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Commit a7270a54 authored by Piotr Gawron's avatar Piotr Gawron
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getModel method added to BioEntity

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1 merge request!186Resolve "upload of sbml"
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converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
+ 357
− 461
View file @ a7270a54
......@@ -6,8 +6,6 @@ import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.Set;
......@@ -16,6 +14,7 @@ import org.apache.xerces.dom.DocumentImpl;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import org.mockito.Mockito;
import org.w3c.dom.Document;
import org.w3c.dom.Node;
......@@ -34,465 +33,362 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Species;
public class RestAnnotationParserTest extends CellDesignerTestFunctions {
Logger logger = Logger.getLogger(RestAnnotationParserTest.class);
@Before
public void setUp() throws Exception {
}
@After
public void tearDown() throws Exception {
}
@Test
public void test() throws Exception {
try {
RestAnnotationParser rap = new RestAnnotationParser();
String response = readFile("testFiles/annotation/sampleDescription.txt");
List<String> synonyms = rap.getSynonyms(response);
assertEquals(3, synonyms.size());
assertTrue(synonyms.contains("CAMK"));
assertTrue(synonyms.contains("CAMKIV"));
List<String> formerSymbols = rap.getFormerSymbols(response);
assertEquals(0, formerSymbols.size());
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testParseNotes() throws Exception {
try {
RestAnnotationParser parser = new RestAnnotationParser();
Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes.xml");
Species proteinAlias = new GenericProtein("id");
parser.processNotes(node.getFirstChild(), proteinAlias);
String notes = proteinAlias.getNotes();
assertNotNull(notes);
assertFalse(notes.contains("body"));
assertTrue(notes.contains("some"));
// after redoing it should be the same
parser.processNotes(node.getFirstChild(), proteinAlias);
notes = proteinAlias.getNotes();
assertNotNull(notes);
assertFalse(notes.contains("body"));
assertTrue(notes.contains("some"));
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testParseNotes2() throws Exception {
try {
RestAnnotationParser parser = new RestAnnotationParser();
Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes3.xml");
Species proteinAlias = new GenericProtein("id");
parser.processNotes(node.getFirstChild(), proteinAlias);
String notes = proteinAlias.getNotes();
assertNotNull(notes);
assertFalse(notes.contains("body"));
assertTrue(notes.contains("some"));
// after redoing it should be the same
parser.processNotes(node.getFirstChild(), proteinAlias);
notes = proteinAlias.getNotes();
assertNotNull(notes);
assertFalse(notes.contains("body"));
assertTrue(notes.contains("some"));
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testParseNotes3() throws Exception {
try {
RestAnnotationParser parser = new RestAnnotationParser();
Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes4.xml");
Species proteinAlias = new GenericProtein("id");
proteinAlias.setNotes("text");
parser.processNotes(node.getFirstChild(), proteinAlias);
String notes = proteinAlias.getNotes();
assertNotNull(notes);
assertFalse(notes.contains("body"));
assertTrue(notes.contains("some"));
// after redoing it should be the same
parser.processNotes(node.getFirstChild(), proteinAlias);
notes = proteinAlias.getNotes();
assertNotNull(notes);
assertFalse(notes.contains("body"));
assertTrue(notes.contains("some"));
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testParseCollisionNotes() throws Exception {
try {
RestAnnotationParser parser = new RestAnnotationParser();
Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes2.xml");
GenericProtein protein = new GenericProtein("pr_id1");
protein.addSynonym("a1");
protein.addFormerSymbol("a1");
protein.setFullName("yyy");
protein.setAbbreviation("aaaa");
protein.setCharge(9);
protein.setSymbol("D");
parser.processNotes(node.getFirstChild(), protein);
assertEquals(1, protein.getSynonyms().size());
assertEquals(1, protein.getFormerSymbols().size());
assertEquals(6, getWarnings().size());
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testParseInvalidNotes1() throws Exception {
try {
RestAnnotationParser parser = new RestAnnotationParser();
Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes_invalid_charge.xml");
Species proteinAlias = new GenericProtein("id");
parser.processNotes(node.getFirstChild(), proteinAlias);
assertEquals(1, getWarnings().size());
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testParseCollisionNotes2() throws Exception {
try {
RestAnnotationParser parser = new RestAnnotationParser();
Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes2.xml");
Reaction reaction = new Reaction();
reaction.addSynonym("a1");
reaction.setAbbreviation("aaaa");
reaction.setSubsystem("sss");
reaction.setGeneProteinReaction("str");
reaction.setFormula("xxx");
reaction.setMechanicalConfidenceScore(-45);
reaction.setUpperBound(4.5);
reaction.setLowerBound(4.5);
parser.processNotes(node.getFirstChild(), reaction);
assertEquals(8, getWarnings().size());
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testMoveAnnotationsFromNotes() throws Exception {
try {
Model model = getModelForFile("testFiles/copyingAnnotationModel.xml");
Set<Element> elements = model.getElements();
for (Element element : elements) {
if (element.getName().equals("blabla")) {
assertEquals(2, element.getMiriamData().size());
element.getMiriamData().add(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, "12345"));
element.getMiriamData().add(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, "333666"));
assertEquals(2, element.getMiriamData().size());
}
assertFalse(element.getNotes().contains("rdf:RDF"));
}
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testProcessRdfDescription() throws Exception {
try {
RestAnnotationParser rap = new RestAnnotationParser();
Species speciesAlias = new GenericProtein("id");
speciesAlias.setNotes(
"begining\n" + "<rdf:RDF>" + "<rdf:Description rdf:about=\"#s2157\">\n" + "<bqmodel:is>\n" + "<rdf:Bag>\n"
+ "<rdf:li rdf:resource=\"urn:miriam:obo.chebi:CHEBI%3A17515\"/>\n" + "</rdf:Bag>\n" + "</bqmodel:is>\n" + "</rdf:Description>\n" + "</rdf:RDF>"
+ "\nend ending");
rap.processRdfDescription(speciesAlias);
assertEquals("begining\n\nend ending", speciesAlias.getNotes());
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testGetMiriamDataFromAnnotation() throws Exception {
try {
RestAnnotationParser rap = new RestAnnotationParser();
String response = readFile("testFiles/annotation/sampleDescription.txt");
Set<MiriamData> set = rap.getMiriamData(response);
for (MiriamData miriamData : set) {
if (miriamData.getDataType().equals(MiriamType.KEGG_GENES)) {
assertTrue(miriamData.getResource().contains("hsa"));
}
}
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testGetMiriamDataFromEmpty() throws Exception {
try {
RestAnnotationParser rap = new RestAnnotationParser();
Set<MiriamData> set = rap.getMiriamData(null);
assertEquals(0, set.size());
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testCreateAnnotationString() throws Exception {
try {
RestAnnotationParser rap = new RestAnnotationParser();
String former1 = "form1";
String former2 = "form2";
GenericProtein element = new GenericProtein("id");
element.addFormerSymbol(former1);
element.addFormerSymbol(former2);
element.setCharge(1);
String str = rap.createAnnotationString(element, true);
assertTrue(str.contains(former1));
assertTrue(str.contains(former2));
for (NoteField field : NoteField.values()) {
if (field.getClazz().isAssignableFrom(element.getClass()) || CellDesignerElement.class.isAssignableFrom(field.getClazz())) {
assertTrue("Export string doesn't contain info about: " + field.getCommonName(), str.indexOf(field.getCommonName()) >= 0);
}
}
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testGetFormerSymbolsFromInvalidStr() throws Exception {
try {
RestAnnotationParser rap = new RestAnnotationParser();
assertEquals(0, rap.getFormerSymbols(null).size());
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testGetNotesInvalid() throws Exception {
try {
RestAnnotationParser rap = new RestAnnotationParser();
Document xmlDoc = new DocumentImpl();
Node node = xmlDoc.createElement("bla");
rap.getNotes(node);
fail("Exception expected");
} catch (InvalidArgumentException e) {
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testProcessNotesForInvalidElement() throws Exception {
try {
RestAnnotationParser parser = new RestAnnotationParser();
Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes4.xml");
parser.processNotes(node.getFirstChild(), new BioEntity() {
/**
*
*/
private static final long serialVersionUID = 1L;
@Override
public void setSynonyms(List<String> synonyms) {
}
@Override
public void setSymbol(String symbol) {
}
@Override
public void setNotes(String notes) {
}
@Override
public void setName(String name) {
}
@Override
public void setFormula(String formula) {
}
@Override
public void setAbbreviation(String abbreviation) {
}
@Override
public List<String> getSynonyms() {
return new ArrayList<>();
}
@Override
public String getSymbol() {
return "";
}
@Override
public String getNotes() {
return "";
}
@Override
public String getName() {
return "";
}
@Override
public Collection<MiriamData> getMiriamData() {
return null;
}
@Override
public String getFormula() {
return null;
}
@Override
public String getAbbreviation() {
return null;
}
@Override
public void addMiriamData(MiriamData md) {
}
@Override
public void addMiriamData(Collection<MiriamData> miriamData) {
}
@Override
public int getId() {
// TODO Auto-generated method stub
return 0;
}
@Override
public String getStringType() {
// TODO Auto-generated method stub
return null;
}
@Override
public void setVisibilityLevel(String zoomLevelVisibility) {
// TODO Auto-generated method stub
}
@Override
public String getVisibilityLevel() {
// TODO Auto-generated method stub
return null;
}
@Override
public void setVisibilityLevel(Integer zoomLevelVisibility) {
// TODO Auto-generated method stub
}
@Override
public String getElementId() {
// TODO Auto-generated method stub
return null;
Logger logger = Logger.getLogger(RestAnnotationParserTest.class);
@Before
public void setUp() throws Exception {
}
@After
public void tearDown() throws Exception {
}
@Test
public void test() throws Exception {
try {
RestAnnotationParser rap = new RestAnnotationParser();
String response = readFile("testFiles/annotation/sampleDescription.txt");
List<String> synonyms = rap.getSynonyms(response);
assertEquals(3, synonyms.size());
assertTrue(synonyms.contains("CAMK"));
assertTrue(synonyms.contains("CAMKIV"));
List<String> formerSymbols = rap.getFormerSymbols(response);
assertEquals(0, formerSymbols.size());
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testParseNotes() throws Exception {
try {
RestAnnotationParser parser = new RestAnnotationParser();
Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes.xml");
Species proteinAlias = new GenericProtein("id");
parser.processNotes(node.getFirstChild(), proteinAlias);
String notes = proteinAlias.getNotes();
assertNotNull(notes);
assertFalse(notes.contains("body"));
assertTrue(notes.contains("some"));
// after redoing it should be the same
parser.processNotes(node.getFirstChild(), proteinAlias);
notes = proteinAlias.getNotes();
assertNotNull(notes);
assertFalse(notes.contains("body"));
assertTrue(notes.contains("some"));
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testParseNotes2() throws Exception {
try {
RestAnnotationParser parser = new RestAnnotationParser();
Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes3.xml");
Species proteinAlias = new GenericProtein("id");
parser.processNotes(node.getFirstChild(), proteinAlias);
String notes = proteinAlias.getNotes();
assertNotNull(notes);
assertFalse(notes.contains("body"));
assertTrue(notes.contains("some"));
// after redoing it should be the same
parser.processNotes(node.getFirstChild(), proteinAlias);
notes = proteinAlias.getNotes();
assertNotNull(notes);
assertFalse(notes.contains("body"));
assertTrue(notes.contains("some"));
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testParseNotes3() throws Exception {
try {
RestAnnotationParser parser = new RestAnnotationParser();
Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes4.xml");
Species proteinAlias = new GenericProtein("id");
proteinAlias.setNotes("text");
parser.processNotes(node.getFirstChild(), proteinAlias);
String notes = proteinAlias.getNotes();
assertNotNull(notes);
assertFalse(notes.contains("body"));
assertTrue(notes.contains("some"));
// after redoing it should be the same
parser.processNotes(node.getFirstChild(), proteinAlias);
notes = proteinAlias.getNotes();
assertNotNull(notes);
assertFalse(notes.contains("body"));
assertTrue(notes.contains("some"));
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testParseCollisionNotes() throws Exception {
try {
RestAnnotationParser parser = new RestAnnotationParser();
Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes2.xml");
GenericProtein protein = new GenericProtein("pr_id1");
protein.addSynonym("a1");
protein.addFormerSymbol("a1");
protein.setFullName("yyy");
protein.setAbbreviation("aaaa");
protein.setCharge(9);
protein.setSymbol("D");
parser.processNotes(node.getFirstChild(), protein);
assertEquals(1, protein.getSynonyms().size());
assertEquals(1, protein.getFormerSymbols().size());
assertEquals(6, getWarnings().size());
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testParseInvalidNotes1() throws Exception {
try {
RestAnnotationParser parser = new RestAnnotationParser();
Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes_invalid_charge.xml");
Species proteinAlias = new GenericProtein("id");
parser.processNotes(node.getFirstChild(), proteinAlias);
assertEquals(1, getWarnings().size());
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testParseCollisionNotes2() throws Exception {
try {
RestAnnotationParser parser = new RestAnnotationParser();
Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes2.xml");
Reaction reaction = new Reaction();
reaction.addSynonym("a1");
reaction.setAbbreviation("aaaa");
reaction.setSubsystem("sss");
reaction.setGeneProteinReaction("str");
reaction.setFormula("xxx");
reaction.setMechanicalConfidenceScore(-45);
reaction.setUpperBound(4.5);
reaction.setLowerBound(4.5);
parser.processNotes(node.getFirstChild(), reaction);
assertEquals(8, getWarnings().size());
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testMoveAnnotationsFromNotes() throws Exception {
try {
Model model = getModelForFile("testFiles/copyingAnnotationModel.xml");
Set<Element> elements = model.getElements();
for (Element element : elements) {
if (element.getName().equals("blabla")) {
assertEquals(2, element.getMiriamData().size());
element.getMiriamData()
.add(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, "12345"));
element.getMiriamData()
.add(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, "333666"));
assertEquals(2, element.getMiriamData().size());
}
});
fail("Exception expected");
} catch (NotImplementedException e) {
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testProcessInvalidNotes() throws Exception {
try {
RestAnnotationParser parser = new RestAnnotationParser();
String str = super.readFile("testFiles/xmlNodeTestExamples/notes5.xml");
parser.processNotes(str, new GenericProtein("id"));
assertEquals(1, getWarnings().size());
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testProcessNotes() throws Exception {
try {
String newNotes = "new notes";
String oldNotes = "old notes";
RestAnnotationParser parser = new RestAnnotationParser();
String str = "Description: " + newNotes + "\n" + oldNotes;
GenericProtein protein = new GenericProtein("id");
parser.processNotes(str, protein);
assertTrue(protein.getNotes().contains(newNotes));
assertTrue(protein.getNotes().contains(oldNotes));
assertFalse(protein.getNotes().contains("Description"));
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
assertFalse(element.getNotes().contains("rdf:RDF"));
}
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testProcessRdfDescription() throws Exception {
try {
RestAnnotationParser rap = new RestAnnotationParser();
Species speciesAlias = new GenericProtein("id");
speciesAlias.setNotes("begining\n" + "<rdf:RDF>" + "<rdf:Description rdf:about=\"#s2157\">\n" + "<bqmodel:is>\n"
+ "<rdf:Bag>\n" + "<rdf:li rdf:resource=\"urn:miriam:obo.chebi:CHEBI%3A17515\"/>\n" + "</rdf:Bag>\n"
+ "</bqmodel:is>\n" + "</rdf:Description>\n" + "</rdf:RDF>" + "\nend ending");
rap.processRdfDescription(speciesAlias);
assertEquals("begining\n\nend ending", speciesAlias.getNotes());
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testGetMiriamDataFromAnnotation() throws Exception {
try {
RestAnnotationParser rap = new RestAnnotationParser();
String response = readFile("testFiles/annotation/sampleDescription.txt");
Set<MiriamData> set = rap.getMiriamData(response);
for (MiriamData miriamData : set) {
if (miriamData.getDataType().equals(MiriamType.KEGG_GENES)) {
assertTrue(miriamData.getResource().contains("hsa"));
}
}
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testGetMiriamDataFromEmpty() throws Exception {
try {
RestAnnotationParser rap = new RestAnnotationParser();
Set<MiriamData> set = rap.getMiriamData(null);
assertEquals(0, set.size());
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testCreateAnnotationString() throws Exception {
try {
RestAnnotationParser rap = new RestAnnotationParser();
String former1 = "form1";
String former2 = "form2";
GenericProtein element = new GenericProtein("id");
element.addFormerSymbol(former1);
element.addFormerSymbol(former2);
element.setCharge(1);
String str = rap.createAnnotationString(element, true);
assertTrue(str.contains(former1));
assertTrue(str.contains(former2));
for (NoteField field : NoteField.values()) {
if (field.getClazz().isAssignableFrom(element.getClass())
|| CellDesignerElement.class.isAssignableFrom(field.getClazz())) {
assertTrue("Export string doesn't contain info about: " + field.getCommonName(),
str.indexOf(field.getCommonName()) >= 0);
}
}
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testGetFormerSymbolsFromInvalidStr() throws Exception {
try {
RestAnnotationParser rap = new RestAnnotationParser();
assertEquals(0, rap.getFormerSymbols(null).size());
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testGetNotesInvalid() throws Exception {
try {
RestAnnotationParser rap = new RestAnnotationParser();
Document xmlDoc = new DocumentImpl();
Node node = xmlDoc.createElement("bla");
rap.getNotes(node);
fail("Exception expected");
} catch (InvalidArgumentException e) {
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testProcessNotesForInvalidElement() throws Exception {
try {
RestAnnotationParser parser = new RestAnnotationParser();
Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes4.xml");
BioEntity bioEntity = Mockito.mock(BioEntity.class);
Mockito.when(bioEntity.getNotes()).thenReturn("");
parser.processNotes(node.getFirstChild(), bioEntity);
fail("Exception expected");
} catch (NotImplementedException e) {
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testProcessInvalidNotes() throws Exception {
try {
RestAnnotationParser parser = new RestAnnotationParser();
String str = super.readFile("testFiles/xmlNodeTestExamples/notes5.xml");
parser.processNotes(str, new GenericProtein("id"));
assertEquals(1, getWarnings().size());
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testProcessNotes() throws Exception {
try {
String newNotes = "new notes";
String oldNotes = "old notes";
RestAnnotationParser parser = new RestAnnotationParser();
String str = "Description: " + newNotes + "\n" + oldNotes;
GenericProtein protein = new GenericProtein("id");
parser.processNotes(str, protein);
assertTrue(protein.getNotes().contains(newNotes));
assertTrue(protein.getNotes().contains(oldNotes));
assertFalse(protein.getNotes().contains("Description"));
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
}
model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
+ 154
− 144
View file @ a7270a54
......@@ -4,6 +4,8 @@ import java.io.Serializable;
import java.util.Collection;
import java.util.List;
import lcsb.mapviewer.model.map.model.Model;
/**
* Interface that describes bio entity on the map (like Protein or Reaction).
*
......@@ -11,149 +13,149 @@ import java.util.List;
*
*/
public interface BioEntity extends Serializable {
/**
* Returns list of {@link MiriamData annotations} for the object.
*
* @return list of {@link MiriamData annotations} for the object
*/
Collection<MiriamData> getMiriamData();
/**
* Adds miriam annotations to the element.
*
* @param miriamData
* set of miriam annotations to be added
*/
void addMiriamData(Collection<MiriamData> miriamData);
/**
* Adds miriam annotation to the element.
*
* @param md
* miriam annotation to be added
*/
void addMiriamData(MiriamData md);
/**
* Returns the name of the object.
*
* @return the name of the object
*/
String getName();
/**
* Returns notes about the object.
*
* @return notes about the object
*/
String getNotes();
/**
* Sets notes about the object.
*
* @param notes
* new notes
*/
void setNotes(String notes);
/**
* Returns the symbol of the element.
*
* @return the symbol of the element
*/
String getSymbol();
/**
* Sets symbol of the element.
*
* @param symbol
* new symbol
*/
void setSymbol(String symbol);
/**
* Get list of synonyms.
*
* @return list of synonyms
*/
List<String> getSynonyms();
/**
* Sets list of synonyms to the element.
*
* @param synonyms
* new list
*/
void setSynonyms(List<String> synonyms);
/**
* Returns the abbreviation.
*
* @return the abbreviation
*/
String getAbbreviation();
/**
* Sets abbreviation.
*
* @param abbreviation
* new abbreviation
*/
void setAbbreviation(String abbreviation);
/**
* Sets formula.
*
* @param formula
* new formula
*/
void setFormula(String formula);
/**
* Returns the formula.
*
* @return the formula
*/
String getFormula();
/**
* Sets the name to the object.
*
* @param name
* name of the object
*
*/
void setName(String name);
/**
* Returns database identifier of the object.
*
* @return database identifier of the object
*/
int getId();
/**
* Return human readable {@link String} representing class.
*
* @return human readable {@link String} representing class
*/
String getStringType();
/**
* Sets semantic zoom level visibility.
*
* @param zoomLevelVisibility
* semantic zoom level visibility
*/
void setVisibilityLevel(String zoomLevelVisibility);
/**
* Sets semantic zoom level visibility.
*
* @param zoomLevelVisibility
* semantic zoom level visibility
*/
void setVisibilityLevel(Integer zoomLevelVisibility);
/**
* Returns list of {@link MiriamData annotations} for the object.
*
* @return list of {@link MiriamData annotations} for the object
*/
Collection<MiriamData> getMiriamData();
/**
* Adds miriam annotations to the element.
*
* @param miriamData
* set of miriam annotations to be added
*/
void addMiriamData(Collection<MiriamData> miriamData);
/**
* Adds miriam annotation to the element.
*
* @param md
* miriam annotation to be added
*/
void addMiriamData(MiriamData md);
/**
* Returns the name of the object.
*
* @return the name of the object
*/
String getName();
/**
* Returns notes about the object.
*
* @return notes about the object
*/
String getNotes();
/**
* Sets notes about the object.
*
* @param notes
* new notes
*/
void setNotes(String notes);
/**
* Returns the symbol of the element.
*
* @return the symbol of the element
*/
String getSymbol();
/**
* Sets symbol of the element.
*
* @param symbol
* new symbol
*/
void setSymbol(String symbol);
/**
* Get list of synonyms.
*
* @return list of synonyms
*/
List<String> getSynonyms();
/**
* Sets list of synonyms to the element.
*
* @param synonyms
* new list
*/
void setSynonyms(List<String> synonyms);
/**
* Returns the abbreviation.
*
* @return the abbreviation
*/
String getAbbreviation();
/**
* Sets abbreviation.
*
* @param abbreviation
* new abbreviation
*/
void setAbbreviation(String abbreviation);
/**
* Sets formula.
*
* @param formula
* new formula
*/
void setFormula(String formula);
/**
* Returns the formula.
*
* @return the formula
*/
String getFormula();
/**
* Sets the name to the object.
*
* @param name
* name of the object
*
*/
void setName(String name);
/**
* Returns database identifier of the object.
*
* @return database identifier of the object
*/
int getId();
/**
* Return human readable {@link String} representing class.
*
* @return human readable {@link String} representing class
*/
String getStringType();
/**
* Sets semantic zoom level visibility.
*
* @param zoomLevelVisibility
* semantic zoom level visibility
*/
void setVisibilityLevel(String zoomLevelVisibility);
/**
* Sets semantic zoom level visibility.
*
* @param zoomLevelVisibility
* semantic zoom level visibility
*/
void setVisibilityLevel(Integer zoomLevelVisibility);
/**
* Returns semantic zoom level visibility.
......@@ -161,6 +163,14 @@ public interface BioEntity extends Serializable {
* @return semantic zoom level visibility
*/
String getVisibilityLevel();
String getElementId();
/**
* Returns the {@link Model} where BioEntity is located.
*
* @return the model
*/
Model getModel();
}
model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
+ 1
− 5
View file @ a7270a54
......@@ -727,12 +727,8 @@ public class Reaction implements BioEntity {
this.model = model2.getModelData();
}
/**
* Returns model where reaction is locacted.
*
* @return model where reaction is locacted.
*/
@XmlTransient
@Override
public Model getModel() {
return model.getModel();
}
......
model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
+ 1
− 4
View file @ a7270a54
......@@ -767,11 +767,8 @@ public abstract class Element implements BioEntity, Serializable {
this.transparencyLevel = transparencyLevel;
}
/**
* @return the model
* @see #model
*/
@XmlTransient
@Override
public Model getModel() {
return model.getModel();
}
......
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