<commit_before> ####################
### BIOJAVA Mapping ###
 #####################

# -----------------------------------------------------------------------------------------------
# general / Change to your needs!
# -----------------------------------------------------------------------------------------------


# logging global: on, off (increase performance, error and fatal errors are still logged)
logging=off

### memory mode

# memoryMode=true    all data is dumped and is held in the memory; 
#                    (up to 200MB RAM per 20mbps of a Chromosome with about 50.000 features) 
#                    once it is instatiated, queries can be executed extremely fast.

# memoryMode=false   all data is queried lazily and filters are mapped dynamically to equivalent FlyMine queries.
#                    instatiation is quick, memory requirements are low 
#                    complex queries and very general queries (e.g. or filter) can last much longer than in memory mode.
memoryMode=true

### annotation bundle of each feature (true/false)

# hasA - if true, all hasA relations of a Feature are added to the annotation bundle. Example: A Gene hasA Transcript(s)
# Annotationbundle in BioJava is a map; therefore - key: "hasA:Transcript" value: FeatureHolderFMAnno
hasA=true

# inverse hasA
invHasA=true

# synonyms
synonyms=true

# -----------------------------------------------------------------------------------------------
# file paths
# -----------------------------------------------------------------------------------------------

log4j.properties.path=resources/runtime/log4j.properties

intermine.properties.path=/home/markus/intermine.properties

sofa.ontology.path=model/so/sofa.ontology
<commit_msg>default properties for FlyMineObjects -> BioJava<commit_after> ####################
### BIOJAVA Mapping ###
 #####################

# -----------------------------------------------------------------------------------------------
# general / Change to your needs!
# -----------------------------------------------------------------------------------------------


# logging global: on, off (increase performance, error and fatal errors are still logged)
logging=off

### memory mode

# memoryMode=true    all data is dumped and is held in the memory; 
#                    (up to 200MB RAM per 20mbps of a Chromosome with about 50.000 features) 
#                    once it is instatiated, queries can be executed extremely fast.

# memoryMode=false   all data is queried lazily and filters are mapped dynamically to equivalent FlyMine queries.
#                    instatiation is quick, memory requirements are low 
#                    complex queries and very general queries (e.g. or filter) can last much longer than in memory mode.
memoryMode=false

### annotation bundle of each feature (true/false)

# hasA - if true, all hasA relations of a Feature are added to the annotation bundle. Example: A Gene hasA Transcript(s)
# Annotationbundle in BioJava is a map; therefore - key: "hasA:Transcript" value: FeatureHolderFMAnno
hasA=false

# inverse hasA
invHasA=false

# synonyms
synonyms=false

# -----------------------------------------------------------------------------------------------
# file paths
# -----------------------------------------------------------------------------------------------

log4j.properties.path=resources/runtime/log4j.properties

intermine.properties.path=/home/markus/intermine.properties

sofa.ontology.path=model/so/sofa.ontology

{'fraction_non_alphanumeric': 0.29426860564585117, 'fraction_numerical': 0.006843455945252352, 'mean_word_length': 1.5587162654996354, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 4, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '667500', 'n_tokens_mistral': 818, 'n_tokens_neox': 769, 'n_words': 296}