1 /* ---------------------------------------------------------------------------- 2 * This file was automatically generated by SWIG (http://www.swig.org). 3 * Version 4.0.2 4 * 5 * Do not make changes to this file unless you know what you are doing--modify 6 * the SWIG interface file instead. 7 * ----------------------------------------------------------------------------- */ 8 9 package btllib; 10 11 public class btllibJNI { SeqReader_SeqReaderFlag_FOLD_CASE_get()12 public final static native long SeqReader_SeqReaderFlag_FOLD_CASE_get(); SeqReader_SeqReaderFlag_NO_FOLD_CASE_get()13 public final static native long SeqReader_SeqReaderFlag_NO_FOLD_CASE_get(); SeqReader_SeqReaderFlag_NO_TRIM_MASKED_get()14 public final static native long SeqReader_SeqReaderFlag_NO_TRIM_MASKED_get(); SeqReader_SeqReaderFlag_TRIM_MASKED_get()15 public final static native long SeqReader_SeqReaderFlag_TRIM_MASKED_get(); SeqReader_SeqReaderFlag_SHORT_MODE_get()16 public final static native long SeqReader_SeqReaderFlag_SHORT_MODE_get(); SeqReader_SeqReaderFlag_LONG_MODE_get()17 public final static native long SeqReader_SeqReaderFlag_LONG_MODE_get(); new_SeqReaderFlag()18 public final static native long new_SeqReaderFlag(); delete_SeqReader_SeqReaderFlag(long jarg1)19 public final static native void delete_SeqReader_SeqReaderFlag(long jarg1); new_SeqReader__SWIG_0(String jarg1, long jarg2, long jarg3)20 public final static native long new_SeqReader__SWIG_0(String jarg1, long jarg2, long jarg3); new_SeqReader__SWIG_1(String jarg1, long jarg2)21 public final static native long new_SeqReader__SWIG_1(String jarg1, long jarg2); new_SeqReader__SWIG_2(String jarg1)22 public final static native long new_SeqReader__SWIG_2(String jarg1); delete_SeqReader(long jarg1)23 public final static native void delete_SeqReader(long jarg1); SeqReader_close(long jarg1, SeqReader jarg1_)24 public final static native void SeqReader_close(long jarg1, SeqReader jarg1_); SeqReader_fold_case(long jarg1, SeqReader jarg1_)25 public final static native boolean SeqReader_fold_case(long jarg1, SeqReader jarg1_); SeqReader_trim_masked(long jarg1, SeqReader jarg1_)26 public final static native boolean SeqReader_trim_masked(long jarg1, SeqReader jarg1_); SeqReader_short_mode(long jarg1, SeqReader jarg1_)27 public final static native boolean SeqReader_short_mode(long jarg1, SeqReader jarg1_); SeqReader_long_mode(long jarg1, SeqReader jarg1_)28 public final static native boolean SeqReader_long_mode(long jarg1, SeqReader jarg1_); SeqReader_get_format(long jarg1, SeqReader jarg1_)29 public final static native int SeqReader_get_format(long jarg1, SeqReader jarg1_); SeqReader_SeqReaderRecord_num_set(long jarg1, SeqReader.SeqReaderRecord jarg1_, long jarg2)30 public final static native void SeqReader_SeqReaderRecord_num_set(long jarg1, SeqReader.SeqReaderRecord jarg1_, long jarg2); SeqReader_SeqReaderRecord_num_get(long jarg1, SeqReader.SeqReaderRecord jarg1_)31 public final static native long SeqReader_SeqReaderRecord_num_get(long jarg1, SeqReader.SeqReaderRecord jarg1_); SeqReader_SeqReaderRecord_name_set(long jarg1, SeqReader.SeqReaderRecord jarg1_, String jarg2)32 public final static native void SeqReader_SeqReaderRecord_name_set(long jarg1, SeqReader.SeqReaderRecord jarg1_, String jarg2); SeqReader_SeqReaderRecord_name_get(long jarg1, SeqReader.SeqReaderRecord jarg1_)33 public final static native String SeqReader_SeqReaderRecord_name_get(long jarg1, SeqReader.SeqReaderRecord jarg1_); SeqReader_SeqReaderRecord_comment_set(long jarg1, SeqReader.SeqReaderRecord jarg1_, String jarg2)34 public final static native void SeqReader_SeqReaderRecord_comment_set(long jarg1, SeqReader.SeqReaderRecord jarg1_, String jarg2); SeqReader_SeqReaderRecord_comment_get(long jarg1, SeqReader.SeqReaderRecord jarg1_)35 public final static native String SeqReader_SeqReaderRecord_comment_get(long jarg1, SeqReader.SeqReaderRecord jarg1_); SeqReader_SeqReaderRecord_seq_set(long jarg1, SeqReader.SeqReaderRecord jarg1_, String jarg2)36 public final static native void SeqReader_SeqReaderRecord_seq_set(long jarg1, SeqReader.SeqReaderRecord jarg1_, String jarg2); SeqReader_SeqReaderRecord_seq_get(long jarg1, SeqReader.SeqReaderRecord jarg1_)37 public final static native String SeqReader_SeqReaderRecord_seq_get(long jarg1, SeqReader.SeqReaderRecord jarg1_); SeqReader_SeqReaderRecord_qual_set(long jarg1, SeqReader.SeqReaderRecord jarg1_, String jarg2)38 public final static native void SeqReader_SeqReaderRecord_qual_set(long jarg1, SeqReader.SeqReaderRecord jarg1_, String jarg2); SeqReader_SeqReaderRecord_qual_get(long jarg1, SeqReader.SeqReaderRecord jarg1_)39 public final static native String SeqReader_SeqReaderRecord_qual_get(long jarg1, SeqReader.SeqReaderRecord jarg1_); new_SeqReaderRecord()40 public final static native long new_SeqReaderRecord(); delete_SeqReader_SeqReaderRecord(long jarg1)41 public final static native void delete_SeqReader_SeqReaderRecord(long jarg1); SeqReader_read(long jarg1, SeqReader jarg1_)42 public final static native long SeqReader_read(long jarg1, SeqReader jarg1_); SeqReader_MAX_SIMULTANEOUS_SEQREADERS_get()43 public final static native long SeqReader_MAX_SIMULTANEOUS_SEQREADERS_get(); BIT_MASKS_get()44 public final static native long BIT_MASKS_get(); KMER_BLOOM_FILTER_MAGIC_HEADER_get()45 public final static native String KMER_BLOOM_FILTER_MAGIC_HEADER_get(); SEED_BLOOM_FILTER_MAGIC_HEADER_get()46 public final static native String SEED_BLOOM_FILTER_MAGIC_HEADER_get(); MAX_HASH_VALUES_get()47 public final static native long MAX_HASH_VALUES_get(); pop_cnt_byte(long jarg1)48 public final static native long pop_cnt_byte(long jarg1); new_BloomFilter__SWIG_0()49 public final static native long new_BloomFilter__SWIG_0(); new_BloomFilter__SWIG_1(long jarg1, long jarg2)50 public final static native long new_BloomFilter__SWIG_1(long jarg1, long jarg2); new_BloomFilter__SWIG_2(String jarg1)51 public final static native long new_BloomFilter__SWIG_2(String jarg1); delete_BloomFilter(long jarg1)52 public final static native void delete_BloomFilter(long jarg1); BloomFilter_insert__SWIG_0(long jarg1, BloomFilter jarg1_, long jarg2)53 public final static native void BloomFilter_insert__SWIG_0(long jarg1, BloomFilter jarg1_, long jarg2); BloomFilter_insert__SWIG_1(long jarg1, BloomFilter jarg1_, long jarg2)54 public final static native void BloomFilter_insert__SWIG_1(long jarg1, BloomFilter jarg1_, long jarg2); BloomFilter_contains__SWIG_0(long jarg1, BloomFilter jarg1_, long jarg2)55 public final static native boolean BloomFilter_contains__SWIG_0(long jarg1, BloomFilter jarg1_, long jarg2); BloomFilter_contains__SWIG_1(long jarg1, BloomFilter jarg1_, long jarg2)56 public final static native boolean BloomFilter_contains__SWIG_1(long jarg1, BloomFilter jarg1_, long jarg2); BloomFilter_get_bytes(long jarg1, BloomFilter jarg1_)57 public final static native long BloomFilter_get_bytes(long jarg1, BloomFilter jarg1_); BloomFilter_get_pop_cnt(long jarg1, BloomFilter jarg1_)58 public final static native long BloomFilter_get_pop_cnt(long jarg1, BloomFilter jarg1_); BloomFilter_get_occupancy(long jarg1, BloomFilter jarg1_)59 public final static native double BloomFilter_get_occupancy(long jarg1, BloomFilter jarg1_); BloomFilter_get_hash_num(long jarg1, BloomFilter jarg1_)60 public final static native long BloomFilter_get_hash_num(long jarg1, BloomFilter jarg1_); BloomFilter_get_fpr(long jarg1, BloomFilter jarg1_)61 public final static native double BloomFilter_get_fpr(long jarg1, BloomFilter jarg1_); BloomFilter_write(long jarg1, BloomFilter jarg1_, String jarg2)62 public final static native void BloomFilter_write(long jarg1, BloomFilter jarg1_, String jarg2); BloomFilter_parse_header(long jarg1, String jarg2)63 public final static native long BloomFilter_parse_header(long jarg1, String jarg2); new_KmerBloomFilter__SWIG_0()64 public final static native long new_KmerBloomFilter__SWIG_0(); new_KmerBloomFilter__SWIG_1(long jarg1, long jarg2, long jarg3)65 public final static native long new_KmerBloomFilter__SWIG_1(long jarg1, long jarg2, long jarg3); new_KmerBloomFilter__SWIG_2(String jarg1)66 public final static native long new_KmerBloomFilter__SWIG_2(String jarg1); KmerBloomFilter_insert__SWIG_0(long jarg1, KmerBloomFilter jarg1_, String jarg2, long jarg3)67 public final static native void KmerBloomFilter_insert__SWIG_0(long jarg1, KmerBloomFilter jarg1_, String jarg2, long jarg3); KmerBloomFilter_insert__SWIG_1(long jarg1, KmerBloomFilter jarg1_, String jarg2)68 public final static native void KmerBloomFilter_insert__SWIG_1(long jarg1, KmerBloomFilter jarg1_, String jarg2); KmerBloomFilter_contains__SWIG_0(long jarg1, KmerBloomFilter jarg1_, String jarg2, long jarg3)69 public final static native long KmerBloomFilter_contains__SWIG_0(long jarg1, KmerBloomFilter jarg1_, String jarg2, long jarg3); KmerBloomFilter_contains__SWIG_1(long jarg1, KmerBloomFilter jarg1_, String jarg2)70 public final static native long KmerBloomFilter_contains__SWIG_1(long jarg1, KmerBloomFilter jarg1_, String jarg2); KmerBloomFilter_contains__SWIG_2(long jarg1, KmerBloomFilter jarg1_, long jarg2)71 public final static native boolean KmerBloomFilter_contains__SWIG_2(long jarg1, KmerBloomFilter jarg1_, long jarg2); KmerBloomFilter_contains__SWIG_3(long jarg1, KmerBloomFilter jarg1_, long jarg2)72 public final static native boolean KmerBloomFilter_contains__SWIG_3(long jarg1, KmerBloomFilter jarg1_, long jarg2); KmerBloomFilter_get_bytes(long jarg1, KmerBloomFilter jarg1_)73 public final static native long KmerBloomFilter_get_bytes(long jarg1, KmerBloomFilter jarg1_); KmerBloomFilter_get_pop_cnt(long jarg1, KmerBloomFilter jarg1_)74 public final static native long KmerBloomFilter_get_pop_cnt(long jarg1, KmerBloomFilter jarg1_); KmerBloomFilter_get_occupancy(long jarg1, KmerBloomFilter jarg1_)75 public final static native double KmerBloomFilter_get_occupancy(long jarg1, KmerBloomFilter jarg1_); KmerBloomFilter_get_hash_num(long jarg1, KmerBloomFilter jarg1_)76 public final static native long KmerBloomFilter_get_hash_num(long jarg1, KmerBloomFilter jarg1_); KmerBloomFilter_get_fpr(long jarg1, KmerBloomFilter jarg1_)77 public final static native double KmerBloomFilter_get_fpr(long jarg1, KmerBloomFilter jarg1_); KmerBloomFilter_get_k(long jarg1, KmerBloomFilter jarg1_)78 public final static native long KmerBloomFilter_get_k(long jarg1, KmerBloomFilter jarg1_); KmerBloomFilter_get_bloom_filter(long jarg1, KmerBloomFilter jarg1_)79 public final static native long KmerBloomFilter_get_bloom_filter(long jarg1, KmerBloomFilter jarg1_); KmerBloomFilter_write(long jarg1, KmerBloomFilter jarg1_, String jarg2)80 public final static native void KmerBloomFilter_write(long jarg1, KmerBloomFilter jarg1_, String jarg2); delete_KmerBloomFilter(long jarg1)81 public final static native void delete_KmerBloomFilter(long jarg1); new_SeedBloomFilter__SWIG_0()82 public final static native long new_SeedBloomFilter__SWIG_0(); new_SeedBloomFilter__SWIG_1(long jarg1, long jarg2, long jarg3, long jarg4)83 public final static native long new_SeedBloomFilter__SWIG_1(long jarg1, long jarg2, long jarg3, long jarg4); new_SeedBloomFilter__SWIG_2(String jarg1)84 public final static native long new_SeedBloomFilter__SWIG_2(String jarg1); SeedBloomFilter_insert__SWIG_0(long jarg1, SeedBloomFilter jarg1_, String jarg2, long jarg3)85 public final static native void SeedBloomFilter_insert__SWIG_0(long jarg1, SeedBloomFilter jarg1_, String jarg2, long jarg3); SeedBloomFilter_insert__SWIG_1(long jarg1, SeedBloomFilter jarg1_, String jarg2)86 public final static native void SeedBloomFilter_insert__SWIG_1(long jarg1, SeedBloomFilter jarg1_, String jarg2); SeedBloomFilter_contains__SWIG_0(long jarg1, SeedBloomFilter jarg1_, String jarg2, long jarg3)87 public final static native long SeedBloomFilter_contains__SWIG_0(long jarg1, SeedBloomFilter jarg1_, String jarg2, long jarg3); SeedBloomFilter_contains__SWIG_1(long jarg1, SeedBloomFilter jarg1_, String jarg2)88 public final static native long SeedBloomFilter_contains__SWIG_1(long jarg1, SeedBloomFilter jarg1_, String jarg2); SeedBloomFilter_contains__SWIG_2(long jarg1, SeedBloomFilter jarg1_, long jarg2)89 public final static native boolean SeedBloomFilter_contains__SWIG_2(long jarg1, SeedBloomFilter jarg1_, long jarg2); SeedBloomFilter_contains__SWIG_3(long jarg1, SeedBloomFilter jarg1_, long jarg2)90 public final static native boolean SeedBloomFilter_contains__SWIG_3(long jarg1, SeedBloomFilter jarg1_, long jarg2); SeedBloomFilter_get_bytes(long jarg1, SeedBloomFilter jarg1_)91 public final static native long SeedBloomFilter_get_bytes(long jarg1, SeedBloomFilter jarg1_); SeedBloomFilter_get_pop_cnt(long jarg1, SeedBloomFilter jarg1_)92 public final static native long SeedBloomFilter_get_pop_cnt(long jarg1, SeedBloomFilter jarg1_); SeedBloomFilter_get_occupancy(long jarg1, SeedBloomFilter jarg1_)93 public final static native double SeedBloomFilter_get_occupancy(long jarg1, SeedBloomFilter jarg1_); SeedBloomFilter_get_hash_num(long jarg1, SeedBloomFilter jarg1_)94 public final static native long SeedBloomFilter_get_hash_num(long jarg1, SeedBloomFilter jarg1_); SeedBloomFilter_get_fpr(long jarg1, SeedBloomFilter jarg1_)95 public final static native double SeedBloomFilter_get_fpr(long jarg1, SeedBloomFilter jarg1_); SeedBloomFilter_get_k(long jarg1, SeedBloomFilter jarg1_)96 public final static native long SeedBloomFilter_get_k(long jarg1, SeedBloomFilter jarg1_); SeedBloomFilter_get_seeds(long jarg1, SeedBloomFilter jarg1_)97 public final static native long SeedBloomFilter_get_seeds(long jarg1, SeedBloomFilter jarg1_); SeedBloomFilter_get_parsed_seeds(long jarg1, SeedBloomFilter jarg1_)98 public final static native long SeedBloomFilter_get_parsed_seeds(long jarg1, SeedBloomFilter jarg1_); SeedBloomFilter_get_hash_num_per_seed(long jarg1, SeedBloomFilter jarg1_)99 public final static native long SeedBloomFilter_get_hash_num_per_seed(long jarg1, SeedBloomFilter jarg1_); SeedBloomFilter_get_kmer_bloom_filter(long jarg1, SeedBloomFilter jarg1_)100 public final static native long SeedBloomFilter_get_kmer_bloom_filter(long jarg1, SeedBloomFilter jarg1_); SeedBloomFilter_write(long jarg1, SeedBloomFilter jarg1_, String jarg2)101 public final static native void SeedBloomFilter_write(long jarg1, SeedBloomFilter jarg1_, String jarg2); delete_SeedBloomFilter(long jarg1)102 public final static native void delete_SeedBloomFilter(long jarg1); COMPLEMENTS_get()103 public final static native String COMPLEMENTS_get(); CAPITALS_get()104 public final static native String CAPITALS_get(); reverse_complement(long jarg1)105 public final static native void reverse_complement(long jarg1); get_reverse_complement(String jarg1)106 public final static native String get_reverse_complement(String jarg1); KMER_COUNTING_BLOOM_FILTER_MAGIC_HEADER_get()107 public final static native String KMER_COUNTING_BLOOM_FILTER_MAGIC_HEADER_get(); Indexlr_IndexlrFlag_ID_get()108 public final static native long Indexlr_IndexlrFlag_ID_get(); Indexlr_IndexlrFlag_NO_ID_get()109 public final static native long Indexlr_IndexlrFlag_NO_ID_get(); Indexlr_IndexlrFlag_BX_get()110 public final static native long Indexlr_IndexlrFlag_BX_get(); Indexlr_IndexlrFlag_NO_BX_get()111 public final static native long Indexlr_IndexlrFlag_NO_BX_get(); Indexlr_IndexlrFlag_SEQ_get()112 public final static native long Indexlr_IndexlrFlag_SEQ_get(); Indexlr_IndexlrFlag_NO_SEQ_get()113 public final static native long Indexlr_IndexlrFlag_NO_SEQ_get(); Indexlr_IndexlrFlag_FILTER_IN_get()114 public final static native long Indexlr_IndexlrFlag_FILTER_IN_get(); Indexlr_IndexlrFlag_NO_FILTER_IN_get()115 public final static native long Indexlr_IndexlrFlag_NO_FILTER_IN_get(); Indexlr_IndexlrFlag_FILTER_OUT_get()116 public final static native long Indexlr_IndexlrFlag_FILTER_OUT_get(); Indexlr_IndexlrFlag_NO_FILTER_OUT_get()117 public final static native long Indexlr_IndexlrFlag_NO_FILTER_OUT_get(); Indexlr_IndexlrFlag_SHORT_MODE_get()118 public final static native long Indexlr_IndexlrFlag_SHORT_MODE_get(); Indexlr_IndexlrFlag_LONG_MODE_get()119 public final static native long Indexlr_IndexlrFlag_LONG_MODE_get(); new_IndexlrFlag()120 public final static native long new_IndexlrFlag(); delete_Indexlr_IndexlrFlag(long jarg1)121 public final static native void delete_Indexlr_IndexlrFlag(long jarg1); Indexlr_output_id(long jarg1, Indexlr jarg1_)122 public final static native boolean Indexlr_output_id(long jarg1, Indexlr jarg1_); Indexlr_output_bx(long jarg1, Indexlr jarg1_)123 public final static native boolean Indexlr_output_bx(long jarg1, Indexlr jarg1_); Indexlr_output_seq(long jarg1, Indexlr jarg1_)124 public final static native boolean Indexlr_output_seq(long jarg1, Indexlr jarg1_); Indexlr_filter_in(long jarg1, Indexlr jarg1_)125 public final static native boolean Indexlr_filter_in(long jarg1, Indexlr jarg1_); Indexlr_filter_out(long jarg1, Indexlr jarg1_)126 public final static native boolean Indexlr_filter_out(long jarg1, Indexlr jarg1_); Indexlr_short_mode(long jarg1, Indexlr jarg1_)127 public final static native boolean Indexlr_short_mode(long jarg1, Indexlr jarg1_); Indexlr_long_mode(long jarg1, Indexlr jarg1_)128 public final static native boolean Indexlr_long_mode(long jarg1, Indexlr jarg1_); new_Indexlr_Minimizer__SWIG_0()129 public final static native long new_Indexlr_Minimizer__SWIG_0(); new_Indexlr_Minimizer__SWIG_1(long jarg1, long jarg2, long jarg3, boolean jarg4, String jarg5)130 public final static native long new_Indexlr_Minimizer__SWIG_1(long jarg1, long jarg2, long jarg3, boolean jarg4, String jarg5); Indexlr_Minimizer_min_hash_set(long jarg1, Indexlr.Minimizer jarg1_, long jarg2)131 public final static native void Indexlr_Minimizer_min_hash_set(long jarg1, Indexlr.Minimizer jarg1_, long jarg2); Indexlr_Minimizer_min_hash_get(long jarg1, Indexlr.Minimizer jarg1_)132 public final static native long Indexlr_Minimizer_min_hash_get(long jarg1, Indexlr.Minimizer jarg1_); Indexlr_Minimizer_out_hash_set(long jarg1, Indexlr.Minimizer jarg1_, long jarg2)133 public final static native void Indexlr_Minimizer_out_hash_set(long jarg1, Indexlr.Minimizer jarg1_, long jarg2); Indexlr_Minimizer_out_hash_get(long jarg1, Indexlr.Minimizer jarg1_)134 public final static native long Indexlr_Minimizer_out_hash_get(long jarg1, Indexlr.Minimizer jarg1_); Indexlr_Minimizer_pos_set(long jarg1, Indexlr.Minimizer jarg1_, long jarg2)135 public final static native void Indexlr_Minimizer_pos_set(long jarg1, Indexlr.Minimizer jarg1_, long jarg2); Indexlr_Minimizer_pos_get(long jarg1, Indexlr.Minimizer jarg1_)136 public final static native long Indexlr_Minimizer_pos_get(long jarg1, Indexlr.Minimizer jarg1_); Indexlr_Minimizer_forward_set(long jarg1, Indexlr.Minimizer jarg1_, boolean jarg2)137 public final static native void Indexlr_Minimizer_forward_set(long jarg1, Indexlr.Minimizer jarg1_, boolean jarg2); Indexlr_Minimizer_forward_get(long jarg1, Indexlr.Minimizer jarg1_)138 public final static native boolean Indexlr_Minimizer_forward_get(long jarg1, Indexlr.Minimizer jarg1_); Indexlr_Minimizer_seq_set(long jarg1, Indexlr.Minimizer jarg1_, String jarg2)139 public final static native void Indexlr_Minimizer_seq_set(long jarg1, Indexlr.Minimizer jarg1_, String jarg2); Indexlr_Minimizer_seq_get(long jarg1, Indexlr.Minimizer jarg1_)140 public final static native String Indexlr_Minimizer_seq_get(long jarg1, Indexlr.Minimizer jarg1_); delete_Indexlr_Minimizer(long jarg1)141 public final static native void delete_Indexlr_Minimizer(long jarg1); new_Indexlr_IndexlrRecord__SWIG_0()142 public final static native long new_Indexlr_IndexlrRecord__SWIG_0(); new_Indexlr_IndexlrRecord__SWIG_1(long jarg1, String jarg2, String jarg3, long jarg4, long jarg5)143 public final static native long new_Indexlr_IndexlrRecord__SWIG_1(long jarg1, String jarg2, String jarg3, long jarg4, long jarg5); Indexlr_IndexlrRecord_num_set(long jarg1, Indexlr.IndexlrRecord jarg1_, long jarg2)144 public final static native void Indexlr_IndexlrRecord_num_set(long jarg1, Indexlr.IndexlrRecord jarg1_, long jarg2); Indexlr_IndexlrRecord_num_get(long jarg1, Indexlr.IndexlrRecord jarg1_)145 public final static native long Indexlr_IndexlrRecord_num_get(long jarg1, Indexlr.IndexlrRecord jarg1_); Indexlr_IndexlrRecord_id_set(long jarg1, Indexlr.IndexlrRecord jarg1_, String jarg2)146 public final static native void Indexlr_IndexlrRecord_id_set(long jarg1, Indexlr.IndexlrRecord jarg1_, String jarg2); Indexlr_IndexlrRecord_id_get(long jarg1, Indexlr.IndexlrRecord jarg1_)147 public final static native String Indexlr_IndexlrRecord_id_get(long jarg1, Indexlr.IndexlrRecord jarg1_); Indexlr_IndexlrRecord_barcode_set(long jarg1, Indexlr.IndexlrRecord jarg1_, String jarg2)148 public final static native void Indexlr_IndexlrRecord_barcode_set(long jarg1, Indexlr.IndexlrRecord jarg1_, String jarg2); Indexlr_IndexlrRecord_barcode_get(long jarg1, Indexlr.IndexlrRecord jarg1_)149 public final static native String Indexlr_IndexlrRecord_barcode_get(long jarg1, Indexlr.IndexlrRecord jarg1_); Indexlr_IndexlrRecord_readlen_set(long jarg1, Indexlr.IndexlrRecord jarg1_, long jarg2)150 public final static native void Indexlr_IndexlrRecord_readlen_set(long jarg1, Indexlr.IndexlrRecord jarg1_, long jarg2); Indexlr_IndexlrRecord_readlen_get(long jarg1, Indexlr.IndexlrRecord jarg1_)151 public final static native long Indexlr_IndexlrRecord_readlen_get(long jarg1, Indexlr.IndexlrRecord jarg1_); Indexlr_IndexlrRecord_minimizers_set(long jarg1, Indexlr.IndexlrRecord jarg1_, long jarg2)152 public final static native void Indexlr_IndexlrRecord_minimizers_set(long jarg1, Indexlr.IndexlrRecord jarg1_, long jarg2); Indexlr_IndexlrRecord_minimizers_get(long jarg1, Indexlr.IndexlrRecord jarg1_)153 public final static native long Indexlr_IndexlrRecord_minimizers_get(long jarg1, Indexlr.IndexlrRecord jarg1_); delete_Indexlr_IndexlrRecord(long jarg1)154 public final static native void delete_Indexlr_IndexlrRecord(long jarg1); Indexlr_get_minimizers(long jarg1, Indexlr jarg1_)155 public final static native long Indexlr_get_minimizers(long jarg1, Indexlr jarg1_); new_Indexlr__SWIG_0(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5, boolean jarg6, long jarg7, BloomFilter jarg7_, long jarg8, BloomFilter jarg8_)156 public final static native long new_Indexlr__SWIG_0(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5, boolean jarg6, long jarg7, BloomFilter jarg7_, long jarg8, BloomFilter jarg8_); new_Indexlr__SWIG_1(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5, boolean jarg6, long jarg7, BloomFilter jarg7_)157 public final static native long new_Indexlr__SWIG_1(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5, boolean jarg6, long jarg7, BloomFilter jarg7_); new_Indexlr__SWIG_2(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5, boolean jarg6)158 public final static native long new_Indexlr__SWIG_2(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5, boolean jarg6); new_Indexlr__SWIG_3(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5)159 public final static native long new_Indexlr__SWIG_3(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5); new_Indexlr__SWIG_4(String jarg1, long jarg2, long jarg3, long jarg4)160 public final static native long new_Indexlr__SWIG_4(String jarg1, long jarg2, long jarg3, long jarg4); new_Indexlr__SWIG_5(String jarg1, long jarg2, long jarg3)161 public final static native long new_Indexlr__SWIG_5(String jarg1, long jarg2, long jarg3); delete_Indexlr(long jarg1)162 public final static native void delete_Indexlr(long jarg1); Indexlr_MAX_SIMULTANEOUS_INDEXLRS_get()163 public final static native long Indexlr_MAX_SIMULTANEOUS_INDEXLRS_get(); CP_OFF_get()164 public final static native long CP_OFF_get(); MULTISHIFT_get()165 public final static native int MULTISHIFT_get(); MULTISEED_get()166 public final static native long MULTISEED_get(); SEED_A_get()167 public final static native long SEED_A_get(); SEED_C_get()168 public final static native long SEED_C_get(); SEED_G_get()169 public final static native long SEED_G_get(); SEED_T_get()170 public final static native long SEED_T_get(); SEED_N_get()171 public final static native long SEED_N_get(); ASCII_SIZE_get()172 public final static native int ASCII_SIZE_get(); SEED_TAB_get()173 public final static native long SEED_TAB_get(); A33R_get()174 public final static native long A33R_get(); A31L_get()175 public final static native long A31L_get(); C33R_get()176 public final static native long C33R_get(); C31L_get()177 public final static native long C31L_get(); G33R_get()178 public final static native long G33R_get(); G31L_get()179 public final static native long G31L_get(); T33R_get()180 public final static native long T33R_get(); T31L_get()181 public final static native long T31L_get(); N33R_get()182 public final static native long N33R_get(); N31L_get()183 public final static native long N31L_get(); MS_TAB_33R_get()184 public final static native long MS_TAB_33R_get(); MS_TAB_31L_get()185 public final static native long MS_TAB_31L_get(); RC_CONVERT_TAB_get()186 public final static native long RC_CONVERT_TAB_get(); CONVERT_TAB_get()187 public final static native long CONVERT_TAB_get(); DIMER_TAB_get()188 public final static native long DIMER_TAB_get(); TRIMER_TAB_get()189 public final static native long TRIMER_TAB_get(); TETRAMER_TAB_get()190 public final static native long TETRAMER_TAB_get(); rol1(long jarg1)191 public final static native long rol1(long jarg1); rolx(long jarg1, long jarg2)192 public final static native long rolx(long jarg1, long jarg2); ror1(long jarg1)193 public final static native long ror1(long jarg1); rol31(long jarg1, long jarg2)194 public final static native long rol31(long jarg1, long jarg2); rol33(long jarg1, long jarg2)195 public final static native long rol33(long jarg1, long jarg2); swapbits033(long jarg1)196 public final static native long swapbits033(long jarg1); swapbits3263(long jarg1)197 public final static native long swapbits3263(long jarg1); swapxbits033(long jarg1, long jarg2)198 public final static native long swapxbits033(long jarg1, long jarg2); ntf64__SWIG_0(String jarg1, long jarg2)199 public final static native long ntf64__SWIG_0(String jarg1, long jarg2); ntr64__SWIG_0(String jarg1, long jarg2)200 public final static native long ntr64__SWIG_0(String jarg1, long jarg2); ntf64__SWIG_1(long jarg1, long jarg2, short jarg3, short jarg4)201 public final static native long ntf64__SWIG_1(long jarg1, long jarg2, short jarg3, short jarg4); ntr64__SWIG_1(long jarg1, long jarg2, short jarg3, short jarg4)202 public final static native long ntr64__SWIG_1(long jarg1, long jarg2, short jarg3, short jarg4); ntc64__SWIG_0(String jarg1, long jarg2)203 public final static native long ntc64__SWIG_0(String jarg1, long jarg2); ntc64__SWIG_1(String jarg1, long jarg2, long jarg3, long jarg4)204 public final static native long ntc64__SWIG_1(String jarg1, long jarg2, long jarg3, long jarg4); ntc64__SWIG_2(short jarg1, short jarg2, long jarg3, long jarg4, long jarg5)205 public final static native long ntc64__SWIG_2(short jarg1, short jarg2, long jarg3, long jarg4, long jarg5); ntf64l(long jarg1, long jarg2, short jarg3, short jarg4)206 public final static native long ntf64l(long jarg1, long jarg2, short jarg3, short jarg4); ntr64l(long jarg1, long jarg2, short jarg3, short jarg4)207 public final static native long ntr64l(long jarg1, long jarg2, short jarg3, short jarg4); ntc64l(short jarg1, short jarg2, long jarg3, long jarg4, long jarg5)208 public final static native long ntc64l(short jarg1, short jarg2, long jarg3, long jarg4, long jarg5); ntf64__SWIG_2(String jarg1, long jarg2, long jarg3)209 public final static native long ntf64__SWIG_2(String jarg1, long jarg2, long jarg3); ntc64__SWIG_3(String jarg1, long jarg2, long jarg3)210 public final static native long ntc64__SWIG_3(String jarg1, long jarg2, long jarg3); ntm64__SWIG_0(String jarg1, long jarg2, long jarg3, long jarg4)211 public final static native void ntm64__SWIG_0(String jarg1, long jarg2, long jarg3, long jarg4); nte64(long jarg1, long jarg2, long jarg3)212 public final static native long nte64(long jarg1, long jarg2, long jarg3); ntm64__SWIG_1(short jarg1, short jarg2, long jarg3, long jarg4, long jarg5)213 public final static native void ntm64__SWIG_1(short jarg1, short jarg2, long jarg3, long jarg4, long jarg5); ntmc64__SWIG_0(String jarg1, long jarg2, long jarg3, long jarg4)214 public final static native void ntmc64__SWIG_0(String jarg1, long jarg2, long jarg3, long jarg4); ntmc64__SWIG_1(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5, long jarg6)215 public final static native void ntmc64__SWIG_1(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5, long jarg6); ntmc64__SWIG_2(short jarg1, short jarg2, long jarg3, long jarg4, long jarg5, long jarg6, long jarg7)216 public final static native void ntmc64__SWIG_2(short jarg1, short jarg2, long jarg3, long jarg4, long jarg5, long jarg6, long jarg7); ntc64__SWIG_4(String jarg1, long jarg2, long jarg3, long jarg4)217 public final static native boolean ntc64__SWIG_4(String jarg1, long jarg2, long jarg3, long jarg4); ntmc64__SWIG_3(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5)218 public final static native boolean ntmc64__SWIG_3(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5); ntc64__SWIG_5(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5, long jarg6)219 public final static native boolean ntc64__SWIG_5(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5, long jarg6); ntmc64__SWIG_4(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5, long jarg6, long jarg7)220 public final static native boolean ntmc64__SWIG_4(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5, long jarg6, long jarg7); ntmc64__SWIG_5(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5, long jarg6, long jarg7, long jarg8)221 public final static native boolean ntmc64__SWIG_5(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5, long jarg6, long jarg7, long jarg8); ntmc64__SWIG_6(short jarg1, short jarg2, long jarg3, long jarg4, long jarg5, long jarg6, long jarg7, long jarg8)222 public final static native void ntmc64__SWIG_6(short jarg1, short jarg2, long jarg3, long jarg4, long jarg5, long jarg6, long jarg7, long jarg8); mask_hash(long jarg1, long jarg2, String jarg3, String jarg4, long jarg5)223 public final static native long mask_hash(long jarg1, long jarg2, String jarg3, String jarg4, long jarg5); sub_hash(long jarg1, long jarg2, String jarg3, long jarg4, long jarg5, long jarg6, long jarg7, long jarg8)224 public final static native void sub_hash(long jarg1, long jarg2, String jarg3, long jarg4, long jarg5, long jarg6, long jarg7, long jarg8); nts64__SWIG_0(String jarg1, long jarg2, long jarg3, long jarg4)225 public final static native long nts64__SWIG_0(String jarg1, long jarg2, long jarg3, long jarg4); nts64__SWIG_1(String jarg1, long jarg2, short jarg3, short jarg4, long jarg5, long jarg6)226 public final static native long nts64__SWIG_1(String jarg1, long jarg2, short jarg3, short jarg4, long jarg5, long jarg6); ntms64__SWIG_0(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5, long jarg6, long jarg7, long jarg8, long jarg9)227 public final static native boolean ntms64__SWIG_0(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5, long jarg6, long jarg7, long jarg8, long jarg9); ntms64__SWIG_1(String jarg1, long jarg2, short jarg3, short jarg4, long jarg5, long jarg6, long jarg7, long jarg8, long jarg9, long jarg10)228 public final static native void ntms64__SWIG_1(String jarg1, long jarg2, short jarg3, short jarg4, long jarg5, long jarg6, long jarg7, long jarg8, long jarg9, long jarg10); ntmsm64__SWIG_0(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5, long jarg6, long jarg7, long jarg8, long jarg9)229 public final static native boolean ntmsm64__SWIG_0(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5, long jarg6, long jarg7, long jarg8, long jarg9); ntmsm64__SWIG_1(String jarg1, long jarg2, short jarg3, short jarg4, long jarg5, long jarg6, long jarg7, long jarg8, long jarg9, long jarg10)230 public final static native void ntmsm64__SWIG_1(String jarg1, long jarg2, short jarg3, short jarg4, long jarg5, long jarg6, long jarg7, long jarg8, long jarg9, long jarg10); parse_seeds(long jarg1)231 public final static native long parse_seeds(long jarg1); new_NtHash__SWIG_0(String jarg1, long jarg2, long jarg3, long jarg4)232 public final static native long new_NtHash__SWIG_0(String jarg1, long jarg2, long jarg3, long jarg4); new_NtHash__SWIG_1(String jarg1, long jarg2, long jarg3)233 public final static native long new_NtHash__SWIG_1(String jarg1, long jarg2, long jarg3); NtHash_roll(long jarg1, NtHash jarg1_)234 public final static native boolean NtHash_roll(long jarg1, NtHash jarg1_); NtHash_sub(long jarg1, NtHash jarg1_, long jarg2, long jarg3)235 public final static native void NtHash_sub(long jarg1, NtHash jarg1_, long jarg2, long jarg3); NtHash_hashes(long jarg1, NtHash jarg1_)236 public final static native long NtHash_hashes(long jarg1, NtHash jarg1_); NtHash_get_pos(long jarg1, NtHash jarg1_)237 public final static native long NtHash_get_pos(long jarg1, NtHash jarg1_); NtHash_forward(long jarg1, NtHash jarg1_)238 public final static native boolean NtHash_forward(long jarg1, NtHash jarg1_); NtHash_get_k(long jarg1, NtHash jarg1_)239 public final static native long NtHash_get_k(long jarg1, NtHash jarg1_); NtHash_get_hash_num(long jarg1, NtHash jarg1_)240 public final static native long NtHash_get_hash_num(long jarg1, NtHash jarg1_); delete_NtHash(long jarg1)241 public final static native void delete_NtHash(long jarg1); new_SeedNtHash__SWIG_0(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5, long jarg6)242 public final static native long new_SeedNtHash__SWIG_0(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5, long jarg6); new_SeedNtHash__SWIG_1(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5)243 public final static native long new_SeedNtHash__SWIG_1(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5); new_SeedNtHash__SWIG_2(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5)244 public final static native long new_SeedNtHash__SWIG_2(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5); new_SeedNtHash__SWIG_3(String jarg1, long jarg2, long jarg3, long jarg4)245 public final static native long new_SeedNtHash__SWIG_3(String jarg1, long jarg2, long jarg3, long jarg4); new_SeedNtHash__SWIG_4(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5, long jarg6)246 public final static native long new_SeedNtHash__SWIG_4(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5, long jarg6); new_SeedNtHash__SWIG_5(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5)247 public final static native long new_SeedNtHash__SWIG_5(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5); new_SeedNtHash__SWIG_6(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5)248 public final static native long new_SeedNtHash__SWIG_6(String jarg1, long jarg2, long jarg3, long jarg4, long jarg5); new_SeedNtHash__SWIG_7(String jarg1, long jarg2, long jarg3, long jarg4)249 public final static native long new_SeedNtHash__SWIG_7(String jarg1, long jarg2, long jarg3, long jarg4); SeedNtHash_hashes(long jarg1, SeedNtHash jarg1_)250 public final static native long SeedNtHash_hashes(long jarg1, SeedNtHash jarg1_); SeedNtHash_get_pos(long jarg1, SeedNtHash jarg1_)251 public final static native long SeedNtHash_get_pos(long jarg1, SeedNtHash jarg1_); SeedNtHash_forward(long jarg1, SeedNtHash jarg1_)252 public final static native boolean SeedNtHash_forward(long jarg1, SeedNtHash jarg1_); SeedNtHash_get_k(long jarg1, SeedNtHash jarg1_)253 public final static native long SeedNtHash_get_k(long jarg1, SeedNtHash jarg1_); SeedNtHash_get_hash_num(long jarg1, SeedNtHash jarg1_)254 public final static native long SeedNtHash_get_hash_num(long jarg1, SeedNtHash jarg1_); SeedNtHash_get_hash_num_per_seed(long jarg1, SeedNtHash jarg1_)255 public final static native long SeedNtHash_get_hash_num_per_seed(long jarg1, SeedNtHash jarg1_); SeedNtHash_roll(long jarg1, SeedNtHash jarg1_)256 public final static native boolean SeedNtHash_roll(long jarg1, SeedNtHash jarg1_); delete_SeedNtHash(long jarg1)257 public final static native void delete_SeedNtHash(long jarg1); new_SeqWriter__SWIG_0(String jarg1, int jarg2, boolean jarg3)258 public final static native long new_SeqWriter__SWIG_0(String jarg1, int jarg2, boolean jarg3); new_SeqWriter__SWIG_1(String jarg1, int jarg2)259 public final static native long new_SeqWriter__SWIG_1(String jarg1, int jarg2); new_SeqWriter__SWIG_2(String jarg1)260 public final static native long new_SeqWriter__SWIG_2(String jarg1); SeqWriter_close(long jarg1, SeqWriter jarg1_)261