       // query logic
       // rawSequenceInts = indexer.whatever()
       String q = controller.sequenceQueryFromInts(rawSequenceInts);
       QueryResponse response;
       if (space.get(page) != null)
           response = controller.makeQuery(q, space.get("page"), space.get("num_rows") )
       else if (space.get("num_rows") != null){
           response = controller.makeQuery(q, space.get("num_rows"));
       }
       else {
           response = controller.makeQuery(q, DEFAULT_NUM_ROWS);
       }

     // check if index directory exsits  
     // load initial json logic, for first time it's run
     boolean success = controller.loadJSONDir(jsonDir);

     // add file to index logic
     // // indexer.whatever(inputFastas);

[averagehat]

this was integrated