org.obolibrary.oboformat.model.OBODoc Maven / Gradle / Ivy
package org.obolibrary.oboformat.model;
import static org.semanticweb.owlapi.util.OWLAPIPreconditions.verifyNotNull;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.Map;
import java.util.Set;
import javax.annotation.Nullable;
import org.obolibrary.obo2owl.OboInOwlCardinalityTools;
import org.obolibrary.oboformat.model.Frame.FrameType;
import org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag;
/**
* An OBODoc is a container for a header frame and zero or more entity frames.
*/
public class OBODoc {
/**
* The term frame map.
*/
protected final Map termFrameMap = new HashMap<>();
/**
* The typedef frame map.
*/
protected final Map typedefFrameMap = new HashMap<>();
/**
* The instance frame map.
*/
protected final Map instanceFrameMap = new HashMap<>();
/**
* The annotation frames.
*/
protected final Collection annotationFrames = new LinkedList<>();
/**
* The imported obo docs.
*/
protected final Collection importedOBODocs = new LinkedList<>();
/**
* The header frame.
*/
@Nullable
protected Frame headerFrame;
private static void freezeFrameMap(Map frameMap) {
for (Frame frame : frameMap.values()) {
frame.freeze();
}
}
/**
* Looks up the ID prefix to IRI prefix mapping. Header-Tag: idspace
*
* @param prefix prefix
* @return IRI prefix as string
*/
@Nullable
public static String getIDSpace(String prefix) {
// built-in
if (prefix.equals("RO")) {
return "http://purl.obolibrary.org/obo/RO_";
}
// TODO
return null;
}
/**
* @param prefix the prefix
* @return true, if is treat xrefs as equivalent
*/
public static boolean isTreatXrefsAsEquivalent(@Nullable String prefix) {
if ("RO".equals(prefix)) {
return true;
}
return false;
}
/**
* @return the header frame
*/
@Nullable
public Frame getHeaderFrame() {
return headerFrame;
}
/**
* @param headerFrame the new header frame
*/
public void setHeaderFrame(Frame headerFrame) {
this.headerFrame = headerFrame;
}
/**
* @return the term frames
*/
public Collection getTermFrames() {
return termFrameMap.values();
}
/**
* @return the typedef frames
*/
public Collection getTypedefFrames() {
return typedefFrameMap.values();
}
/**
* @return the instance frames
*/
public Collection getInstanceFrames() {
return instanceFrameMap.values();
}
/**
* Freezing an OBODoc signals that the document has become quiescent, and
* that the system may optimize data structures for performance or space.
*/
public void freezeFrames() {
verifyNotNull(headerFrame,
"headerFrame cannot be null at this stage. Setting the headr frame has been skipped")
.freeze();
freezeFrameMap(termFrameMap);
freezeFrameMap(typedefFrameMap);
freezeFrameMap(instanceFrameMap);
for (Frame frame : annotationFrames) {
frame.freeze();
}
}
/**
* @param id the id
* @return the term frame
*/
@Nullable
public Frame getTermFrame(String id) {
return getTermFrame(id, false);
}
/**
* @param id the id
* @param followImport the follow import
* @return the term frame
*/
@Nullable
public Frame getTermFrame(String id, boolean followImport) {
if (!followImport) {
return termFrameMap.get(id);
}
// this set is used to check for cycles
Set visited = new HashSet<>();
visited.add(getHeaderDescriptor());
return getTermFrame(id, visited);
}
/**
* @param id the id
* @param visitedDocs the visited docs
* @return the frame
*/
@Nullable
private Frame getTermFrame(String id, Set visitedDocs) {
Frame f = termFrameMap.get(id);
if (f != null) {
return f;
}
for (OBODoc doc : importedOBODocs) {
String headerDescriptor = doc.getHeaderDescriptor();
if (!visitedDocs.contains(headerDescriptor)) {
visitedDocs.add(headerDescriptor);
f = doc.getTermFrame(id, true);
}
if (f != null) {
return f;
}
}
return null;
}
/**
* @param id the id
* @return the typedef frame
*/
@Nullable
public Frame getTypedefFrame(String id) {
return getTypedefFrame(id, false);
}
/**
* @param id the id
* @param followImports the follow imports
* @return the typedef frame
*/
@Nullable
public Frame getTypedefFrame(String id, boolean followImports) {
if (!followImports) {
return typedefFrameMap.get(id);
}
// this set is used to check for cycles
Set visited = new HashSet<>();
visited.add(getHeaderDescriptor());
return getTypedefFrame(id, visited);
}
/**
* @param id the id
* @param visitedDocs the visited docs
* @return the frame
*/
@Nullable
private Frame getTypedefFrame(String id, Set visitedDocs) {
Frame f = typedefFrameMap.get(id);
if (f != null) {
return f;
}
for (OBODoc doc : importedOBODocs) {
String headerDescriptor = doc.getHeaderDescriptor();
if (!visitedDocs.contains(headerDescriptor)) {
visitedDocs.add(headerDescriptor);
f = doc.getTypedefFrame(id, true);
}
if (f != null) {
return f;
}
}
return null;
}
/**
* @param id the id
* @return the instance frame
*/
public Frame getInstanceFrame(String id) {
return instanceFrameMap.get(id);
}
/**
* @return the imported obo docs
*/
public Collection getImportedOBODocs() {
return importedOBODocs;
}
/**
* @param importedOBODocs the new imported obo docs
*/
public void setImportedOBODocs(Collection importedOBODocs) {
this.importedOBODocs.clear();
this.importedOBODocs.addAll(importedOBODocs);
}
/**
* Adds the imported obo doc.
*
* @param doc the doc
*/
public void addImportedOBODoc(OBODoc doc) {
importedOBODocs.add(doc);
}
/**
* Adds the frame.
*
* @param f the frame
* @throws FrameMergeException the frame merge exception
*/
public void addFrame(Frame f) throws FrameMergeException {
if (f.getType() == FrameType.TERM) {
addTermFrame(f);
} else if (f.getType() == FrameType.TYPEDEF) {
addTypedefFrame(f);
} else if (f.getType() == FrameType.INSTANCE) {
addInstanceFrame(f);
}
}
/**
* Adds the term frame.
*
* @param f the frame
* @throws FrameMergeException the frame merge exception
*/
public void addTermFrame(Frame f) throws FrameMergeException {
String id = f.getId();
if (termFrameMap.containsKey(id)) {
termFrameMap.get(id).merge(f);
} else {
termFrameMap.put(id, f);
}
}
/**
* Adds the typedef frame.
*
* @param f the frame
* @throws FrameMergeException the frame merge exception
*/
public void addTypedefFrame(Frame f) throws FrameMergeException {
String id = f.getId();
if (typedefFrameMap.containsKey(id)) {
typedefFrameMap.get(id).merge(f);
} else {
typedefFrameMap.put(id, f);
}
}
/**
* Adds the instance frame.
*
* @param f the frame
* @throws FrameMergeException the frame merge exception
*/
public void addInstanceFrame(Frame f) throws FrameMergeException {
String id = f.getId();
if (instanceFrameMap.containsKey(id)) {
instanceFrameMap.get(id).merge(f);
} else {
instanceFrameMap.put(id, f);
}
}
/**
* Merge contents.
*
* @param extDoc the external doc
* @throws FrameMergeException the frame merge exception
*/
public void mergeContents(OBODoc extDoc) throws FrameMergeException {
for (Frame f : extDoc.getTermFrames()) {
addTermFrame(f);
}
for (Frame f : extDoc.getTypedefFrames()) {
addTypedefFrame(f);
}
for (Frame f : extDoc.getInstanceFrames()) {
addInstanceFrame(f);
}
}
/**
* Adds the default ontology header.
*
* @param defaultOnt the default ont
*/
public void addDefaultOntologyHeader(String defaultOnt) {
Frame hf = verifyNotNull(getHeaderFrame());
Clause ontClause = hf.getClause(OboFormatTag.TAG_ONTOLOGY);
if (ontClause == null) {
ontClause = new Clause(OboFormatTag.TAG_ONTOLOGY, defaultOnt);
hf.addClause(ontClause);
}
}
/**
* Check this document for violations, i.e. cardinality constraint
* violations.
*
* @see OboInOwlCardinalityTools for equivalent checks in OWL
*/
public void check() {
verifyNotNull(headerFrame).check();
for (Frame f : getTermFrames()) {
f.check();
}
for (Frame f : getTypedefFrames()) {
f.check();
}
for (Frame f : getInstanceFrames()) {
f.check();
}
}
@Override
public String toString() {
return getHeaderDescriptor();
}
/**
* @return the header descriptor
*/
private String getHeaderDescriptor() {
return "OBODoc(" + headerFrame + ')';
}
}