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org.obolibrary.oboformat.parser.OBOFormatConstants Maven / Gradle / Ivy
package org.obolibrary.oboformat.parser;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.Comparator;
import java.util.EnumSet;
import java.util.Map;
import java.util.Set;
import java.util.function.Function;
import java.util.function.ToIntFunction;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import javax.annotation.Nullable;
/**
* OBOformat constants.
*/
public class OBOFormatConstants {
private static final Map TAGSTABLE = Stream.of(OboFormatTag.values())
.collect(Collectors.toConcurrentMap(OboFormatTag::getTag, Function.identity()));
private static int map(String s, ToIntFunction f) {
OboFormatTag t = TAGSTABLE.get(s);
if (t == null) {
return 10000;
}
return f.applyAsInt(t);
}
/**
* Header priority comparator.
*/
public static Comparator headerPriority = (a, b) -> Integer
.compare(map(a, OboFormatTag::headerPriority), map(b, OboFormatTag::headerPriority));
/**
* Tag priority comparator.
*/
public static Comparator tagPriority = (a, b) -> Integer
.compare(map(a, OboFormatTag::tagPriority), map(b, OboFormatTag::tagPriority));
/**
* typedef priority comparator.
*/
public static Comparator typeDefPriority = (a, b) -> Integer
.compare(map(a, OboFormatTag::typeDefPriority), map(b, OboFormatTag::typeDefPriority));
/**
* tags
*/
public static final Set TAGS = TAGSTABLE.keySet();
/**
* @param tag tag
* @return oboformat tag
*/
@Nullable
public static OboFormatTag getTag(String tag) {
return TAGSTABLE.get(tag);
}
/**
* @return Date format for OboFormatTag.TAG_DATE
*/
public static final DateFormat headerDateFormat() {
return new SimpleDateFormat("dd:MM:yyyy HH:mm");
}
/**
* OBOformat tags.
*/
public enum OboFormatTag {
//@formatter:off
/**TAG_FORMAT_VERSION. */ TAG_FORMAT_VERSION ("format-version", 0),
// moved from pos 5 to emulate OBO-Edit behavior
/**TAG_ONTOLOGY. */ TAG_ONTOLOGY ("ontology", 85),
/**TAG_DATA_VERSION. */ TAG_DATA_VERSION ("data-version", 10),
/**TAG_DATE. */ TAG_DATE ("date", 15),
/**TAG_SAVED_BY. */ TAG_SAVED_BY ("saved-by", 20),
/**TAG_AUTO_GENERATED_BY. */ TAG_AUTO_GENERATED_BY ("auto-generated-by", 25),
// moved from pos 30 to emulate OBO-Edit behavior
/**TAG_IMPORT. */ TAG_IMPORT ("import", 80),
/**TAG_SUBSETDEF. */ TAG_SUBSETDEF ("subsetdef", 35),
/**TAG_SYNONYMTYPEDEF. */ TAG_SYNONYMTYPEDEF ("synonymtypedef", 40),
/**TAG_DEFAULT_NAMESPACE. */ TAG_DEFAULT_NAMESPACE ("default-namespace", 45),
/**TAG_IDSPACE. */ TAG_IDSPACE ("idspace", 50),
/**TAG_TREAT_XREFS_AS_EQUIVALENT. */ TAG_TREAT_XREFS_AS_EQUIVALENT ("treat-xrefs-as-equivalent", 55),
/**XREFS_AS_REVERSE_GENUS_DIFFERENTIA. */ TAG_TREAT_XREFS_AS_REVERSE_GENUS_DIFFERENTIA ("treat-xrefs-as-reverse-genus-differentia"),
/**TAG_TREAT_XREFS_AS_GENUS_DIFFERENTIA. */ TAG_TREAT_XREFS_AS_GENUS_DIFFERENTIA ("treat-xrefs-as-genus-differentia", 60),
/**TAG_TREAT_XREFS_AS_RELATIONSHIP. */ TAG_TREAT_XREFS_AS_RELATIONSHIP ("treat-xrefs-as-relationship", 65),
/**TAG_TREAT_XREFS_AS_IS_A. */ TAG_TREAT_XREFS_AS_IS_A ("treat-xrefs-as-is_a", 70),
/**TAG_TREAT_XREFS_AS_HAS_SUBCLASS. */ TAG_TREAT_XREFS_AS_HAS_SUBCLASS( "treat-xrefs-as-has-subclass"),
/**TAG_OWL_AXIOMS. */ TAG_OWL_AXIOMS ("owl-axioms", 110),
/**TAG_REMARK. */ TAG_REMARK ("remark", 75),
/**TAG_ID. */ TAG_ID ("id", 10000, 5, 5),
/**TAG_NAME. */ TAG_NAME ("name", 10000, 15, 15),
/**TAG_NAMESPACE. */ TAG_NAMESPACE ("namespace", 10000, 20, 20),
/**TAG_ALT_ID. */ TAG_ALT_ID ("alt_id", 10000, 25, 25),
/**TAG_DEF. */ TAG_DEF ("def", 10000, 30, 30),
/**TAG_COMMENT. */ TAG_COMMENT ("comment", 10000, 35, 35),
/**TAG_SUBSET. */ TAG_SUBSET ("subset", 10000, 40, 40),
/**TAG_SYNONYM. */ TAG_SYNONYM ("synonym", 10000, 45, 45),
/**TAG_XREF. */ TAG_XREF ("xref", 10000, 50, 50),
/**TAG_BUILTIN. */ TAG_BUILTIN ("builtin", 10000, 55, 70),
/**TAG_PROPERTY_VALUE. */ TAG_PROPERTY_VALUE ("property_value", 100, 98, 55),
/**TAG_IS_A. */ TAG_IS_A ("is_a", 10000, 65, 115),
/**TAG_INTERSECTION_OF. */ TAG_INTERSECTION_OF ("intersection_of", 10000, 70, 120),
/**TAG_UNION_OF. */ TAG_UNION_OF ("union_of", 10000, 80, 125),
/**TAG_EQUIVALENT_TO. */ TAG_EQUIVALENT_TO ("equivalent_to", 10000, 85, 130),
/**TAG_DISJOINT_FROM. */ TAG_DISJOINT_FROM ("disjoint_from", 10000, 90, 135),
/**TAG_RELATIONSHIP. */ TAG_RELATIONSHIP ("relationship", 10000, 95, 165),
/**TAG_CREATED_BY. */ TAG_CREATED_BY ("created_by", 10000, 130, 191),
/**TAG_CREATION_DATE. */ TAG_CREATION_DATE ("creation_date", 10000, 140, 192),
/**TAG_IS_OBSELETE. */ TAG_IS_OBSELETE ("is_obsolete", 10000, 110, 169),
/**TAG_REPLACED_BY. */ TAG_REPLACED_BY ("replaced_by", 10000, 115, 185),
/**TAG_IS_ANONYMOUS. */ TAG_IS_ANONYMOUS ("is_anonymous", 10000, 10, 10),
/**TAG_DOMAIN. */ TAG_DOMAIN ("domain", 10000, 10000, 60),
/**TAG_RANGE. */ TAG_RANGE ("range", 10000, 10000, 65),
/**TAG_IS_ANTI_SYMMETRIC. */ TAG_IS_ANTI_SYMMETRIC ("is_anti_symmetric", 10000, 10000, 75),
/**TAG_IS_CYCLIC. */ TAG_IS_CYCLIC ("is_cyclic", 10000, 10000, 80),
/**TAG_IS_REFLEXIVE. */ TAG_IS_REFLEXIVE ("is_reflexive", 10000, 10000, 85),
/**TAG_IS_SYMMETRIC. */ TAG_IS_SYMMETRIC ("is_symmetric", 10000, 10000, 90),
/**TAG_IS_TRANSITIVE. */ TAG_IS_TRANSITIVE ("is_transitive", 10000, 10000, 100),
/**TAG_IS_FUNCTIONAL. */ TAG_IS_FUNCTIONAL ("is_functional", 10000, 10000, 105),
/**TAG_IS_INVERSE_FUNCTIONAL. */ TAG_IS_INVERSE_FUNCTIONAL ("is_inverse_functional", 10000, 10000, 110),
/**TAG_TRANSITIVE_OVER. */ TAG_TRANSITIVE_OVER ("transitive_over", 10000, 10000, 145),
/**TAG_HOLDS_OVER_CHAIN. */ TAG_HOLDS_OVER_CHAIN ("holds_over_chain", 10000, 60, 71),
/**TAG_EQUIVALENT_TO_CHAIN. */ TAG_EQUIVALENT_TO_CHAIN ("equivalent_to_chain", 10000, 10000, 155),
/**TAG_DISJOINT_OVER. */ TAG_DISJOINT_OVER ("disjoint_over", 10000, 10000, 160),
/**TAG_EXPAND_ASSERTION_TO. */ TAG_EXPAND_ASSERTION_TO ("expand_assertion_to", 10000, 10000, 195),
/**TAG_EXPAND_EXPRESSION_TO. */ TAG_EXPAND_EXPRESSION_TO ("expand_expression_to", 10000, 10000, 200),
/**TAG_IS_CLASS_LEVEL_TAG. */ TAG_IS_CLASS_LEVEL_TAG ("is_class_level", 10000, 10000, 210),
/**TAG_IS_METADATA_TAG. */ TAG_IS_METADATA_TAG ("is_metadata_tag", 10000, 10000, 205),
/**TAG_CONSIDER. */ TAG_CONSIDER ("consider", 10000, 120, 190),
/**TAG_INVERSE_OF. */ TAG_INVERSE_OF ("inverse_of", 10000, 10000, 140),
/**TAG_IS_ASYMMETRIC. */ TAG_IS_ASYMMETRIC("is_asymmetric"),
/**TAG_NAMESPACE_ID_RULE. */ TAG_NAMESPACE_ID_RULE ("namespace-id-rule", 46),
/**TAG_LOGICAL_DEFINITION_VIEW_RELATION. */ TAG_LOGICAL_DEFINITION_VIEW_RELATION("logical-definition-view-relation"),
//@formatter:on
// these are keywords, not tags, but we keep them here for convenience
/**
* Scope.
*/
TAG_SCOPE("scope"),
/**
* Implicit, in synonymtypedef.
*/
TAG_HAS_SYNONYM_TYPE("has_synonym_type"),
/** implicit, in synonym. */
/**
* Broad.
*/
TAG_BROAD("BROAD"),
/**
* Narrow.
*/
TAG_NARROW("NARROW"),
/**
* Exact.
*/
TAG_EXACT("EXACT"),
/**
* Related.
*/
TAG_RELATED("RELATED");
/**
* Term frames.
*/
public static final EnumSet TERM_FRAMES = EnumSet.of(TAG_INTERSECTION_OF,
TAG_UNION_OF, TAG_EQUIVALENT_TO, TAG_DISJOINT_FROM, TAG_RELATIONSHIP, TAG_IS_A);
/**
* Typedef frames.
*/
public static final EnumSet TYPEDEF_FRAMES =
EnumSet.of(TAG_INTERSECTION_OF, TAG_UNION_OF, TAG_EQUIVALENT_TO, TAG_DISJOINT_FROM,
TAG_INVERSE_OF, TAG_TRANSITIVE_OVER, TAG_DISJOINT_OVER, TAG_IS_A);
private final String tag;
private final int headerTagsPriority;
private final int tagsPriority;
private final int typeDefTagsPriority;
OboFormatTag(String tag) {
this(tag, 10000, 10000, 10000);
}
OboFormatTag(String tag, int header) {
this(tag, header, 10000, 10000);
}
OboFormatTag(String tag, int header, int priority, int typedef) {
this.tag = tag;
headerTagsPriority = header;
tagsPriority = priority;
typeDefTagsPriority = typedef;
}
/**
* @return header priority
*/
public int headerPriority() {
return headerTagsPriority;
}
/**
* @return tag priority
*/
public int tagPriority() {
return tagsPriority;
}
/**
* @return typedef priority
*/
public int typeDefPriority() {
return typeDefTagsPriority;
}
/**
* @return tag
*/
public String getTag() {
return tag;
}
@Override
public String toString() {
return tag;
}
}
}
