removed compilation errors

not tested so far

.classpath

@@ -19,5 +19,6 @@
  <attribute name="org.eclipse.jst.component.dependency" value="/WEB-INF/lib"/>
  </attributes>
  </classpathentry>
+ <classpathentry combineaccessrules="false" exported="true" kind="src" path="/javautil_pheno"/>
  <classpathentry kind="output" path="build/classes"/>
 </classpath>

src/hpoweb/HpowebUI.java

@@ -1,25 +1,5 @@
 package hpoweb;
 
-import hpoweb.data.HpData;
-import hpoweb.data.dataprovider.IDiseaseDataProvider;
-import hpoweb.data.dataprovider.IEntityDataProvider;
-import hpoweb.data.dataprovider.IGeneDataProvider;
-import hpoweb.data.dataprovider.IHpClassDataProvider;
-import hpoweb.data.dataprovider.impl.DiseaseDataProvider;
-import hpoweb.data.dataprovider.impl.FakeDiseaseDataProvider;
-import hpoweb.data.dataprovider.impl.FakeGeneDataProvider;
-import hpoweb.data.dataprovider.impl.FakeHpClassDataProvider;
-import hpoweb.data.dataprovider.impl.GeneDataProvider;
-import hpoweb.data.dataprovider.impl.HpClassDataProvider;
-import hpoweb.data.entities.SearchableEntity;
-import hpoweb.uicontent.SearchBarFactory;
-import hpoweb.uicontent.graph.GraphtestUI;
-import hpoweb.uicontent.tabs.disease.DiseaseTabFactory;
-import hpoweb.uicontent.tabs.gene.GeneTabFactory;
-import hpoweb.uicontent.tabs.hpoclass.HpoClassTabFactory;
-import hpoweb.util.CONSTANTS;
-import hpoweb.util.TableUtils;
-
 import java.util.Map;
 
 import javax.servlet.annotation.WebServlet;
@@ -57,7 +37,26 @@
 import com.vaadin.ui.Window;
 import com.vaadin.ui.themes.ValoTheme;
 
-import de.charite.phenowl.annotations.DiseaseId;
+import hpo.DiseaseId;
+import hpoweb.data.HpData;
+import hpoweb.data.dataprovider.IDiseaseDataProvider;
+import hpoweb.data.dataprovider.IEntityDataProvider;
+import hpoweb.data.dataprovider.IGeneDataProvider;
+import hpoweb.data.dataprovider.IHpClassDataProvider;
+import hpoweb.data.dataprovider.impl.DiseaseDataProvider;
+import hpoweb.data.dataprovider.impl.FakeDiseaseDataProvider;
+import hpoweb.data.dataprovider.impl.FakeGeneDataProvider;
+import hpoweb.data.dataprovider.impl.FakeHpClassDataProvider;
+import hpoweb.data.dataprovider.impl.GeneDataProvider;
+import hpoweb.data.dataprovider.impl.HpClassDataProvider;
+import hpoweb.data.entities.SearchableEntity;
+import hpoweb.uicontent.SearchBarFactory;
+import hpoweb.uicontent.graph.GraphtestUI;
+import hpoweb.uicontent.tabs.disease.DiseaseTabFactory;
+import hpoweb.uicontent.tabs.gene.GeneTabFactory;
+import hpoweb.uicontent.tabs.hpoclass.HpoClassTabFactory;
+import hpoweb.util.CONSTANTS;
+import hpoweb.util.TableUtils;
 
 @SuppressWarnings("serial")
 @Theme("hpoweb")
@@ -143,11 +142,13 @@ protected void init(VaadinRequest request) {
  hpoClassTabFactory.addTermInfoElements(gridContainer, (IHpClassDataProvider) dataProvider);
 
  addExtraButtons(gridContainer, (IHpClassDataProvider) dataProvider);
- } else if (dataProvider instanceof IDiseaseDataProvider) {
+ }
+ else if (dataProvider instanceof IDiseaseDataProvider) {
 
  DiseaseTabFactory diseaseTabFactory = new DiseaseTabFactory(tableUtils);
  diseaseTabFactory.addDiseaseInfoElements(gridContainer, (IDiseaseDataProvider) dataProvider);
- } else if (dataProvider instanceof IGeneDataProvider) {
+ }
+ else if (dataProvider instanceof IGeneDataProvider) {
 
  GeneTabFactory geneTabFactory = new GeneTabFactory(tableUtils);
  geneTabFactory.addGeneInfoElements(gridContainer, (IGeneDataProvider) dataProvider);
@@ -160,7 +161,8 @@ protected void init(VaadinRequest request) {
  String ontologyVersion;
  if (doParseHpo) {
  ontologyVersion = hpData.getExtOwlOntology().getOntologyVersionIri().toString();
- } else
+ }
+ else
 
  {
  ontologyVersion = "some ontology version here";
@@ -257,44 +259,52 @@ private IEntityDataProvider setupDataProvider(VaadinRequest request, Map<String,
 
  if (doParseHpo) {
  dataProvider = new HpClassDataProvider(hpClass, hpData);
- } else {
+ }
+ else {
  dataProvider = new FakeHpClassDataProvider();
  }
 
- } else if (parameterMap.containsKey(CONSTANTS.geneRequestId)) {
+ }
+ else if (parameterMap.containsKey(CONSTANTS.geneRequestId)) {
 
  Integer geneId = parseGeneId(request);
  if (geneId == null && doParseHpo) {
- new Notification("Invalid gene id input", "<br/><br/>Can't parse gene id from '" + request.getParameter(CONSTANTS.geneRequestId)
- + "'", Notification.Type.ERROR_MESSAGE, true).show(Page.getCurrent());
+ new Notification("Invalid gene id input",
+ "<br/><br/>Can't parse gene id from '" + request.getParameter(CONSTANTS.geneRequestId) + "'", Notification.Type.ERROR_MESSAGE,
+ true).show(Page.getCurrent());
  return null;
  }
 
  if (doParseHpo) {
 
  dataProvider = new GeneDataProvider(geneId, hpData);
- } else {
+ }
+ else {
  dataProvider = new FakeGeneDataProvider();
  }
 
- } else if (parameterMap.containsKey(CONSTANTS.diseaseRequestId)) {
+ }
+ else if (parameterMap.containsKey(CONSTANTS.diseaseRequestId)) {
 
  DiseaseId diseaseId = parseDiseaseId(request);
  if (diseaseId == null && doParseHpo) {
- new Notification("Invalid disease id input", "<br/><br/>Can't parse disease id from '"
- + request.getParameter(CONSTANTS.geneRequestId) + "'", Notification.Type.ERROR_MESSAGE, true).show(Page.getCurrent());
+ new Notification("Invalid disease id input",
+ "<br/><br/>Can't parse disease id from '" + request.getParameter(CONSTANTS.geneRequestId) + "'",
+ Notification.Type.ERROR_MESSAGE, true).show(Page.getCurrent());
  return null;
  }
 
  if (doParseHpo) {
  dataProvider = new DiseaseDataProvider(diseaseId, hpData);
- } else {
+ }
+ else {
  dataProvider = new FakeDiseaseDataProvider();
  }
- } else {
+ }
+ else {
  new Notification("Invalid URL", "<br/><br/>You have to provide one URL parameter (" + CONSTANTS.hpRequestId + ","
- + CONSTANTS.geneRequestId + ", or " + CONSTANTS.diseaseRequestId + ") ! ", Notification.Type.WARNING_MESSAGE, true).show(Page
- .getCurrent());
+ + CONSTANTS.geneRequestId + ", or " + CONSTANTS.diseaseRequestId + ") ! ", Notification.Type.WARNING_MESSAGE, true)
+  .show(Page.getCurrent());
  return null;
  }
  return dataProvider;

src/hpoweb/data/HpData.java

@@ -9,9 +9,9 @@
 import com.vaadin.server.VaadinService;
 
 import de.charite.phenowl.annotations.AnnotationUtils;
-import de.charite.phenowl.annotations.DiseaseGeneMapper;
 import de.charite.phenowl.hpowl.util.ExtendedOwlOntology;
 import de.charite.phenowl.hpowl.util.OwlAxiomClass;
+import hpo.DiseaseGeneMapper;
 
 public class HpData {
 
@@ -44,7 +44,6 @@ public HpData() {
  DiseaseGeneMapper.setOrphanetPath(datapath);
  annotationUtils.setDataPath(datapath);
  annotationUtils.parseAssociation();
- annotationUtils.getDiseaseGeneMapper().addCancerGeneAssociationsToDiseaseGenes();
  }
 
  public ExtendedOwlOntology getExtOwlOntology() {

src/hpoweb/data/dataprovider/IGeneDataProvider.java

@@ -1,16 +1,15 @@
 package hpoweb.data.dataprovider;
 
-import hpoweb.uicontent.table.HpoClassTableEntry;
-
 import java.util.Collection;
 import java.util.List;
 
-import de.charite.phenowl.annotations.DiseaseEntry;
+import de.charite.phenowl.annotations.OwlAnnotatedDiseaseEntry;
+import hpoweb.uicontent.table.HpoClassTableEntry;
 
 public interface IGeneDataProvider extends IEntityDataProvider {
 
  List<HpoClassTableEntry> getAssociatedHpoClasses();
 
- Collection<DiseaseEntry> getAssociatedDiseases();
+ Collection<OwlAnnotatedDiseaseEntry> getAssociatedDiseases();
 
 }

src/hpoweb/data/dataprovider/LazySearchbarService.java

@@ -1,9 +1,5 @@
 package hpoweb.data.dataprovider;
 
-import hpoweb.data.HpData;
-import hpoweb.data.entities.SearchableEntity;
-import hpoweb.data.entities.SearchableEntity.SearchableEntityType;
-
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
@@ -13,10 +9,13 @@
 import org.semanticweb.owlapi.model.OWLClass;
 
 import de.charite.phenowl.annotations.AnnotationUtils;
-import de.charite.phenowl.annotations.DiseaseEntry;
-import de.charite.phenowl.annotations.DiseaseGeneMapper;
-import de.charite.phenowl.annotations.DiseaseId;
 import de.charite.phenowl.hpowl.util.OboUtil;
+import hpo.DiseaseEntry;
+import hpo.DiseaseGeneMapper;
+import hpo.DiseaseId;
+import hpoweb.data.HpData;
+import hpoweb.data.entities.SearchableEntity;
+import hpoweb.data.entities.SearchableEntity.SearchableEntityType;
 
 public class LazySearchbarService {
 

src/hpoweb/data/dataprovider/impl/DiseaseDataProvider.java

@@ -1,10 +1,5 @@
 package hpoweb.data.dataprovider.impl;
 
-import hpoweb.data.HpData;
-import hpoweb.data.dataprovider.IDiseaseDataProvider;
-import hpoweb.data.entities.DiseaseGene;
-import hpoweb.uicontent.table.HpoClassTableEntry;
-
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
@@ -16,17 +11,21 @@
 import com.google.common.collect.HashMultimap;
 
 import de.charite.phenowl.annotations.AnnotationUtils;
-import de.charite.phenowl.annotations.DiseaseEntry;
-import de.charite.phenowl.annotations.DiseaseId;
 import de.charite.phenowl.annotations.HPOAnnotation;
+import de.charite.phenowl.annotations.OwlAnnotatedDiseaseEntry;
 import de.charite.phenowl.hpowl.util.OboUtil;
+import hpo.DiseaseId;
+import hpoweb.data.HpData;
+import hpoweb.data.dataprovider.IDiseaseDataProvider;
+import hpoweb.data.entities.DiseaseGene;
+import hpoweb.uicontent.table.HpoClassTableEntry;
 
 public class DiseaseDataProvider implements IDiseaseDataProvider {
 
  private HpData hpData;
  private AnnotationUtils annotationUtils;
  private DiseaseId diseaseId;
- private DiseaseEntry diseaseEntry;
+ private OwlAnnotatedDiseaseEntry diseaseEntry;
  private ArrayList<HPOAnnotation> annotations;
  private HashSet<Integer> diseaseGeneIds;
  private HashSet<DiseaseGene> diseaseGenes;
@@ -36,7 +35,7 @@ public DiseaseDataProvider(DiseaseId diseaseId, HpData hpData) {
  this.diseaseId = diseaseId;
  this.annotationUtils = hpData.getAnnotationUtils();
  this.diseaseEntry = annotationUtils.getDiseaseId2entry().get(diseaseId);
- this.annotations = diseaseEntry.getAnnotations();
+ this.annotations = diseaseEntry.getAnnotationsOwlClasses();
  // genes for this disease
  this.diseaseGeneIds = annotationUtils.getDiseaseGeneMapper().diseaseId2entrezIds.get(diseaseId);
  diseaseGenes = new HashSet<DiseaseGene>();

src/hpoweb/data/dataprovider/impl/FakeGeneDataProvider.java

@@ -1,8 +1,5 @@
 package hpoweb.data.dataprovider.impl;
 
-import hpoweb.data.dataprovider.IGeneDataProvider;
-import hpoweb.uicontent.table.HpoClassTableEntry;
-
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
@@ -11,8 +8,10 @@
 
 import com.google.gwt.thirdparty.guava.common.collect.Lists;
 
-import de.charite.phenowl.annotations.DiseaseEntry;
-import de.charite.phenowl.annotations.DiseaseId;
+import de.charite.phenowl.annotations.OwlAnnotatedDiseaseEntry;
+import hpo.DiseaseId;
+import hpoweb.data.dataprovider.IGeneDataProvider;
+import hpoweb.uicontent.table.HpoClassTableEntry;
 
 public class FakeGeneDataProvider implements IGeneDataProvider {
 
@@ -53,10 +52,10 @@ public List<HpoClassTableEntry> getAssociatedHpoClasses() {
  }
 
  @Override
- public Collection<DiseaseEntry> getAssociatedDiseases() {
+ public Collection<OwlAnnotatedDiseaseEntry> getAssociatedDiseases() {
 
  DiseaseId id = new DiseaseId("OMIM", RandomStringUtils.randomNumeric(6));
- DiseaseEntry entry = new DiseaseEntry(id, null, null);
+ OwlAnnotatedDiseaseEntry entry = new OwlAnnotatedDiseaseEntry(id, null, null);
  entry.setName(RandomStringUtils.randomAlphabetic(8) + " " + RandomStringUtils.randomAlphabetic(4) + " syndrome");
  return Lists.newArrayList(entry);
  }

src/hpoweb/data/dataprovider/impl/FakeHpClassDataProvider.java

@@ -1,11 +1,5 @@
 package hpoweb.data.dataprovider.impl;
 
-import hpoweb.data.dataprovider.IHpClassDataProvider;
-import hpoweb.data.entities.DiseaseGene;
-import hpoweb.uicontent.graph.GraphtestUI;
-import hpoweb.uicontent.table.DiseaseGeneTableEntry;
-import hpoweb.uicontent.table.GeneDiseaseTableEntry;
-
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
@@ -15,8 +9,13 @@
 
 import com.google.common.collect.ImmutableSet;
 
-import de.charite.phenowl.annotations.DiseaseEntry;
-import de.charite.phenowl.annotations.DiseaseId;
+import de.charite.phenowl.annotations.OwlAnnotatedDiseaseEntry;
+import hpo.DiseaseId;
+import hpoweb.data.dataprovider.IHpClassDataProvider;
+import hpoweb.data.entities.DiseaseGene;
+import hpoweb.uicontent.graph.GraphtestUI;
+import hpoweb.uicontent.table.DiseaseGeneTableEntry;
+import hpoweb.uicontent.table.GeneDiseaseTableEntry;
 
 public class FakeHpClassDataProvider implements IHpClassDataProvider {
 
@@ -102,7 +101,8 @@ public List<DiseaseGeneTableEntry> getDiseaseGeneTableContent() {
  ArrayList<DiseaseGene> associatedGenes = new ArrayList<DiseaseGene>();
  if (Math.random() < 0.3) {
  associatedGenes.add(getRandomDiseaseGene());
- } else if (Math.random() < 0.6) {
+ }
+ else if (Math.random() < 0.6) {
  associatedGenes.add(getRandomDiseaseGene());
  associatedGenes.add(getRandomDiseaseGene());
  }
@@ -123,10 +123,11 @@ private DiseaseGene getRandomDiseaseGene() {
  public List<GeneDiseaseTableEntry> getGeneDiseaseTableContent() {
  ArrayList<GeneDiseaseTableEntry> tableEntries = new ArrayList<GeneDiseaseTableEntry>();
  for (int i = 0; i < 250; i++) {
- ArrayList<DiseaseEntry> associatedDiseases = new ArrayList<DiseaseEntry>();
+ ArrayList<OwlAnnotatedDiseaseEntry> associatedDiseases = new ArrayList<OwlAnnotatedDiseaseEntry>();
  if (Math.random() < 0.3) {
  associatedDiseases.add(getRandomDisease());
- } else if (Math.random() < 0.6) {
+ }
+ else if (Math.random() < 0.6) {
  associatedDiseases.add(getRandomDisease());
  associatedDiseases.add(getRandomDisease());
  }
@@ -138,9 +139,9 @@ public List<GeneDiseaseTableEntry> getGeneDiseaseTableContent() {
  return tableEntries;
  }
 
- private DiseaseEntry getRandomDisease() {
+ private OwlAnnotatedDiseaseEntry getRandomDisease() {
  DiseaseId id = new DiseaseId("OMIM", RandomStringUtils.randomNumeric(6));
- DiseaseEntry entry = new DiseaseEntry(id, null, null);
+ OwlAnnotatedDiseaseEntry entry = new OwlAnnotatedDiseaseEntry(id, null, null);
  entry.setName(RandomStringUtils.randomAlphabetic(8) + " " + RandomStringUtils.randomAlphabetic(4) + " syndrome");
  return entry;
  }