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org.obolibrary.oboformat.writer.OBOFormatWriter Maven / Gradle / Ivy
package org.obolibrary.oboformat.writer;
import static org.semanticweb.owlapi.model.parameters.Navigation.IN_SUB_POSITION;
import static org.semanticweb.owlapi.util.OWLAPIPreconditions.checkNotNull;
import static org.semanticweb.owlapi.util.OWLAPIStreamUtils.asList;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.io.Reader;
import java.io.Serializable;
import java.io.Writer;
import java.net.URL;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.Date;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
import javax.annotation.Nullable;
import javax.annotation.ParametersAreNonnullByDefault;
import org.obolibrary.obo2owl.OWLAPIObo2Owl;
import org.obolibrary.oboformat.model.Clause;
import org.obolibrary.oboformat.model.Frame;
import org.obolibrary.oboformat.model.Frame.FrameType;
import org.obolibrary.oboformat.model.OBODoc;
import org.obolibrary.oboformat.model.QualifierValue;
import org.obolibrary.oboformat.model.Xref;
import org.obolibrary.oboformat.parser.OBOFormatConstants;
import org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag;
import org.obolibrary.oboformat.parser.OBOFormatParser;
import org.obolibrary.oboformat.parser.OBOFormatParserException;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom;
import org.semanticweb.owlapi.model.OWLAnnotationSubject;
import org.semanticweb.owlapi.model.OWLAnnotationValue;
import org.semanticweb.owlapi.model.OWLLiteral;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.parameters.Imports;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* The Class OBOFormatWriter.
*
* @author Shahid Manzoor
*/
@ParametersAreNonnullByDefault
public class OBOFormatWriter {
private static final Logger LOG = LoggerFactory.getLogger(OBOFormatWriter.class);
private static final Comparator TAGSINFORMATIVE = buildTagsInformative();
/**
* This comparator sorts clauses with the same tag in the specified write order.
*/
private static final Comparator clauseComparator = (o1, o2) -> compare(o1, o2);
private static Comparator clauseListComparator = Comparator
.comparing(Clause::getTag, OBOFormatConstants.tagPriority).thenComparing(clauseComparator);
private boolean isCheckStructure = true;
private static Set buildTagsInformative() {
Set set = new HashSet<>();
set.add(OboFormatTag.TAG_IS_A.getTag());
set.add(OboFormatTag.TAG_RELATIONSHIP.getTag());
set.add(OboFormatTag.TAG_DISJOINT_FROM.getTag());
set.add(OboFormatTag.TAG_INTERSECTION_OF.getTag());
set.add(OboFormatTag.TAG_UNION_OF.getTag());
set.add(OboFormatTag.TAG_EQUIVALENT_TO.getTag());
// removed OboFormatTag.TAG_REPLACED_BY to be compatible with OBO-Edit
set.add(OboFormatTag.TAG_PROPERTY_VALUE.getTag());
set.add(OboFormatTag.TAG_DOMAIN.getTag());
set.add(OboFormatTag.TAG_RANGE.getTag());
set.add(OboFormatTag.TAG_INVERSE_OF.getTag());
set.add(OboFormatTag.TAG_TRANSITIVE_OVER.getTag());
// removed OboFormatTag.TAG_HOLDS_OVER_CHAIN to be compatible with
// OBO-Edit
set.add(OboFormatTag.TAG_EQUIVALENT_TO_CHAIN.getTag());
set.add(OboFormatTag.TAG_DISJOINT_OVER.getTag());
return set;
}
private static void writeLine(StringBuilder ln, Writer writer) throws IOException {
ln.append('\n');
writer.write(ln.toString());
}
private static void writeLine(String ln, Writer writer) throws IOException {
writer.write(ln + '\n');
}
private static void writeEmptyLine(Writer writer) throws IOException {
writer.write("\n");
}
private static List duplicateTags(Set src) {
return new ArrayList<>(src);
}
private static void writeXRefClause(Clause clause, Writer writer) throws IOException {
Xref xref = clause.getValue(Xref.class);
StringBuilder sb = new StringBuilder();
sb.append(clause.getTag());
sb.append(": ");
String idref = xref.getIdref();
int colonPos = idref.indexOf(':');
if (colonPos > 0) {
sb.append(escapeOboString(idref.substring(0, colonPos), EscapeMode.XREF));
sb.append(':');
sb.append(escapeOboString(idref.substring(colonPos + 1), EscapeMode.XREF));
} else {
sb.append(escapeOboString(idref, EscapeMode.XREF));
}
String annotation = xref.getAnnotation();
if (annotation != null) {
sb.append(" \"");
sb.append(escapeOboString(annotation, EscapeMode.QUOTES));
sb.append('"');
}
appendQualifiers(sb, clause);
writeLine(sb, writer);
}
private static void writeSynonymtypedef(Clause clause, Writer writer) throws IOException {
StringBuilder sb = new StringBuilder();
sb.append(clause.getTag());
sb.append(": ");
Iterator valuesIterator = clause.getValues().iterator();
Collection values = clause.getValues();
for (int i = 0; i < values.size(); i++) {
String value = valuesIterator.next().toString();
if (i == 1) {
sb.append('"');
}
sb.append(escapeOboString(value, EscapeMode.QUOTES));
if (i == 1) {
sb.append('"');
}
if (valuesIterator.hasNext()) {
sb.append(' ');
}
}
appendQualifiers(sb, clause);
writeLine(sb, writer);
}
private static void writeHeaderDate(Clause clause, Writer writer) throws IOException {
StringBuilder sb = new StringBuilder();
sb.append(clause.getTag());
sb.append(": ");
Object value = clause.getValue();
if (value instanceof Date) {
sb.append(OBOFormatConstants.headerDateFormat().format((Date) value));
} else if (value instanceof String) {
sb.append(value);
} else {
if (LOG.isWarnEnabled()) {
LOG.warn("Unknown datatype ('{}') for value in clause: {}",
value.getClass().getName(), clause);
sb.append(value);
}
}
writeLine(sb, writer);
}
private static void writeIdSpace(Clause cl, Writer writer) throws IOException {
StringBuilder sb = new StringBuilder(cl.getTag());
sb.append(": ");
Collection values = cl.getValues();
int i = 0;
Iterator iterator = values.iterator();
while (iterator.hasNext() && i < 3) {
String value = iterator.next().toString();
if (i == 2) {
sb.append('"').append(escapeOboString(value, EscapeMode.QUOTES)).append('"');
} else {
sb.append(escapeOboString(value, EscapeMode.SIMPLE)).append(' ');
}
i++;
}
appendQualifiers(sb, cl);
writeLine(sb, writer);
}
private static void writeClauseWithQuotedString(Clause clause, Writer writer)
throws IOException {
StringBuilder sb = new StringBuilder();
sb.append(clause.getTag());
sb.append(": ");
boolean first = true;
Iterator valuesIterator = clause.getValues().iterator();
while (valuesIterator.hasNext()) {
if (first) {
sb.append('"');
}
String value = valuesIterator.next().toString();
sb.append(escapeOboString(value, EscapeMode.QUOTES));
if (first) {
sb.append('"');
}
if (valuesIterator.hasNext()) {
sb.append(' ');
}
first = false;
}
Collection xrefs = clause.getXrefs();
// if the xrefs value is null, then there should *never* be xrefs at
// this location
// not that the value may be a non-null empty list - here we still want
// to write []
if (!xrefs.isEmpty()) {
appendXrefs(sb, xrefs);
} else if (OboFormatTag.TAG_DEF.getTag().equals(clause.getTag())
|| OboFormatTag.TAG_SYNONYM.getTag().equals(clause.getTag())
|| OboFormatTag.TAG_EXPAND_EXPRESSION_TO.getTag().equals(clause.getTag())
|| OboFormatTag.TAG_EXPAND_ASSERTION_TO.getTag().equals(clause.getTag())) {
sb.append(" []");
}
appendQualifiers(sb, clause);
writeLine(sb, writer);
}
private static void appendXrefs(StringBuilder sb, Collection xrefs) {
List sortedXrefs = new ArrayList<>(xrefs);
Collections.sort(sortedXrefs, XrefComparator.INSTANCE);
sb.append(" [");
Iterator xrefsIterator = sortedXrefs.iterator();
while (xrefsIterator.hasNext()) {
Xref current = xrefsIterator.next();
String idref = current.getIdref();
int colonPos = idref.indexOf(':');
if (colonPos > 0) {
sb.append(escapeOboString(idref.substring(0, colonPos), EscapeMode.XREFLIST));
sb.append(':');
sb.append(escapeOboString(idref.substring(colonPos + 1), EscapeMode.XREFLIST));
} else {
sb.append(escapeOboString(idref, EscapeMode.XREFLIST));
}
String annotation = current.getAnnotation();
if (annotation != null) {
sb.append(' ');
sb.append('"');
sb.append(escapeOboString(annotation, EscapeMode.QUOTES));
sb.append('"');
}
if (xrefsIterator.hasNext()) {
sb.append(", ");
}
}
sb.append(']');
}
/**
* Write def.
*
* @param clause the clause
* @param writer the writer
* @throws IOException Signals that an I/O exception has occurred.
*/
public static void writeDef(Clause clause, Writer writer) throws IOException {
writeClauseWithQuotedString(clause, writer);
}
/**
* Write property value.
*
* @param clause the clause
* @param writer the writer
* @throws IOException Signals that an I/O exception has occurred.
*/
public static void writePropertyValue(Clause clause, Writer writer) throws IOException {
Collection cols = clause.getValues();
if (cols.size() < 2) {
LOG.error("The {} has incorrect number of values: {}",
OboFormatTag.TAG_PROPERTY_VALUE.getTag(), clause);
return;
}
StringBuilder sb = new StringBuilder();
sb.append(clause.getTag());
sb.append(": ");
Iterator it = cols.iterator();
// write property
// TODO replace toString() method
String property = it.next().toString();
sb.append(escapeOboString(property, EscapeMode.SIMPLE));
// write value and optional type
if (it.hasNext()) {
// value
sb.append(' ');
String val = it.next().toString(); // TODO replace toString() method
sb.append('"');
sb.append(escapeOboString(val, EscapeMode.QUOTES));
sb.append('"');
}
while (it.hasNext()) {
// optional type; there should be only one value left in the iterator
sb.append(' ');
String val = it.next().toString(); // TODO replace toString() method
sb.append(escapeOboString(val, EscapeMode.SIMPLE));
}
appendQualifiers(sb, clause);
writeLine(sb, writer);
}
/**
* Write synonym.
*
* @param clause the clause
* @param writer the writer
* @throws IOException Signals that an I/O exception has occurred.
*/
public static void writeSynonym(Clause clause, Writer writer) throws IOException {
writeClauseWithQuotedString(clause, writer);
}
/**
* Write.
*
* @param clause the clause
* @param writer the writer
* @param nameProvider the name provider
* @throws IOException Signals that an I/O exception has occurred.
*/
public static void write(Clause clause, Writer writer, @Nullable NameProvider nameProvider)
throws IOException {
if (OboFormatTag.TAG_IS_OBSELETE.getTag().equals(clause.getTag())) {
// only write the obsolete tag if the value is Boolean.TRUE or
// "true"
Object value = clause.getValue();
if (value instanceof Boolean) {
if (Boolean.FALSE.equals(value)) {
return;
}
} else {
// also check for a String representation of Boolean.TRUE
if (!Boolean.TRUE.toString().equals(value)) {
return;
}
}
}
StringBuilder sb = new StringBuilder();
sb.append(clause.getTag());
sb.append(": ");
Iterator valuesIterator = clause.getValues().iterator();
StringBuilder idsLabel = null;
if (nameProvider != null && TAGSINFORMATIVE.contains(clause.getTag())) {
idsLabel = new StringBuilder();
}
while (valuesIterator.hasNext()) {
String value = valuesIterator.next().toString();
if (idsLabel != null && nameProvider != null) {
String label = nameProvider.getName(value);
if (label != null && (isOpaqueIdentifier(value) || !valuesIterator.hasNext())) {
// only print label if the label exists
// and the label is different from the id
// relationships: ID part_of LABEL part_of
if (idsLabel.length() > 0) {
idsLabel.append(' ');
}
idsLabel.append(label);
}
}
EscapeMode mode = EscapeMode.MOST;
if (OboFormatTag.TAG_COMMENT.getTag().equals(clause.getTag())) {
mode = EscapeMode.PARENTHESIS;
}
sb.append(escapeOboString(value, mode));
if (valuesIterator.hasNext()) {
sb.append(' ');
}
}
Collection xrefs = clause.getXrefs();
if (!xrefs.isEmpty()) {
appendXrefs(sb, xrefs);
}
appendQualifiers(sb, clause);
if (idsLabel != null && idsLabel.length() > 0) {
String trimmed = idsLabel.toString().trim();
if (!trimmed.isEmpty()) {
sb.append(" ! ");
sb.append(trimmed);
}
}
writeLine(sb, writer);
}
private static boolean isOpaqueIdentifier(@Nullable String value) {
boolean result = false;
if (value != null && !value.isEmpty()) {
// check for colon
int colonPos = value.indexOf(':');
// check that the suffix after the colon contains only digits
if (colonPos > 0 && value.length() > colonPos + 1) {
result = true;
for (int i = colonPos; i < value.length(); i++) {
char c = value.charAt(i);
if (!Character.isDigit(c) && c != ':') {
result = false;
break;
}
}
}
}
return result;
}
private static void appendQualifiers(StringBuilder sb, Clause clause) {
Collection qvs = clause.getQualifierValues();
if (!qvs.isEmpty()) {
sb.append(" {");
Iterator qvsIterator = qvs.iterator();
while (qvsIterator.hasNext()) {
QualifierValue qv = qvsIterator.next();
sb.append(qv.getQualifier());
sb.append("=\"");
sb.append(escapeOboString(qv.getValue(), EscapeMode.QUOTES));
sb.append('"');
if (qvsIterator.hasNext()) {
sb.append(", ");
}
}
sb.append('}');
}
}
private static CharSequence escapeOboString(String in, EscapeMode mode) {
String replace = in.replace("\\", "\\\\");
if (mode == EscapeMode.MOST || mode == EscapeMode.QUOTES) {
replace = replace.replace("\"", "\\\"");
}
replace = replace.replace("\n", "\\n");
if (mode == EscapeMode.MOST || mode == EscapeMode.PARENTHESIS) {
replace = replace.replace("{", "\\{").replace("}", "\\}");
}
if (mode == EscapeMode.XREF || mode == EscapeMode.XREFLIST) {
replace = replace.replace(",", "\\,").replace(":", "\\:");
}
if (mode == EscapeMode.XREFLIST) {
replace = replace.replace("[", "\\[").replace("]", "\\]");
}
return replace;
}
/**
* Sort a list of term frame clauses according to in the OBO format specified tag and value
* order.
*
* @param clauses the clauses
*/
public static void sortTermClauses(List clauses) {
Collections.sort(clauses, clauseListComparator);
}
private static int compare(Clause o1, Clause o2) {
// special case for intersections
String tag = o1.getTag();
if (OboFormatTag.TAG_INTERSECTION_OF.getTag().equals(tag)) {
// sort by values size, prefer short ones.
int s1 = o1.getValues().size();
int s2 = o2.getValues().size();
if (s1 < s2) {
return -1;
} else if (s1 > s2) {
return 1;
}
}
// sort by value
int comp = compareValues(o1.getValue(), o2.getValue());
if (comp != 0) {
return comp;
}
return compareValues(o1.getValue2(), o2.getValue2());
}
/**
* Compare values.
*
* @param o1 the o1
* @param o2 the o2
* @return the int
*/
private static int compareValues(@Nullable Object o1, @Nullable Object o2) {
if (o1 == null && o2 == null) {
return 0;
}
if (o1 == null) {
return -1;
}
if (o2 == null) {
return 1;
}
String s1 = toStringRepresentation(o1);
String s2 = toStringRepresentation(o2);
int comp = s1.compareToIgnoreCase(s2);
if (comp == 0) {
// normally ignore case, for sorting
// but if the strings are equal,
// try again with case check
comp = s1.compareTo(s2);
}
return comp;
}
/**
* @param obj the obj
* @return toString representation
*/
private static String toStringRepresentation(@Nullable Object obj) {
if (obj == null) {
return "";
}
if (obj instanceof Xref) {
Xref xref = (Xref) obj;
return xref.getIdref() + ' ' + xref.getAnnotation();
}
if (obj instanceof String) {
return (String) obj;
}
return obj.toString();
}
/**
* @return true, if is check structure
*/
public boolean isCheckStructure() {
return isCheckStructure;
}
/**
* @param isCheckStructure the new check structure
*/
public void setCheckStructure(boolean isCheckStructure) {
this.isCheckStructure = isCheckStructure;
}
/**
* @param fn the file name to read in
* @param writer the writer
* @throws IOException Signals that an I/O exception has occurred.
* @throws OBOFormatParserException the oBO format parser exception
*/
public void write(String fn, Writer writer) throws IOException {
if (fn.startsWith("http:")) {
write(new URL(fn), writer);
} else {
try (FileReader r = new FileReader(new File(fn));
Reader reader = new BufferedReader(r);) {
write(reader, writer);
}
}
}
/**
* Write.
*
* @param url the url
* @param writer the writer
* @throws IOException Signals that an I/O exception has occurred.
* @throws OBOFormatParserException the oBO format parser exception
*/
public void write(URL url, Writer writer) throws IOException {
Reader reader = new BufferedReader(new InputStreamReader(url.openStream()));
write(reader, writer);
}
/**
* @param reader the reader
* @param writer the writer
* @throws IOException Signals that an I/O exception has occurred.
* @throws OBOFormatParserException the oBO format parser exception
*/
public void write(Reader reader, Writer writer) throws IOException {
OBOFormatParser parser = new OBOFormatParser();
OBODoc doc = parser.parse(reader);
write(doc, writer);
}
/**
* @param doc the doc
* @param outFilename the out file name
* @throws IOException Signals that an I/O exception has occurred.
*/
public void write(OBODoc doc, String outFilename) throws IOException {
write(doc, new File(outFilename));
}
/**
* @param doc the doc
* @param outFile the out file
* @throws IOException Signals that an I/O exception has occurred.
*/
public void write(OBODoc doc, File outFile) throws IOException {
try (FileOutputStream os = new FileOutputStream(outFile);
OutputStreamWriter osw = new OutputStreamWriter(os, StandardCharsets.UTF_8);
Writer bw = new BufferedWriter(osw);) {
write(doc, bw);
}
}
/**
* @param doc the doc
* @param writer the writer
* @throws IOException Signals that an I/O exception has occurred.
*/
public void write(OBODoc doc, Writer writer) throws IOException {
NameProvider nameProvider = new OBODocNameProvider(doc);
write(doc, writer, nameProvider);
}
/**
* @param doc the doc
* @param writer the writer
* @param nameProvider the name provider
* @throws IOException Signals that an I/O exception has occurred.
*/
public void write(OBODoc doc, Writer writer, NameProvider nameProvider) throws IOException {
if (isCheckStructure) {
doc.check();
}
Frame headerFrame = doc.getHeaderFrame();
writeHeader(checkNotNull(headerFrame), writer, nameProvider);
List tags = duplicateTags(frame.getTags());
Collections.sort(tags, OBOFormatConstants.headerPriority);
write(new Clause(OboFormatTag.TAG_FORMAT_VERSION.getTag(), "1.2"), writer, nameProvider);
for (String tag : tags) {
if (tag.equals(OboFormatTag.TAG_FORMAT_VERSION.getTag())) {
continue;
}
List clauses = new ArrayList<>(frame.getClauses(tag));
Collections.sort(clauses, clauseComparator);
for (Clause clause : clauses) {
if (tag.equals(OboFormatTag.TAG_SUBSETDEF.getTag())) {
writeSynonymtypedef(clause, writer);
} else if (tag.equals(OboFormatTag.TAG_SYNONYMTYPEDEF.getTag())) {
writeSynonymtypedef(clause, writer);
} else if (tag.equals(OboFormatTag.TAG_DATE.getTag())) {
writeHeaderDate(clause, writer);
} else if (tag.equals(OboFormatTag.TAG_PROPERTY_VALUE.getTag())) {
writePropertyValue(clause, writer);
} else if (tag.equals(OboFormatTag.TAG_IDSPACE.getTag())) {
writeIdSpace(clause, writer);
} else {
write(clause, writer, nameProvider);
}
}
}
writeEmptyLine(writer);
}
/**
* @param frame the frame
* @param writer the writer
* @param nameProvider the name provider
* @throws IOException Signals that an I/O exception has occurred.
*/
public void write(Frame frame, Writer writer, @Nullable NameProvider nameProvider)
throws IOException {
Comparator comparator = null;
if (frame.getType() == FrameType.TERM) {
writeLine("[Term]", writer);
comparator = OBOFormatConstants.tagPriority;
} else if (frame.getType() == FrameType.TYPEDEF) {
writeLine("[Typedef]", writer);
comparator = OBOFormatConstants.typeDefPriority;
} else if (frame.getType() == FrameType.INSTANCE) {
writeLine("[Instance]", writer);
comparator = OBOFormatConstants.typeDefPriority;
}
String id = frame.getId();
if (id != null) {
Object label = frame.getTagValue(OboFormatTag.TAG_NAME);
String extra = "";
if (label == null && nameProvider != null) {
// the name clause may not be present in this OBODoc - however,
// the name provider may be able to provide one, in which case,
// we
// write it as a parser-invisible comment, thus preserving the
// document structure but providing useful information for any
// person that inspects the obo file
label = nameProvider.getName(id);
if (label != null) {
extra = " ! " + label;
}
}
writeLine(OboFormatTag.TAG_ID.getTag() + ": " + id + extra, writer);
}
List tags = duplicateTags(frame.getTags());
Collections.sort(tags, comparator);
String defaultOboNamespace = null;
if (nameProvider != null) {
defaultOboNamespace = nameProvider.getDefaultOboNamespace();
}
for (String tag : tags) {
List clauses = new ArrayList<>(frame.getClauses(tag));
Collections.sort(clauses, clauseComparator);
for (Clause clause : clauses) {
String clauseTag = clause.getTag();
if (OboFormatTag.TAG_ID.getTag().equals(clauseTag)) {
continue;
} else if (OboFormatTag.TAG_DEF.getTag().equals(clauseTag)) {
writeDef(clause, writer);
} else if (OboFormatTag.TAG_SYNONYM.getTag().equals(clauseTag)) {
writeSynonym(clause, writer);
} else if (OboFormatTag.TAG_PROPERTY_VALUE.getTag().equals(clauseTag)) {
writePropertyValue(clause, writer);
} else if (OboFormatTag.TAG_EXPAND_EXPRESSION_TO.getTag().equals(clauseTag)
|| OboFormatTag.TAG_EXPAND_ASSERTION_TO.getTag().equals(clauseTag)) {
writeClauseWithQuotedString(clause, writer);
} else if (OboFormatTag.TAG_XREF.getTag().equals(clauseTag)) {
writeXRefClause(clause, writer);
} else if (OboFormatTag.TAG_NAMESPACE.getTag().equals(clauseTag)) {
// only write OBO namespace,
// if it is different from the default OBO namespace
if (defaultOboNamespace == null
|| !clause.getValue().equals(defaultOboNamespace)) {
write(clause, writer, nameProvider);
}
} else {
write(clause, writer, nameProvider);
}
}
}
writeEmptyLine(writer);
}
//@formatter:off
/** The Enum EscapeMode. */
private enum EscapeMode {
/** all except xref and xrefList. */ MOST,
/** simple + parenthesis. */ PARENTHESIS,
/** simple + quotes. */ QUOTES,
/** simple + comma + colon. */ XREF,
/** xref + closing brackets. */ XREFLIST,
/** newline and backslash. */ SIMPLE
}
//@formatter:on
/**
* Provide names for given OBO identifiers. This abstraction layer allows to find names from
* different sources, including {@link OBODoc}.
*/
public interface NameProvider {
/**
* Try to retrieve the valid name for the given identifier. If not available return null.
*
* @param id identifier
* @return name or null
*/
@Nullable
String getName(String id);
/**
* Retrieve the default OBO namespace.
*
* @return default OBO namespace or null
*/
@Nullable
String getDefaultOboNamespace();
}
/**
* The Class XrefComparator.
*/
private static class XrefComparator implements Comparator, Serializable {
static final XrefComparator INSTANCE = new XrefComparator();
@Override
public int compare(@Nullable Xref o1, @Nullable Xref o2) {
String idref1 = checkNotNull(o1).getIdref();
String idref2 = checkNotNull(o2).getIdref();
return idref1.compareToIgnoreCase(idref2);
}
}
/**
* Default implementation of a {@link NameProvider} using an underlying. {@link OBODoc}.
*/
public static class OBODocNameProvider implements NameProvider {
private final OBODoc oboDoc;
@Nullable
private final String defaultOboNamespace;
/**
* Instantiates a new OBO doc name provider.
*
* @param oboDoc the obo doc
*/
public OBODocNameProvider(OBODoc oboDoc) {
this.oboDoc = oboDoc;
Frame headerFrame = oboDoc.getHeaderFrame();
if (headerFrame != null) {
defaultOboNamespace =
headerFrame.getTagValue(OboFormatTag.TAG_DEFAULT_NAMESPACE, String.class);
} else {
defaultOboNamespace = null;
}
}
@Override
@Nullable
public String getName(String id) {
String name = null;
Frame frame = oboDoc.getTermFrame(id);
if (frame == null) {
frame = oboDoc.getTypedefFrame(id);
}
if (frame != null) {
Clause cl = frame.getClause(OboFormatTag.TAG_NAME);
if (cl != null) {
name = cl.getValue(String.class);
}
}
return name;
}
@Override
@Nullable
public String getDefaultOboNamespace() {
return defaultOboNamespace;
}
}
/**
* Alternative implementation to lookup labels in an {@link OWLOntology}. axioms =
asList(ont.axioms(OWLAnnotationAssertionAxiom.class, OWLAnnotationSubject.class,
iri, Imports.INCLUDED, IN_SUB_POSITION));
for (OWLAnnotationAssertionAxiom axiom : axioms) {
if (axiom.getProperty().isLabel()) {
OWLAnnotationValue value = axiom.getValue();
if (value instanceof OWLLiteral) {
return ((OWLLiteral) value).getLiteral();
}
}
}
return null;
}
@Override
@Nullable
public String getDefaultOboNamespace() {
return defaultOboNamespace;
}
}
}
