org.obolibrary.oboformat.model.OBODoc Maven / Gradle / Ivy
package org.obolibrary.oboformat.model;
import java.util.ArrayList;
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 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 header frame. */
protected Frame headerFrame;
/** The term frame map. */
protected Map termFrameMap = new HashMap();
/** The typedef frame map. */
protected Map typedefFrameMap = new HashMap();
/** The instance frame map. */
protected Map instanceFrameMap = new HashMap();
/** The annotation frames. */
protected Collection annotationFrames = new LinkedList();
/** The imported obo docs. */
protected Collection importedOBODocs = new LinkedList();
/** default constructor. */
public OBODoc() {
super();
}
/** @return the header frame */
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();
}
/**
* @param id
* the id
* @return the term frame
*/
public Frame getTermFrame(String id) {
return getTermFrame(id, false);
}
/**
* @param id
* the id
* @param followImport
* the follow import
* @return the term frame
*/
public Frame getTermFrame(String id, boolean followImport) {
if (followImport == false) {
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
*/
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
*/
public Frame getTypedefFrame(String id) {
return getTypedefFrame(id, false);
}
/**
* @param id
* the id
* @param followImports
* the follow imports
* @return the typedef frame
*/
public Frame getTypedefFrame(String id, boolean followImports) {
if (followImports == false) {
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
*/
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 = importedOBODocs;
}
/**
* Adds the imported obo doc.
*
* @param doc
* the doc
*/
public void addImportedOBODoc(OBODoc doc) {
if (importedOBODocs == null) {
importedOBODocs = new ArrayList();
}
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);
}
}
/**
* Looks up the ID prefix to IRI prefix mapping. Header-Tag: idspace
*
* @param prefix
* prefix
* @return IRI prefix as string
*/
public 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 boolean isTreatXrefsAsEquivalent(String prefix) {
if (prefix != null && prefix.equals("RO")) {
return true;
}
return false;
}
/**
* 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 = 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.
*
* @throws FrameStructureException
* the frame structure exception
* @see OboInOwlCardinalityTools for equivalent checks in OWL
*/
public void check() throws FrameStructureException {
getHeaderFrame().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 + ")";
}
}
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