Definition at line 58 of file Job.hpp.
Public Member Functions |
| | Job (int sequencesCount) |
| virtual | ~Job () |
| void | setWorkPath (string workPath) |
| void | setSpecialRowsPath (string specialRowsPath) |
| void | setSharedPath (string sharedPath) |
| string | getWorkPath () |
| int | initialize () |
| FILE * | fopenStatistics (int stage, int id) |
| int | getSequenceCount () const |
| void | addSequence (Sequence *sequence) |
| Sequence * | getSequence (int index) |
| AlignmentParams * | getAlignmentParams () const |
| Alignment * | getAlignment () const |
| void | setAlignment (Alignment *alignment) |
| void | loadSequenceData (Sequence *sequence) |
| string | getCrosspointFile (int stage, int id, int deep=-1) |
| string | getAlignmentBinaryFile (int id) |
| string | getAlignmentTextFile (int id) |
| SpecialRowsArea * | getSpecialRowsArea (int stage, int id, int deep=-1) |
| void | clearSpecialRowsArea (SpecialRowsArea **area) |
| long long | getSRALimit () |
| long long | getFlushInterval (int step) |
| AlignerPool * | getAlignerPool () |
| int | getPoolWaitId () const |
| void | setPoolWaitId (int id) |
| int | getBufferLimit () const |
| void | setBufferLimit (int bufferLimit) |
Public Attributes |
| int | alignment_start |
| int | alignment_end |
| int | max_alignments |
| long long | ram_limit |
| long long | disk_limit |
| bool | block_pruning |
| bool | dump_blocks |
| string | flush_column_url |
| string | load_column_url |
| int | predicted_traceback |
| int | stage4_maximum_partition_size |
| bool | stage4_orthogonal_execution |
| string | dump_pruning_text_filename |
| int | stage6_output_format |
| string | outputBufferLogFile |
| string | inputBufferLogFile |
| IAligner * | aligner |
| Configs * | configs |
| int | peer_listen_port |
| string | peer_connect |
Private Member Functions |
| string | getSpecialRowsPath (int stage, int id, int deep=-1) |
| void | createPath (string path) |
| void | initializeWorkPath () |
| string | resolve_env (string in) |
| void | clearSpecialRowsAreas () |
| void | calculateFlushIntervals (int max_deep, long long limit, int seq0_len, int seq1_len) |
Private Attributes |
| vector< Sequence * > | sequences |
| AlignmentParams * | alignment_params |
| Alignment * | alignment |
| string | statistics_filename |
| string | status_filename |
| string | info_filename |
| int | last_crosspoint_id |
| string | work_path |
| string | crosspoints_path |
| string | special_rows_path |
| int * | flushIntervals |
| int | maxFlushDeep |
| AlignerPool * | alignerPool |
| string | pool_shared_path |
| int | pool_wait_id |
| int | bufferLimit |
| map< string, SpecialRowsArea * > | specialRowsAreas |
