├── .gitignore ├── README.md ├── datasets ├── Prompts.zip ├── README.md ├── java_hidden.json ├── java_public.json ├── java_similar.json ├── python_hidden.json ├── python_public.json ├── python_similar.json └── rosalind.json ├── evaluation ├── .DS_Store ├── CentralServer │ ├── lambda_queue_handler.py │ └── lambda_queue_handler_dynamodb.py ├── DockerServers │ ├── .DS_Store │ ├── Dockerfile │ ├── docker_runner.py │ └── init_vm_ebs_only.sh ├── Fuzzer │ ├── ba1a.py │ ├── check_golden.py │ ├── find_and_replacer_delete.py │ ├── fuzzer_tester.py │ ├── jiakang_scratch.ipynb │ ├── parsing_strategies_delete.py │ ├── rosalind_testcases.zip │ ├── run_java.sh │ ├── test_functions │ │ ├── java_test_function_1 │ │ │ ├── context.java │ │ │ ├── generated_code.java │ │ │ └── golden_code.java │ │ ├── java_test_function_2 │ │ │ ├── context.java │ │ │ ├── generated_code.java │ │ │ └── golden_code.java │ │ ├── java_test_function_3 │ │ │ ├── context.java │ │ │ ├── generated_code.java │ │ │ └── golden_code.java │ │ ├── java_test_function_4 │ │ │ ├── context.java │ │ │ ├── generated_code.java │ │ │ └── golden_code.java │ │ ├── java_test_function_5 │ │ │ ├── context.java │ │ │ ├── generated_code.java │ │ │ └── golden_code.java │ │ ├── python_test_function_1 │ │ │ ├── context.py │ │ │ ├── generated_code.py │ │ │ └── golden_code.py │ │ ├── python_test_function_2 │ │ │ ├── context.py │ │ │ ├── generated_code.py │ │ │ └── golden_code.py │ │ ├── python_test_function_3 │ │ │ ├── context.py │ │ │ ├── generated_code.py │ │ │ └── golden_code.py │ │ ├── python_test_function_4 │ │ │ ├── context.py │ │ │ ├── generated_code.py │ │ │ └── golden_code.py │ │ ├── python_test_function_5 │ │ │ ├── context.py │ │ │ ├── generated.py │ │ │ └── golden.py │ │ ├── python_test_function_6 │ │ │ ├── context.py │ │ │ ├── generated.py │ │ │ └── golden.py │ │ └── test │ │ │ ├── context.py │ │ │ ├── generated_code.py │ │ │ └── golden_code.py │ ├── test_fuzzer_1.py │ └── test_jiakang.ipynb ├── ImageBuilder │ ├── .DS_Store │ ├── build_data.yaml │ ├── build_docker_image.py │ ├── build_image.sh │ ├── init_build_environment.sh │ ├── requirements.txt │ └── start_test.py ├── TestCaseLoader │ ├── .DS_Store │ ├── download_test_case.py │ ├── gather_results copy.ipynb │ ├── gather_results.ipynb │ ├── load_golden.py │ └── upload_test_cases.py ├── TestRosalind │ ├── run_script.sh │ ├── skeleton.py │ ├── testcases │ │ ├── rosalind_2sat.txt │ │ ├── rosalind_2satsol.txt │ │ ├── rosalind_2sum.txt │ │ ├── rosalind_2sumsol.txt │ │ ├── rosalind_3sum.txt │ │ ├── rosalind_3sumsol.txt │ │ ├── rosalind_afrq.txt │ │ ├── rosalind_afrqsol.txt │ │ ├── rosalind_alph.txt │ │ ├── rosalind_alphsol.txt │ │ ├── rosalind_asmq.txt │ │ ├── rosalind_asmqsol.txt │ │ ├── rosalind_aspc.txt │ │ ├── rosalind_aspcsol.txt │ │ ├── rosalind_ba10a.txt │ │ ├── rosalind_ba10asol.txt │ │ ├── rosalind_ba10b.txt │ │ ├── rosalind_ba10bsol.txt │ │ ├── rosalind_ba10c.txt │ │ ├── rosalind_ba10csol.txt │ │ ├── rosalind_ba10d.txt │ │ ├── rosalind_ba10dsol.txt │ │ ├── rosalind_ba10e.txt │ │ ├── rosalind_ba10esol.txt │ │ ├── rosalind_ba10f.txt │ │ ├── rosalind_ba10fsol.txt │ │ ├── rosalind_ba10g.txt │ │ ├── rosalind_ba10gsol.txt │ │ ├── rosalind_ba10h.txt │ │ ├── rosalind_ba10hsol.txt │ │ ├── rosalind_ba10i.txt │ │ ├── rosalind_ba10isol.txt │ │ ├── rosalind_ba10j.txt │ │ ├── rosalind_ba10jsol.txt │ │ ├── rosalind_ba10k.txt │ │ ├── rosalind_ba10ksol.txt │ │ ├── rosalind_ba11a.txt │ │ ├── rosalind_ba11asol.txt │ │ ├── rosalind_ba11b.txt │ │ ├── rosalind_ba11bsol.txt │ │ ├── rosalind_ba11c.txt │ │ ├── rosalind_ba11csol.txt │ │ ├── rosalind_ba11d.txt │ │ ├── rosalind_ba11dsol.txt │ │ ├── rosalind_ba11e.txt │ │ ├── rosalind_ba11esol.txt │ │ ├── rosalind_ba11f.txt │ │ ├── rosalind_ba11fsol.txt │ │ ├── rosalind_ba11g.txt │ │ ├── rosalind_ba11gsol.txt │ │ ├── rosalind_ba11h.txt │ │ ├── rosalind_ba11hsol.txt │ │ ├── rosalind_ba11i.txt │ │ ├── rosalind_ba11isol.txt │ │ ├── rosalind_ba11j.txt │ │ ├── rosalind_ba11jsol.txt │ │ ├── rosalind_ba1a.txt │ │ ├── rosalind_ba1asol.txt │ │ ├── rosalind_ba1b.txt │ │ ├── rosalind_ba1bsol.txt │ │ ├── rosalind_ba1c.txt │ │ ├── rosalind_ba1csol.txt │ │ ├── rosalind_ba1d.txt │ │ ├── rosalind_ba1dsol.txt │ │ ├── rosalind_ba1e.txt │ │ ├── rosalind_ba1esol.txt │ │ ├── rosalind_ba1f.txt │ │ ├── rosalind_ba1fsol.txt │ │ ├── rosalind_ba1g.txt │ │ ├── rosalind_ba1gsol.txt │ │ ├── rosalind_ba1h.txt │ │ ├── rosalind_ba1hsol.txt │ │ ├── rosalind_ba1i.txt │ │ ├── rosalind_ba1isol.txt │ │ ├── rosalind_ba1j.txt │ │ ├── rosalind_ba1jsol.txt │ │ ├── rosalind_ba1k.txt │ │ ├── rosalind_ba1ksol.txt │ │ ├── rosalind_ba1l.txt │ │ ├── rosalind_ba1lsol.txt │ │ ├── rosalind_ba1m.txt │ │ ├── rosalind_ba1msol.txt │ │ ├── rosalind_ba1n.txt │ │ ├── rosalind_ba1nsol.txt │ │ ├── rosalind_ba2a.txt │ │ ├── rosalind_ba2asol.txt │ │ ├── rosalind_ba2b.txt │ │ ├── rosalind_ba2bsol.txt │ │ ├── rosalind_ba2c.txt │ │ ├── rosalind_ba2csol.txt │ │ ├── rosalind_ba2d.txt │ │ ├── rosalind_ba2dsol.txt │ │ ├── rosalind_ba2e.txt │ │ ├── rosalind_ba2esol.txt │ │ ├── rosalind_ba2f.txt │ │ ├── rosalind_ba2fsol.txt │ │ ├── rosalind_ba2g.txt │ │ ├── rosalind_ba2gsol.txt │ │ ├── rosalind_ba2h.txt │ │ ├── rosalind_ba2hsol.txt │ │ ├── rosalind_ba3a.txt │ │ ├── rosalind_ba3asol.txt │ │ ├── rosalind_ba3b.txt │ │ ├── rosalind_ba3bsol.txt │ │ ├── rosalind_ba3c.txt │ │ ├── rosalind_ba3csol.txt │ │ ├── rosalind_ba3d.txt │ │ ├── rosalind_ba3dsol.txt │ │ ├── rosalind_ba3e.txt │ │ ├── rosalind_ba3esol.txt │ │ ├── rosalind_ba3f.txt │ │ ├── rosalind_ba3fsol.txt │ │ ├── rosalind_ba3g.txt │ │ ├── rosalind_ba3gsol.txt │ │ ├── rosalind_ba3h.txt │ │ ├── rosalind_ba3hsol.txt │ │ ├── rosalind_ba3i.txt │ │ ├── rosalind_ba3isol.txt │ │ ├── rosalind_ba3j.txt │ │ ├── rosalind_ba3jsol.txt │ │ ├── rosalind_ba3k.txt │ │ ├── rosalind_ba3ksol.txt │ │ ├── rosalind_ba3l.txt │ │ ├── rosalind_ba3lsol.txt │ │ ├── rosalind_ba3m.txt │ │ ├── rosalind_ba3msol.txt │ │ ├── rosalind_ba4a.txt │ │ ├── rosalind_ba4asol.txt │ │ ├── rosalind_ba4b.txt │ │ ├── rosalind_ba4bsol.txt │ │ ├── rosalind_ba4c.txt │ │ ├── rosalind_ba4csol.txt │ │ ├── rosalind_ba4d.txt │ │ ├── rosalind_ba4dsol.txt │ │ ├── rosalind_ba4e.txt │ │ ├── rosalind_ba4esol.txt │ │ ├── rosalind_ba4f.txt │ │ ├── rosalind_ba4fsol.txt │ │ ├── rosalind_ba4g.txt │ │ ├── rosalind_ba4gsol.txt │ │ ├── rosalind_ba4h.txt │ │ ├── rosalind_ba4hsol.txt │ │ ├── rosalind_ba4i.txt │ │ ├── rosalind_ba4isol.txt │ │ ├── rosalind_ba4j.txt │ │ ├── rosalind_ba4jsol.txt │ │ ├── rosalind_ba4k.txt │ │ ├── rosalind_ba4ksol.txt │ │ ├── rosalind_ba4l.txt │ │ ├── rosalind_ba4lsol.txt │ │ ├── rosalind_ba4m.txt │ │ ├── rosalind_ba4msol.txt │ │ ├── rosalind_ba5a.txt │ │ ├── rosalind_ba5asol.txt │ │ ├── rosalind_ba5b.txt │ │ ├── rosalind_ba5bsol.txt │ │ ├── rosalind_ba5c.txt │ │ ├── rosalind_ba5csol.txt │ │ ├── rosalind_ba5d.txt │ │ ├── rosalind_ba5dsol.txt │ │ ├── rosalind_ba5e.txt │ │ ├── rosalind_ba5esol.txt │ │ ├── rosalind_ba5f.txt │ │ ├── rosalind_ba5fsol.txt │ │ ├── rosalind_ba5g.txt │ │ ├── rosalind_ba5gsol.txt │ │ ├── rosalind_ba5h.txt │ │ ├── rosalind_ba5hsol.txt │ │ ├── rosalind_ba5i.txt │ │ ├── rosalind_ba5isol.txt │ │ ├── rosalind_ba5j.txt │ │ ├── rosalind_ba5jsol.txt │ │ ├── rosalind_ba5k.txt │ │ ├── rosalind_ba5ksol.txt │ │ ├── rosalind_ba5l.txt │ │ ├── rosalind_ba5lsol.txt │ │ ├── rosalind_ba5m.txt │ │ ├── rosalind_ba5msol.txt │ │ ├── rosalind_ba5n.txt │ │ ├── rosalind_ba5nsol.txt │ │ ├── rosalind_ba6a.txt │ │ ├── rosalind_ba6asol.txt │ │ ├── rosalind_ba6b.txt │ │ ├── rosalind_ba6bsol.txt │ │ ├── rosalind_ba6c.txt │ │ ├── rosalind_ba6csol.txt │ │ ├── rosalind_ba6d.txt │ │ ├── rosalind_ba6dsol.txt │ │ ├── rosalind_ba6e.txt │ │ ├── rosalind_ba6esol.txt │ │ ├── rosalind_ba6f.txt │ │ ├── rosalind_ba6fsol.txt │ │ ├── rosalind_ba6g.txt │ │ ├── rosalind_ba6gsol.txt │ │ ├── rosalind_ba6h.txt │ │ ├── rosalind_ba6hsol.txt │ │ ├── rosalind_ba6i.txt │ │ ├── rosalind_ba6isol.txt │ │ ├── rosalind_ba6j.txt │ │ ├── rosalind_ba6jsol.txt │ │ ├── rosalind_ba6k.txt │ │ ├── rosalind_ba6ksol.txt │ │ ├── rosalind_ba7a.txt │ │ ├── rosalind_ba7asol.txt │ │ ├── rosalind_ba7b.txt │ │ ├── rosalind_ba7bsol.txt │ │ ├── rosalind_ba7c.txt │ │ ├── rosalind_ba7csol.txt │ │ ├── rosalind_ba7d.txt │ │ ├── rosalind_ba7dsol.txt │ │ ├── rosalind_ba7e.txt │ │ ├── rosalind_ba7esol.txt │ │ ├── rosalind_ba7f.txt │ │ ├── rosalind_ba7fsol.txt │ │ ├── rosalind_ba7g.txt │ │ ├── rosalind_ba7gsol.txt │ │ ├── rosalind_ba8a.txt │ │ ├── rosalind_ba8asol.txt │ │ ├── rosalind_ba8b.txt │ │ ├── rosalind_ba8bsol.txt │ │ ├── rosalind_ba8c.txt │ │ ├── rosalind_ba8csol.txt │ │ ├── rosalind_ba8d.txt │ │ ├── rosalind_ba8dsol.txt │ │ ├── rosalind_ba8e.txt │ │ ├── rosalind_ba8esol.txt │ │ ├── rosalind_ba9a.txt │ │ ├── rosalind_ba9asol.txt │ │ ├── rosalind_ba9b.txt │ │ ├── rosalind_ba9bsol.txt │ │ ├── rosalind_ba9c.txt │ │ ├── rosalind_ba9csol.txt │ │ ├── rosalind_ba9d.txt │ │ ├── rosalind_ba9dsol.txt │ │ ├── rosalind_ba9e.txt │ │ ├── rosalind_ba9esol.txt │ │ ├── rosalind_ba9f.txt │ │ ├── rosalind_ba9fsol.txt │ │ ├── rosalind_ba9g.txt │ │ ├── rosalind_ba9gsol.txt │ │ ├── rosalind_ba9h.txt │ │ ├── rosalind_ba9hsol.txt │ │ ├── rosalind_ba9i.txt │ │ ├── rosalind_ba9isol.txt │ │ ├── rosalind_ba9j.txt │ │ ├── rosalind_ba9jsol.txt │ │ ├── rosalind_ba9k.txt │ │ ├── rosalind_ba9ksol.txt │ │ ├── rosalind_ba9l.txt │ │ ├── rosalind_ba9lsol.txt │ │ ├── rosalind_ba9m.txt │ │ ├── rosalind_ba9msol.txt │ │ ├── rosalind_ba9n.txt │ │ ├── rosalind_ba9nsol.txt │ │ ├── rosalind_ba9o.txt │ │ ├── rosalind_ba9osol.txt │ │ ├── rosalind_ba9p.txt │ │ ├── rosalind_ba9psol.txt │ │ ├── rosalind_ba9q.txt │ │ ├── rosalind_ba9qsol.txt │ │ ├── rosalind_ba9r.txt │ │ ├── rosalind_ba9rsol.txt │ │ ├── rosalind_bf.txt │ │ ├── rosalind_bfil.txt │ │ ├── rosalind_bfilsol.txt │ │ ├── rosalind_bfs.txt │ │ ├── rosalind_bfsol.txt │ │ ├── rosalind_bfssol.txt │ │ ├── rosalind_bins.txt │ │ ├── rosalind_binssol.txt │ │ ├── rosalind_bip.txt │ │ ├── rosalind_bipsol.txt │ │ ├── rosalind_bphr.txt │ │ ├── rosalind_bphrsol.txt │ │ ├── rosalind_cat.txt │ │ ├── rosalind_catsol.txt │ │ ├── rosalind_cc.txt │ │ ├── rosalind_ccsol.txt │ │ ├── rosalind_chbp.txt │ │ ├── rosalind_chbpsol.txt │ │ ├── rosalind_clus.txt │ │ ├── rosalind_clussol.txt │ │ ├── rosalind_cntq.txt │ │ ├── rosalind_cntqsol.txt │ │ ├── rosalind_cons.txt │ │ ├── rosalind_conssol.txt │ │ ├── rosalind_conv.txt │ │ ├── rosalind_convsol.txt │ │ ├── rosalind_corr.txt │ │ ├── rosalind_corrsol.txt │ │ ├── rosalind_cset.txt │ │ ├── rosalind_csetsol.txt │ │ ├── rosalind_cstr.txt │ │ ├── rosalind_cstrsol.txt │ │ ├── rosalind_ctbl.txt │ │ ├── rosalind_ctblsol.txt │ │ ├── rosalind_cte.txt │ │ ├── rosalind_ctea.txt │ │ ├── rosalind_cteasol.txt │ │ ├── rosalind_ctesol.txt │ │ ├── rosalind_cunr.txt │ │ ├── rosalind_cunrsol.txt │ │ ├── rosalind_dag.txt │ │ ├── rosalind_dagsol.txt │ │ ├── rosalind_dbru.txt │ │ ├── rosalind_dbrusol.txt │ │ ├── rosalind_ddeg.txt │ │ ├── rosalind_ddegsol.txt │ │ ├── rosalind_deg.txt │ │ ├── rosalind_degsol.txt │ │ ├── rosalind_dij.txt │ │ ├── rosalind_dijsol.txt │ │ ├── rosalind_dna.txt │ │ ├── rosalind_dnasol.txt │ │ ├── rosalind_ebin.txt │ │ ├── rosalind_ebinsol.txt │ │ ├── rosalind_edit.txt │ │ ├── rosalind_editsol.txt │ │ ├── rosalind_edta.txt │ │ ├── rosalind_edtasol.txt │ │ ├── rosalind_eubt.txt │ │ ├── rosalind_eubtsol.txt │ │ ├── rosalind_eval.txt │ │ ├── rosalind_evalsol.txt │ │ ├── rosalind_fib.txt │ │ ├── rosalind_fibd.txt │ │ ├── rosalind_fibdsol.txt │ │ ├── rosalind_fibo.txt │ │ ├── rosalind_fibosol.txt │ │ ├── rosalind_fibsol.txt │ │ ├── rosalind_filt.txt │ │ ├── rosalind_filtsol.txt │ │ ├── rosalind_foun.txt │ │ ├── rosalind_founsol.txt │ │ ├── rosalind_frmt.txt │ │ ├── rosalind_frmtsol.txt │ │ ├── rosalind_full.txt │ │ ├── rosalind_fullsol.txt │ │ ├── rosalind_gaff.txt │ │ ├── rosalind_gaffsol.txt │ │ ├── rosalind_gasm.txt │ │ ├── rosalind_gasmsol.txt │ │ ├── rosalind_gbk.txt │ │ ├── rosalind_gbksol.txt │ │ ├── rosalind_gc.txt │ │ ├── rosalind_gcon.txt │ │ ├── rosalind_gconsol.txt │ │ ├── rosalind_gcsol.txt │ │ ├── rosalind_glob.txt │ │ ├── rosalind_globsol.txt │ │ ├── rosalind_grep.txt │ │ ├── rosalind_grepsol.txt │ │ ├── rosalind_grph.txt │ │ ├── rosalind_grphsol.txt │ │ ├── rosalind_gs.txt │ │ ├── rosalind_gssol.txt │ │ ├── rosalind_hamm.txt │ │ ├── rosalind_hammsol.txt │ │ ├── rosalind_hdag.txt │ │ ├── rosalind_hdagsol.txt │ │ ├── rosalind_hea.txt │ │ ├── rosalind_heasol.txt │ │ ├── rosalind_hs.txt │ │ ├── rosalind_hssol.txt │ │ ├── rosalind_iev.txt │ │ ├── rosalind_ievsol.txt │ │ ├── rosalind_indc.txt │ │ ├── rosalind_indcsol.txt │ │ ├── rosalind_ini.txt │ │ ├── rosalind_ini1.txt │ │ ├── rosalind_ini1sol.txt │ │ ├── rosalind_ini2.txt │ │ ├── rosalind_ini2sol.txt │ │ ├── rosalind_ini3.txt │ │ ├── rosalind_ini3sol.txt │ │ ├── rosalind_ini4.txt │ │ ├── rosalind_ini4sol.txt │ │ ├── rosalind_ini5.txt │ │ ├── rosalind_ini5sol.txt │ │ ├── rosalind_ini6.txt │ │ ├── rosalind_ini6sol.txt │ │ ├── rosalind_inisol.txt │ │ ├── rosalind_inod.txt │ │ ├── rosalind_inodsol.txt │ │ ├── rosalind_ins.txt │ │ ├── rosalind_inssol.txt │ │ ├── rosalind_inv.txt │ │ ├── rosalind_invsol.txt │ │ ├── rosalind_iprb.txt │ │ ├── rosalind_iprbsol.txt │ │ ├── rosalind_itwv.txt │ │ ├── rosalind_itwvsol.txt │ │ ├── rosalind_kmer.txt │ │ ├── rosalind_kmersol.txt │ │ ├── rosalind_kmp.txt │ │ ├── rosalind_kmpsol.txt │ │ ├── rosalind_ksim.txt │ │ ├── rosalind_ksimsol.txt │ │ ├── rosalind_laff.txt │ │ ├── rosalind_laffsol.txt │ │ ├── rosalind_lcsm.txt │ │ ├── rosalind_lcsmsol.txt │ │ ├── rosalind_lcsq.txt │ │ ├── rosalind_lcsqsol.txt │ │ ├── rosalind_lexf.txt │ │ ├── rosalind_lexfsol.txt │ │ ├── rosalind_lexv.txt │ │ ├── rosalind_lexvsol.txt │ │ ├── rosalind_lgis.txt │ │ ├── rosalind_lgissol.txt │ │ ├── rosalind_lia.txt │ │ ├── rosalind_liasol.txt │ │ ├── rosalind_ling.txt │ │ ├── rosalind_lingsol.txt │ │ ├── rosalind_loca.txt │ │ ├── rosalind_locasol.txt │ │ ├── rosalind_long.txt │ │ ├── rosalind_longsol.txt │ │ ├── rosalind_lrep.txt │ │ ├── rosalind_lrepsol.txt │ │ ├── rosalind_lscmsol.txt │ │ ├── rosalind_maj.txt │ │ ├── rosalind_majsol.txt │ │ ├── rosalind_med.txt │ │ ├── rosalind_medsol.txt │ │ ├── rosalind_meme.txt │ │ ├── rosalind_memesol.txt │ │ ├── rosalind_mend.txt │ │ ├── rosalind_mendsol.txt │ │ ├── rosalind_mer.txt │ │ ├── rosalind_mersol.txt │ │ ├── rosalind_mgap.txt │ │ ├── rosalind_mgapsol.txt │ │ ├── rosalind_mmch.txt │ │ ├── rosalind_mmchsol.txt │ │ ├── rosalind_motz.txt │ │ ├── rosalind_motzsol.txt │ │ ├── rosalind_mprt.txt │ │ ├── rosalind_mprtsol.txt │ │ ├── rosalind_mrep.txt │ │ ├── rosalind_mrepsol.txt │ │ ├── rosalind_mrna.txt │ │ ├── rosalind_mrnasol.txt │ │ ├── rosalind_ms.txt │ │ ├── rosalind_mssol.txt │ │ ├── rosalind_mult.txt │ │ ├── rosalind_multsol.txt │ │ ├── rosalind_need.txt │ │ ├── rosalind_needsol.txt │ │ ├── rosalind_nkew.txt │ │ ├── rosalind_nkewsol.txt │ │ ├── rosalind_nwc.txt │ │ ├── rosalind_nwck.txt │ │ ├── rosalind_nwcksol.txt │ │ ├── rosalind_nwcsol.txt │ │ ├── rosalind_oap.txt │ │ ├── rosalind_oapsol.txt │ │ ├── rosalind_orf.txt │ │ ├── rosalind_orfr.txt │ │ ├── rosalind_orfrsol.txt │ │ ├── rosalind_orfsol.txt │ │ ├── rosalind_osym.txt │ │ ├── rosalind_osymsol.txt │ │ ├── rosalind_par.txt │ │ ├── rosalind_par3.txt │ │ ├── rosalind_par3sol.txt │ │ ├── rosalind_parsol.txt │ │ ├── rosalind_pcov.txt │ │ ├── rosalind_pcovsol.txt │ │ ├── rosalind_pdpl.txt │ │ ├── rosalind_pdplsol.txt │ │ ├── rosalind_pdst.txt │ │ ├── rosalind_pdstsol.txt │ │ ├── rosalind_perm.txt │ │ ├── rosalind_permsol.txt │ │ ├── rosalind_phre.txt │ │ ├── rosalind_phresol.txt │ │ ├── rosalind_pmch.txt │ │ ├── rosalind_pmchsol.txt │ │ ├── rosalind_pper.txt │ │ ├── rosalind_ppersol.txt │ │ ├── rosalind_prob.txt │ │ ├── rosalind_probsol.txt │ │ ├── rosalind_prot.txt │ │ ├── rosalind_protsol.txt │ │ ├── rosalind_prsm.txt │ │ ├── rosalind_prsmsol.txt │ │ ├── rosalind_prtm.txt │ │ ├── rosalind_prtmsol.txt │ │ ├── rosalind_ps.txt │ │ ├── rosalind_pssol.txt │ │ ├── rosalind_ptra.txt │ │ ├── rosalind_ptrasol.txt │ │ ├── rosalind_qrt.txt │ │ ├── rosalind_qrtd.txt │ │ ├── rosalind_qrtdsol.txt │ │ ├── rosalind_qrtsol.txt │ │ ├── rosalind_qs.txt │ │ ├── rosalind_qssol.txt │ │ ├── rosalind_rear.txt │ │ ├── rosalind_rearsol.txt │ │ ├── rosalind_revc.txt │ │ ├── rosalind_revcsol.txt │ │ ├── rosalind_revp.txt │ │ ├── rosalind_revpsol.txt │ │ ├── rosalind_rna.txt │ │ ├── rosalind_rnas.txt │ │ ├── rosalind_rnasol.txt │ │ ├── rosalind_rnassol.txt │ │ ├── rosalind_root.txt │ │ ├── rosalind_rootsol.txt │ │ ├── rosalind_rstr.txt │ │ ├── rosalind_rstrsol.txt │ │ ├── rosalind_rsub.txt │ │ ├── rosalind_rsubsol.txt │ │ ├── rosalind_rvco.txt │ │ ├── rosalind_rvcosol.txt │ │ ├── rosalind_sc.txt │ │ ├── rosalind_scc.txt │ │ ├── rosalind_sccsol.txt │ │ ├── rosalind_scsol.txt │ │ ├── rosalind_scsp.txt │ │ ├── rosalind_scspsol.txt │ │ ├── rosalind_sdag.txt │ │ ├── rosalind_sdagsol.txt │ │ ├── rosalind_seto.txt │ │ ├── rosalind_setosol.txt │ │ ├── rosalind_sexl.txt │ │ ├── rosalind_sexlsol.txt │ │ ├── rosalind_sgra.txt │ │ ├── rosalind_sgrasol.txt │ │ ├── rosalind_sign.txt │ │ ├── rosalind_signsol.txt │ │ ├── rosalind_sims.txt │ │ ├── rosalind_simssol.txt │ │ ├── rosalind_smgb.txt │ │ ├── rosalind_smgbsol.txt │ │ ├── rosalind_sort.txt │ │ ├── rosalind_sortsol.txt │ │ ├── rosalind_spec.txt │ │ ├── rosalind_specsol.txt │ │ ├── rosalind_splc.txt │ │ ├── rosalind_splcsol.txt │ │ ├── rosalind_sptd.txt │ │ ├── rosalind_sptdsol.txt │ │ ├── rosalind_sq.txt │ │ ├── rosalind_sqsol.txt │ │ ├── rosalind_sseq.txt │ │ ├── rosalind_sseqsol.txt │ │ ├── rosalind_sset.txt │ │ ├── rosalind_ssetsol.txt │ │ ├── rosalind_subo.txt │ │ ├── rosalind_subosol.txt │ │ ├── rosalind_subs.txt │ │ ├── rosalind_subssol.txt │ │ ├── rosalind_suff.txt │ │ ├── rosalind_suffsol.txt │ │ ├── rosalind_tfsq.txt │ │ ├── rosalind_tfsqsol.txt │ │ ├── rosalind_tran.txt │ │ ├── rosalind_transol.txt │ │ ├── rosalind_tree.txt │ │ ├── rosalind_treesol.txt │ │ ├── rosalind_trie.txt │ │ ├── rosalind_triesol.txt │ │ ├── rosalind_ts.txt │ │ ├── rosalind_tssol.txt │ │ ├── rosalind_wfmd.txt │ │ └── rosalind_wfmdsol.txt │ └── tester.py └── upload_files.py ├── inference ├── final_batch_run.py └── requirements.txt ├── parsing ├── .DS_Store ├── FunctionExtractor │ └── methods_data │ │ └── .DS_Store ├── FunctionExtractors │ ├── JavaFunctionExtractor │ │ ├── .idea │ │ │ ├── .gitignore │ │ │ ├── compiler.xml │ │ │ ├── encodings.xml │ │ │ ├── jarRepositories.xml │ │ │ ├── libraries │ │ │ │ ├── apache_directory_studio_commons_io.xml │ │ │ │ ├── github_javaparser_core.xml │ │ │ │ └── github_javaparser_symbol_solver_core.xml │ │ │ ├── misc.xml │ │ │ └── vcs.xml │ │ ├── README.md │ │ ├── java_functions_filter.py │ │ ├── methods_data │ │ │ └── merge_data.py │ │ ├── pom.xml │ │ ├── src │ │ │ └── main │ │ │ │ └── java │ │ │ │ └── com │ │ │ │ └── lilbillbiscuit │ │ │ │ ├── BundleStructures.java │ │ │ │ ├── DirExplorer.java │ │ │ │ ├── JSONTesting.java │ │ │ │ ├── Main2.java │ │ │ │ ├── SearchDirectory.java │ │ │ │ ├── Testing.java │ │ │ │ └── TestingHTSOnly.java │ │ └── target │ │ │ └── classes │ │ │ └── com │ │ │ └── lilbillbiscuit │ │ │ ├── BundleStructures.class │ │ │ ├── DirExplorer$FileHandler.class │ │ │ ├── DirExplorer$Filter.class │ │ │ ├── DirExplorer.class │ │ │ ├── FunctionObj.class │ │ │ ├── ImportData.class │ │ │ ├── ImportObj.class │ │ │ ├── JSONTesting.class │ │ │ ├── Main2$1.class │ │ │ ├── Main2$2.class │ │ │ ├── Main2.class │ │ │ ├── MethodObj.class │ │ │ ├── SearchDirectory.class │ │ │ ├── SingleImportClass.class │ │ │ ├── Testing.class │ │ │ └── TestingHTSOnly.class │ └── PythonFunctionExtractor │ │ ├── README.md │ │ └── parse.py ├── FunctionProcessing │ ├── PromptGeneration │ │ ├── generate_prompts.py │ │ └── parse.py │ ├── chatGPT_filtering_python.ipynb │ ├── dictionary.txt │ ├── filter_by_keyword.py │ ├── gpt_filter.py │ ├── java_functions_filtering.ipynb │ └── keyword scraping │ │ ├── __pycache__ │ │ └── keyword_scraper.cpython-310.pyc │ │ ├── draw_association_graph.py │ │ 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-------------------------------------------------------------------------------- 1 | GGGA: -------------------------------------------------------------------------------- /evaluation/TestRosalind/testcases/rosalind_ba9c.txt: -------------------------------------------------------------------------------- 1 | AATCAATC$ -------------------------------------------------------------------------------- /evaluation/TestRosalind/testcases/rosalind_ba9csol.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gersteinlab/BioCoder/HEAD/evaluation/TestRosalind/testcases/rosalind_ba9csol.txt -------------------------------------------------------------------------------- /evaluation/TestRosalind/testcases/rosalind_ba9d.txt: -------------------------------------------------------------------------------- 1 | swtA -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | ACGT 2 | GG AC 3 | 1 -------------------------------------------------------------------------------- /evaluation/TestRosalind/testcases/rosalind_ba9osol.txt: -------------------------------------------------------------------------------- 1 | GG: 1 2 2 | AC: 0 -------------------------------------------------------------------------------- /evaluation/TestRosalind/testcases/rosalind_ba9p.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gersteinlab/BioCoder/HEAD/evaluation/TestRosalind/testcases/rosalind_ba9p.txt -------------------------------------------------------------------------------- /evaluation/TestRosalind/testcases/rosalind_ba9psol.txt: -------------------------------------------------------------------------------- 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