/**
* Copyright (C) 2012-2013 Selventa, Inc.
*
* This file is part of the OpenBEL Framework.
*
* This program is free software; you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* The OpenBEL Framework is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
* License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with the OpenBEL Framework. If not, see <http://www.gnu.org/licenses/>.
*
* Additional Terms under LGPL v3:
*
* This license does not authorize you and you are prohibited from using the
* name, trademarks, service marks, logos or similar indicia of Selventa, Inc.,
* or, in the discretion of other licensors or authors of the program, the
* name, trademarks, service marks, logos or similar indicia of such authors or
* licensors, in any marketing or advertising materials relating to your
* distribution of the program or any covered product. This restriction does
* not waive or limit your obligation to keep intact all copyright notices set
* forth in the program as delivered to you.
*
* If you distribute the program in whole or in part, or any modified version
* of the program, and you assume contractual liability to the recipient with
* respect to the program or modified version, then you will indemnify the
* authors and licensors of the program for any liabilities that these
* contractual assumptions directly impose on those licensors and authors.
*/
package org.openbel.framework.common;
import static org.openbel.framework.common.cfg.SystemConfiguration.RESOURCE_INDEX_URL_DESC;
/**
* This class defines the set of strings used throughout BEL.
* <p>
* TODO: restore formatting sanity - some of these string definitions go out to
* hundreds of columns.
* </p>
*/
public class Strings {
/**
* {@value}
*/
public static final String ABUNDANCE = "abundance";
/**
* {@value}
*/
public static final String ABUNDANCE_ABBREV = "a";
/**
* {@value}
*/
public static final String ALL_DOCUMENTS_FAILED_CONVERSION =
"All documents failed conversion";
/**
* {@value}
*/
public static final String ALL_DOCUMENTS_FAILED_VALIDATION =
"All documents failed validation";
/**
* {@value}
*/
public static final String ALL_DOCUMENTS_PASSED_VALIDATION =
"All documents passed validation";
/**
* {@value}
*/
public static final String ANNOTATION_WARNING =
"%s is not found in annotation type %s";
/**
* {@value}
*/
public static final String BAD_INPUT_PATH = "Bad input path: ";
/**
* {@value}
*/
public static final String BAD_OUTPUT_DIR = "Bad output directory";
/**
* {@value}
*/
public static final String BIOLOGICAL_PROCESS = "biologicalProcess";
/**
* {@value}
*/
public static final String BIOLOGICAL_PROCESS_ABBREV = "bp";
/**
* {@value}
*/
public final static String CANT_WRITE_TO_PATH = "Can't write to path: ";
/**
* {@value}
*/
public static final String CATALYTIC_ACTIVITY = "catalyticActivity";
/**
* {@value}
*/
public static final String CATALYTIC_ACTIVITY_ABBREV = "cat";
/**
* {@value}
*/
public static final String CELL_SECRETION = "cellSecretion";
/**
* {@value}
*/
public static final String CELL_SECRETION_ABBREV = "sec";
/**
* {@value}
*/
public static final String CELL_SURFACE_EXPRESSION =
"cellSurfaceExpression";
/**
* {@value}
*/
public static final String CELL_SURFACE_EXPRESSION_ABBREV = "surf";
/**
* {@value}
*/
public static final String CHAPERONE_ACTIVITY = "chaperoneActivity";
/**
* {@value}
*/
public static final String CHAPERONE_ACTIVITY_ABBREV = "chap";
/**
* {@value}
*/
public static final String CHECK_PEDANTIC = "Enables pedantic mode. "
+ "This mode treats warnings as errors and will return a failure "
+ "code if a syntax or semantic warning is detected in the input "
+ "file.\nThe default is to disable pedantic mode.";
/**
* {@value}
*/
public static final String CHECK_PEDANTIC_PERMISSIVE_ERROR =
"Choose one of --pedantic or --permissive for document checking.";
/**
* {@value}
*/
public static final String CHECK_PERMISSIVE = "Enables permissive mode. "
+ "This mode will return a success code if syntactic or semantic "
+ "warnings are detected in the input file.\nThe default is to "
+ "disable permissive mode.";
/**
* {@value}
*/
public static final String CHECK_QUIET = "Enables quiet mode. "
+ "This mode supresses warnings and errors sent to the output.\n"
+ "The default is to disable quiet mode.";
/**
* {@value}
*/
public static final String CHECK_SUMMARY = "Optional. This switch will "
+ "output the number of warnings and errors detected in the "
+ "input file. The summary will still be written if the --quiet "
+ "switch is set.";
/**
* {@value}
*/
public static final String COMPLEX_ABUNDANCE = "complexAbundance";
/**
* {@value}
*/
public static final String COMPLEX_ABUNDANCE_ABBREV = "complex";
/**
* {@value}
*/
public static final String COMPOSITE_ABUNDANCE = "compositeAbundance";
/**
* {@value}
*/
public static final String COMPOSITE_ABUNDANCE_ABBREV = "composite";
/**
* {@value}
*/
public static final String DEBUG_HELP =
"Enables debug mode.\nThe default is to disable debug mode.";
/**
* {@value}
*/
public static final String DEGRADATION = "degradation";
/**
* {@value}
*/
public static final String DEGRADATION_ABBREV = "deg";
/**
* {@value}
*/
public static final String DIRECTORY_CREATION_FAILED =
"Failed to create directory: ";
/**
* {@value}
*/
public static final String DIRECTORY_DELETION_FAILED =
"Failed to delete directory: ";
/**
* {@value}
*/
public static final String DOCUMENT_CONTAINS_ERRORS =
"Document contains %d error(s)";
/**
* {@value}
*/
public static final String DOCUMENT_CONTAINS_WARNINGS =
"Document contains %d warning(s)";
/**
* {@value}
*/
public final static String ERROR_DOWNLOADING_RESOURCE =
"Error downloading resource";
/**
* {@value}
*/
public static final String EXPAND_NAMED_COMPLEXES_HELP =
"Modifies Phase III to inject named complex members and associated hasComponent edges when a member of a named complex is defined in a BEL Document.\nThe default is to not inject named complex nodes and edges.";
/**
* {@value}
*/
public static final String EXPAND_PROTEIN_FAMILIES_HELP =
"Modifies Phase III to inject protein family nodes, members, and associated hasMember edges when a member of a protein family is defined in a BEL Document.\nThe default is to not inject protein family nodes and edges.";
/**
* {@value}
*/
public static final String EXPECTED_ONE_NETWORK =
"Expected one merged network";
/**
* {@value}
*/
public static final String EXPORT_BEL_SCRIPT =
"Write all BEL Documents using BEL Script format.\n" +
"The default is to write as XBEL format.";
/**
* {@value}
*/
public static final String EXPORT_DOCUMENT_GROUPS =
"Optional. A list of Document Groups in the BEL Document Store to export the BEL Document(s) from.";
/**
* {@value}
*/
public static final String EXPORT_DOCUMENTS =
"Optional. A list of BEL Documents to export.";
/**
* {@value}
*/
public static final String EXPORT_NO_PRESERVE =
"If present, if a BEL Document with the same name exists in the output directory it will be overwritten.\n"
+
"The default is to preserve the BEL Document in the output directory and to generate a warning.";
/**
* {@value}
*/
public static final String EXPORT_OUTPUT =
"The path to a directory where the BEL Document file(s) will be written. This directory must exist and be writable";
/**
* {@value}
*/
public static final String EXPORT_XBEL =
"Write all BEL Documents using XBEL format. This is the default.";
/**
* {@value}
*/
public static final String FUSION = "fusion";
/**
* {@value}
*/
public static final String FUSION_ABBREV = "fus";
/**
* {@value}
*/
public static final String GENE_ABUNDANCE = "geneAbundance";
/**
* {@value}
*/
public static final String GENE_ABUNDANCE_ABBREV = "g";
/**
* {@value}
*/
public static final String GENERAL_FAILURE = "General failure";
/**
* {@value}
*/
public static final String GS_INJECTION_DISABLED =
"Gene scaffolding injection disabled";
/**
* {@value}
*/
public static final String GTP_BOUND_ACTIVITY = "gtpBoundActivity";
/**
* {@value}
*/
public static final String GTP_BOUND_ACTIVITY_ABBREV = "gtp";
/**
* {@value}
*/
public static final String HASH =
"Generate a checksum for the specified file.";
/**
* {@value}
*/
public static final String IMPORT_DOCUMENT_GROUP =
"Optional name of a Document Group in the Document Store to add the BEL Document(s) to. "
+
"If not specified, the BEL Document(s) will be added without being assigned to any Document Groups.";
/**
* {@value}
*/
public static final String IMPORT_NO_PRESERVE =
"If present, if a BEL Document with the same name and version exists in the Document Store it will be overwritten.\n"
+
"The default is to preserve the existing BEL Document in the Document Store and generate a warning.";
/**
* {@value}
*/
public static final String IMPORT_PEDANTIC =
"Enables pedantic mode. This mode treats warnings as errors and will terminate the import of a BEL Document "
+
"if a syntax or semantic warning is detected in the input file.\n"
+
"The default is to disable pedantic mode.";
/**
* {@value}
*/
public static final String IMPORT_PEDANTIC_PERMISSIVE_ERROR =
"Choose one of --pedantic or --permissive for document import.";
/**
* {@value}
*/
public static final String IMPORT_PERMISSIVE =
"Enables permissive mode. This mode will allow the import of documents which contain syntax errors at the BEL Statement level.\n"
+
"The default is to disable permissive mode.";
/**
* {@value}
*/
public static final String INJECTIONS_DISABLED = "Injections disabled";
/**
* {@value}
*/
public static final String INPUT_FILE_UNREADABLE =
"Input file cannot be read: ";
/**
* {@value}
*/
public static final String INVALID_ANNOTATIONS =
"%d invalid annotation(s)";
/**
* {@value}
*/
public static final String INVALID_NAMESPACE_RESOURCE_LOCATION =
"Invalid namespace resource location '%s'";
/**
* {@value}
*/
public static final String INVALID_NAMESPACE_VALUE =
"Invalid namespace value '%s'";
/**
* {@value}
*/
public static final String INVALID_SYMBOLS =
"%d invalid symbol(s)";
/**
* {@value}
*/
public final static String IO_ERROR = "I/O error";
/**
* {@value}
*/
public static final String KAM_CATALOG_LOAD_FAILED =
"Error loading into KAM catalog";
/**
* {@value}
*/
public static final String KAM_CONNECTION_FAILURE =
"Error connecting to KAM store";
/**
* {@value}
*/
public static final String KAM_DESCRIPTION_HELP =
"A description for the KAM that will be created. Put the description in quotes. It may be necessary "
+
"to escape the quotes (i.e. \\\") for the full description to be recognized by BELC.";
/**
* {@value}
*/
public static final String KAM_LOAD_FAILURE = "Error loading KAM";
/**
* {@value}
*/
public static final String KAM_NAME = "KAM Store name";
/*
* {@value}
*/
public static final String KAM_NAME_ALREADY_EXISTS = "KAM name already exists.\n";
/**
* {@value}
*/
public static final String KAM_NAME_HELP = "Name of the KAM to create."
+ " If a KAM with same name exists it will be overwritten if the"
+ " --no-preserve option is set.";
/**
* {@value}
*/
public static final String KAM_PASSWORD = "password for KAM Store";
/**
* {@value}
*/
public static final String KAM_REQUEST_NO_HANDLE = "KAM handle is required";
/**
* {@value}
*/
public static final String KAM_REQUEST_NO_KAM =
"'kam' is required";
/**
* {@value}
*/
public static final String KAM_REQUEST_NO_KAM_FOR_HANDLE =
"no KAM found with handle \"%s\"";
/**
* {@value}
*/
public static final String DIALECT_REQUEST_NO_DIALECT_FOR_HANDLE =
"no Dialect found with handle \"%s\"";
/**
* {@value}
*/
public static final String KAM_REQUEST_NO_KAM_FOR_NAME =
"no KAM found with name \"%s\"";
/**
* {@value}
*/
public static final String KAM_REQUEST_NO_NAME =
"KAM 'name' is required";
/**
* {@value}
*/
public static final String KAM_URL = "database URL";
/**
* {@value}
*/
public static final String KAM_USER = "user for KAM Store";
/**
* {@value}
*/
public static final String KINASE_ACTIVITY = "kinaseActivity";
/**
* {@value}
*/
public static final String KINASE_ACTIVITY_ABBREV = "kin";
/**
* {@value}
*/
public static final String LIST = "list";
/**
* {@value}
*/
public static final String LIST_CACHE = "List the resources in the cache";
/**
* {@value}
*/
public static final String LOAD_INDEX_FILE =
"Read the index file specified by the URL and cache all resources "
+
"identified in the index file.";
/**
* {@value}
*/
public static final String LOAD_INDEX_FROM_SYSCONFIG = "Read the index"
+ " file referenced using the " + RESOURCE_INDEX_URL_DESC + " of"
+ " the system configuration file and cache all resources"
+ " identified in the index file.";
/**
* {@value}
*/
public static final String LOAD_RESOURCE = "Add the resource specified"
+ " by URL to the cache. If the resource "
+
"already exists in the cache it will be updated.";
/**
* {@value}
*/
public static final String MICRO_RNA_ABUNDANCE = "microRNAAbundance";
/*
* {@value}
*/
public final static String LONG_OPT_KAM_NAME = "kam-name";
/**
* {@value}
*/
public final static String LONG_OPT_NO_PRESERVE = "no-preserve";
/**
* {@value}
*/
public static final String MICRO_RNA_ABUNDANCE_ABBREV = "m";
/**
* {@value}
*/
public static final String MISSING_KAM_DESCRIPTION =
"Missing KAM description";
/**
* {@value}
*/
public static final String MISSING_KAM_NAME = "Missing KAM name";
/**
* {@value}
*/
public final static String MISSING_SYSCFG = "Missing system configuration";
/**
* {@value}
*/
public static final String MOLECULAR_ACTIVITY = "molecularActivity";
/**
* {@value}
*/
public static final String MOLECULAR_ACTIVITY_ABBREV = "act";
/**
* {@value}
*/
public static final String NC_INJECTION_DISABLED =
"Named complex injection disabled";
/**
* {@value}
*/
public static final String NETWORK_MERGE_FAILURE =
"Failed merging proto-networks";
/**
* {@value}
*/
public static final String NO_DOCUMENT_FILES = "No documents found";
/**
* {@value}
*/
public static final String NO_GENE_SCAFFOLDING_HELP =
"Modifies Phase III to omit expanding the composite network to " +
"include gene activation pathways for gene products identified " +
"in BEL Document input to the compiler.\nThe default is to " +
"expand gene activation pathways for identified gene products.";
/**
* {@value}
*/
public static final String NO_GLOBAL_PROTO_NETWORK =
"No merged network file";
/**
* {@value}
*/
public static final String NO_NAMED_COMPLEXES_HELP =
"Modifies Phase III to omit coupling named complexes to its " +
"components in the composite network.\nThe default is to " +
"automatically create edges from named complexes, in a BEL " +
"Document, to their components.";
/**
* {@value}
*/
public static final String NO_NETWORKS_SAVED = "No proto-networks saved";
/**
* {@value}
*/
public static final String NO_ORTHOLOGY_HELP =
"Modifies Phase III to omit coupling orthologous family members " +
"to existing nodes in the composite network. The default is to " +
"add orthologous edges to the network.";
/**
* {@value}
*/
public static final String NO_PHASE_THREE =
"Executes Phase III in pass-through mode. This is the same as " +
"specifying --no-gene-scaffolding, --no-named-complexes, " +
"--no-protein-families, and --no-orthology.";
/**
* {@value}
*/
public static final String NO_PRESERVE_HELP =
"If present, if a KAM with the same name exists it will be " +
"overwritten.\nThe default is to preserve the KAM and exit with " +
"an error if the existing KAM will be overwritten.";
/**
* {@value}
*/
public static final String NO_PROTEIN_FAMILIES_HELP =
"Modifies Phase III to omit coupling protein family members to " +
"existing nodes in the composite network.\nThe default is to " +
"automatically create edges from protein family nodes to their " +
"members.";
/**
* {@value}
*/
public static final String NO_PROTO_NETWORKS = "No proto-networks";
/**
* {@value}
*/
public static final String NO_XBEL_DOCUMENTS = "No XBEL documents";
/**
* {@value}
*/
public static final String NO_XBEL_INPUT = "No XBEL input provided";
/**
* {@value}
*/
public static final String NOT_A_DIRECTORY = "Not a directory";
/**
* {@value}
*/
public final static String NOT_A_NUMBER = "Not a number: ";
/**
* {@value}
*/
public static final String NOT_A_PHASE1_DIR = "Not a phase one directory";
/**
* {@value}
*/
public static final String NOT_A_PHASE2_DIR = "Not a phase two directory";
/**
* {@value}
*/
public static final String OOM = "Out of memory";
/**
* {@value}
*/
public static final String ORTHO_INJECTION_DISABLED = "Orthology scaffolding disabled";
/**
* {@value}
*/
public static final String OXIDOREDUCTASE_ACTIVITY =
"oxidoreductaseActivity";
/**
* {@value}
*/
public static final String OXIDOREDUCTASE_ACTIVITY_ABBREV = "oxi";
/**
* {@value}
*/
public static final String PARSE_ERROR =
"Error parsing command-line arguments";
/**
* {@value}
*/
public static final String ERROR_INIT_LOGGING =
"Error initializing logging (%s), attempting to continue";
/**
* {@value}
*/
public static final String PATHOLOGY = "pathology";
/**
* {@value}
*/
public static final String PATHOLOGY_ABBREV = "path";
/**
* {@value}
*/
public final static String PEDANTIC_CONVERSION_FAILURE =
"Conversion failure";
/**
* {@value}
*/
public final static String PEDANTIC_NAMESPACE_INDEXING_FAILURE =
"Namespace indexing failure";
/**
* {@value}
*/
public final static String PEDANTIC_NAMESPACE_RESOLUTION_FAILURE =
"Namespace resolution failure";
/**
* {@value}
*/
public final static String PEDANTIC_PROTO_NETWORK_SAVE_FAILURE =
"Proto-network save failure";
/**
* {@value}
*/
public final static String PEDANTIC_SEMANTIC_VERIFICATION_FAILURE =
"Semantic verification failure";
/**
* {@value}
*/
public final static String PEDANTIC_STATEMENT_EXPANSION_FAILURE =
"Statement expansion failure";
/**
* {@value}
*/
public final static String PEDANTIC_SYMBOL_VERIFICATION_FAILURE =
"Symbol verification failure";
/**
* {@value}
*/
public final static String PEDANTIC_TERM_EXPANSION_FAILURE =
"Term expansion failure";
/**
* {@value}
*/
public final static String PEDANTIC_VALIDATION_FAILURE =
"Validation failure";
/**
* {@value}
*/
public static final String PEPTIDASE_ACTIVITY = "peptidaseActivity";
/**
* {@value}
*/
public static final String PEPTIDASE_ACTIVITY_ABBREV = "pep";
/**
* {@value}
*/
public static final String PF_INJECTION_DISABLED =
"Protein family injection disabled";
/**
* {@value}
*/
public static final String PHASE_1_DISABLE_NESTED_STMTS = "Modifies Phase"
+ " I to force the compiler not to create a relationship between"
+ " the subject term of a statement with a nested statement as an"
+ " object, to the object term of the nested statement.\n"
+ "The default is to couple nested statements.";
/**
* {@value}
*/
public static final String PHASE_1_INPUT_FILE =
"File name of an XBEL or BEL Script file to compile."
+ " This option may be used multiple times.";
/**
* {@value}
*/
public static final String PHASE_1_INPUT_PATH = "Path to a folder"
+ " containing one or more XBEL or BEL Script files to compile."
+ " This option may be used multiple times.";
/**
* {@value}
*/
public static final String PHASE_1_NO_SEMANTICS = "Bypasses the semantic"
+ " checker. When set, this option will omit checking for semantic"
+ " errors in the input documents.\nThe default is to enable"
+ " semantic checking.";
/**
* {@value}
*/
public static final String PHASE_1_NO_SYNTAX = "Bypasses the syntax"
+ " checker. When set, this option will omit checking for"
+ " syntax errors in the input documents. This is not recommended"
+ " as it can lead to unpredictable KAM topologies.\n"
+ "The default is to enable syntax checking.";
/**
* {@value}
*/
public final static String PHASE1_STAGE1_HDR = "Validation";
/**
* {@value}
*/
public final static String PHASE1_STAGE2_HDR = "Namespace compilation";
/**
* {@value}
*/
public final static String PHASE1_STAGE3_HDR = "Symbol verification";
/**
* {@value}
*/
public final static String PHASE1_STAGE4_HDR = "Semantic verification";
/**
* {@value}
*/
public final static String PHASE1_STAGE5_HDR = "Building proto-networks";
/**
* {@value}
*/
public final static String PHASE1_STAGE6_HDR = "Expansion";
/**
* {@value}
*/
public final static String PHASE1_STAGE7_HDR = "Saving proto-networks";
/**
* {@value}
*/
public final static String PHASE2_STAGE1_HDR = "Merging proto-networks";
/**
* {@value}
*/
public final static String PHASE2_STAGE2_HDR = "Loading equivalence index";
/**
* {@value}
*/
public final static String PHASE2_STAGE3_HDR =
"Equivalencing merged network";
/**
* {@value}
*/
public final static String PHASE2_STAGE4_HDR = "Saving merged network";
/**
* {@value}
*/
public final static String PHASE3_STAGE1_HDR =
"Processing protein families";
/**
* {@value}
*/
public final static String PHASE3_STAGE2_HDR = "Processing named complexes";
/**
* {@value}
*/
public final static String PHASE3_STAGE3_HDR =
"Processing gene scaffolding";
/**
* {@value}
*/
public final static String PHASE3_STAGE4_HDR = "Incorporating orthology information";
/**
* {@value}
*/
public final static String PHASE3_STAGE5_HDR =
"Equivalencing merged network";
/**
* {@value}
*/
public final static String PHASE3_STAGE6_HDR = "Saving augmented network";
/**
* {@value}
*/
public final static String PHASE3_NO_ORTHOLOGY_LONG_OPTION = "no-orthology";
/**
* {@value}
*/
public final static String PHASE4_SHORT_NAME = "Phase IV";
/**
* {@value}
*/
public final static String PHASE4_NAME = PHASE4_SHORT_NAME
+ ": Exporting final network to the KAM Store";
/**
* {@value}
*/
public final static String PHASE4_DESCRIPTION = "Exports a completed network to the KAM Store.";
/**
* {@value}
*/
public final static String PHASE4_STAGE1_HDR = "Building final KAM";
/**
* {@value}
*/
public static final String PHOSPHATASE_ACTIVITY = "phosphataseActivity";
/**
* {@value}
*/
public static final String PHOSPHATASE_ACTIVITY_ABBREV = "phos";
/**
* {@value}
*/
public static final String PRODUCTS = "products";
/**
* {@value}
*/
public static final String PROTEIN_ABUNDANCE = "proteinAbundance";
/**
* {@value}
*/
public static final String PROTEIN_ABUNDANCE_ABBREV = "p";
/**
* {@value}
*/
public static final String PROTEIN_MODIFICATION = "proteinModification";
/**
* {@value}
*/
public static final String PROTEIN_MODIFICATION_ABBREV = "pmod";
/**
* {@value}
*/
public static final String PURGE_CACHE =
"Removes all resources from the cache";
/**
* {@value}
*/
public final static String RC_READ_FAILURE =
"Failed to read runtime configuration";
/**
* {@value}
*/
public static final String REACTANTS = "reactants";
/**
* {@value}
*/
public static final String REACTION = "reaction";
/**
* {@value}
*/
public static final String REACTION_ABBREV = "rxn";
/**
* {@value}
*/
public static final String RIBOSYLATION_ACTIVITY = "ribosylationActivity";
/**
* {@value}
*/
public static final String RIBOSYLATION_ACTIVITY_ABBREV = "ribo";
/**
* {@value}
*/
public static final String RNA_ABUNDANCE = "rnaAbundance";
/**
* {@value}
*/
public static final String RNA_ABUNDANCE_ABBREV = "r";
/**
* {@value}
*/
public static final String SEMANTIC_CHECKS_DISABLED =
"Semantic checks disabled";
/**
* {@value}
*/
public static final String SEMANTIC_CODE_NOT_AA =
"\"%s\" is not a valid amino acid";
/**
* {@value}
*/
public static final String SEMANTIC_LIST_IMPROPER_CONTEXT =
"statement uses the LIST function in an improper context";
/**
* {@value}
*/
public final static String SEMANTIC_NESTED_REQUIRE_CAUSAL =
"nested statements require causal relationships";
public final static String SEMANTIC_MULTI_NESTED =
"statements with multiple nesting are not valid";
/**
* {@value}
*/
public static final String SEMANTIC_NOT_AA = "expected a valid amino acid";
/**
* {@value}
*/
public static final String SEMANTIC_NOT_CM =
"expected a covalent modification";
/**
* {@value}
*/
public static final String SEMANTIC_NOT_INT =
"expected a positive whole number";
/**
* {@value}
*/
public static final String SEMANTIC_POS_NOT_INT =
"\"%s\" is not a positive whole number";
/**
* {@value}
*/
public static final String SEMANTIC_PTYPE_NOT_CM =
"\"%s\" is not a covalent modification";
/**
* {@value}
*/
public final static String SEMANTIC_STATEMENT_PROVIDES_RELATIONSHIP =
"statement provides relationship when object is missing";
/**
* {@value}
*/
public final static String SEMANTIC_STATEMENT_REQUIRES_RELATIONSHIP =
"statement requires relationship when object is present";
/**
* {@value}
*/
public final static String SEMANTIC_TERM_FAILURE =
"term failed semantic checks: %s";
/**
* {@value}
*/
public final static String SHA_256 = "SHA-256";
/*
* {@value}
*/
public final static String SHORT_OPT_KAM_NAME = "k";
/**
* {@value}
*/
public static final String SUBSTITUTION = "substitution";
/**
* {@value}
*/
public static final String SUBSTITUTION_ABBREV = "sub";
/**
* {@value}
*/
public static final String SUCCESS = "Success";
/**
* {@value}
*/
public static final String SYMBOL_CHECKS_DISABLED =
"Symbol checks disabled";
/**
* {@value}
*/
public final static String SYSCFG_READ_FAILURE =
"Failed to read system configuration";
/**
* {@value}
*/
public static final String SYSTEM_CONFIG_PATH = "Optional. Allows the"
+ " user to specify the path to a system configuration file"
+ " to use to specify the OpenBEL Framework configuration.\n"
+ "The default is to use the default systems configuration file"
+ " found in [installdir]/config.";
/**
* {@value}
*/
public static final String TIME_HELP = "Enables timing mode. This mode"
+ " outputs times in seconds for each reported phase of the"
+ " compiler/assembler. Usually used in conjunction with"
+ " --verbose.\nThe default is to disable timing mode.";
/**
* {@value}
*/
public static final String TRANSCRIPTIONAL_ACTIVITY =
"transcriptionalActivity";
/**
* {@value}
*/
public static final String TRANSCRIPTIONAL_ACTIVITY_ABBREV = "tscript";
/**
* {@value}
*/
public static final String TRANSLOCATION = "translocation";
/**
* {@value}
*/
public static final String TRANSLOCATION_ABBREV = "tloc";
/**
* {@value}
*/
public static final String TRANSPORT_ACTIVITY = "transportActivity";
/**
* {@value}
*/
public static final String TRANSPORT_ACTIVITY_ABBREV = "tport";
/**
* {@value}
*/
public static final String TRUNCATION = "truncation";
/**
* {@value}
*/
public static final String TRUNCATION_ABBREV = "trunc";
/**
* {@value}
*/
public final static String UNRECOVERABLE_ERROR_MSG = "Unrecoverable error";
/**
* {@value}
*/
public static final String UPDATE_CACHE =
"Update cache with the latest resources";
/**
* {@value}
*/
public static final String UTF_8 = "UTF-8";
/**
* {@value}
*/
public static final String VERBOSE_HELP = "Enables verbose mode. This mode"
+ " outputs additional information as the application runs.\nThe"
+ " default is to disable verbose mode.";
/**
* {@value}
*/
public static final String WARNINGS_AS_ERRORS = "Enables pedantic mode."
+ " This mode treats warnings as errors and will terminate the"
+ " compiler/assembler at the end of a phase if a warning is"
+ " generated in the phase.\nThe default is to disable pedantic"
+ " mode.";
/**
* Default private constructor.
*/
private Strings() {
}
}