Loading dbs/gydb_arh_chdcr/gydb_arh_chdcr.fa +3110 −3126 File changed.Preview size limit exceeded, changes collapsed. Show changes dbs/gydb_arh_chdcr/gydb_arh_chdcr.fa.phr −857 B (195 KiB) File changed.No diff preview for this file type. View original file View changed file dbs/gydb_arh_chdcr/gydb_arh_chdcr.fa.pin −64 B (13.5 KiB) File changed.No diff preview for this file type. View original file View changed file dbs/gydb_arh_chdcr/gydb_arh_chdcr.fa.psq −773 B (259 KiB) File changed.No diff preview for this file type. View original file View changed file nested/core/module_management/modules.py +12 −0 Original line number Original line Diff line number Diff line Loading @@ -17,6 +17,10 @@ from nested.core.tools.mite_finder import MiteFinder from nested.entities.mite import Mite from nested.entities.mite import Mite from nested.output.output_generators.mite_output_generator import MiteOutputGenerator from nested.output.output_generators.mite_output_generator import MiteOutputGenerator from nested.core.tools.retro_te_domains import RetroTeDomains from nested.entities.domain_dante import DomainDante from nested.output.output_generators.retro_domain_output_generator import RetroDomainOutputGenerator from nested.core.tools.nester.nester import Nester from nested.core.tools.nester.nester import Nester from nested.entities.te import TE from nested.entities.te import TE from nested.output.output_generators.nester_output_generator import NesterOutputGenerator from nested.output.output_generators.nester_output_generator import NesterOutputGenerator Loading @@ -32,6 +36,7 @@ class Modules: def _prepare_modules(self) -> NoReturn: def _prepare_modules(self) -> NoReturn: self._create_trf_module() self._create_trf_module() self._create_mite_module() self._create_mite_module() self._create_retro_domain_module() self._create_solo_ltr_module() self._create_solo_ltr_module() self._create_nester_module() self._create_nester_module() Loading Loading @@ -68,6 +73,13 @@ class Modules: module_mite = Module("mite", mite, type_mite, output_mite) module_mite = Module("mite", mite, type_mite, output_mite) self.modules.append(module_mite) self.modules.append(module_mite) def _create_retro_domain_module(self) -> NoReturn: retro_domain = RetroTeDomains(self.arguments["sequence"]) output_retro_domain = RetroDomainOutputGenerator(self.arguments["output_folder"]) type_retro_domain = DomainDante module_retro_domain = Module("retro_te_domain", retro_domain, type_retro_domain, output_retro_domain) self.modules.append(module_retro_domain) def _create_nester_module(self) -> NoReturn: def _create_nester_module(self) -> NoReturn: nester = Nester(self.arguments["sequence"], self.arguments["initial_threshold"], nester = Nester(self.arguments["sequence"], self.arguments["initial_threshold"], self.arguments["threshold_multiplier"], self.arguments["dependency_resolver"]) self.arguments["threshold_multiplier"], self.arguments["dependency_resolver"]) Loading Loading
dbs/gydb_arh_chdcr/gydb_arh_chdcr.fa +3110 −3126 File changed.Preview size limit exceeded, changes collapsed. Show changes
dbs/gydb_arh_chdcr/gydb_arh_chdcr.fa.phr −857 B (195 KiB) File changed.No diff preview for this file type. View original file View changed file
dbs/gydb_arh_chdcr/gydb_arh_chdcr.fa.pin −64 B (13.5 KiB) File changed.No diff preview for this file type. View original file View changed file
dbs/gydb_arh_chdcr/gydb_arh_chdcr.fa.psq −773 B (259 KiB) File changed.No diff preview for this file type. View original file View changed file
nested/core/module_management/modules.py +12 −0 Original line number Original line Diff line number Diff line Loading @@ -17,6 +17,10 @@ from nested.core.tools.mite_finder import MiteFinder from nested.entities.mite import Mite from nested.entities.mite import Mite from nested.output.output_generators.mite_output_generator import MiteOutputGenerator from nested.output.output_generators.mite_output_generator import MiteOutputGenerator from nested.core.tools.retro_te_domains import RetroTeDomains from nested.entities.domain_dante import DomainDante from nested.output.output_generators.retro_domain_output_generator import RetroDomainOutputGenerator from nested.core.tools.nester.nester import Nester from nested.core.tools.nester.nester import Nester from nested.entities.te import TE from nested.entities.te import TE from nested.output.output_generators.nester_output_generator import NesterOutputGenerator from nested.output.output_generators.nester_output_generator import NesterOutputGenerator Loading @@ -32,6 +36,7 @@ class Modules: def _prepare_modules(self) -> NoReturn: def _prepare_modules(self) -> NoReturn: self._create_trf_module() self._create_trf_module() self._create_mite_module() self._create_mite_module() self._create_retro_domain_module() self._create_solo_ltr_module() self._create_solo_ltr_module() self._create_nester_module() self._create_nester_module() Loading Loading @@ -68,6 +73,13 @@ class Modules: module_mite = Module("mite", mite, type_mite, output_mite) module_mite = Module("mite", mite, type_mite, output_mite) self.modules.append(module_mite) self.modules.append(module_mite) def _create_retro_domain_module(self) -> NoReturn: retro_domain = RetroTeDomains(self.arguments["sequence"]) output_retro_domain = RetroDomainOutputGenerator(self.arguments["output_folder"]) type_retro_domain = DomainDante module_retro_domain = Module("retro_te_domain", retro_domain, type_retro_domain, output_retro_domain) self.modules.append(module_retro_domain) def _create_nester_module(self) -> NoReturn: def _create_nester_module(self) -> NoReturn: nester = Nester(self.arguments["sequence"], self.arguments["initial_threshold"], nester = Nester(self.arguments["sequence"], self.arguments["initial_threshold"], self.arguments["threshold_multiplier"], self.arguments["dependency_resolver"]) self.arguments["threshold_multiplier"], self.arguments["dependency_resolver"]) Loading
