improve vis

.externalToolBuilders/org.eclipse.m2e.core.maven2Builder.launch

@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.ant.AntBuilderLaunchConfigurationType">
+<booleanAttribute key="org.eclipse.ui.externaltools.ATTR_BUILDER_ENABLED" value="false"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_DISABLED_BUILDER" value="org.eclipse.m2e.core.maven2Builder"/>
+<mapAttribute key="org.eclipse.ui.externaltools.ATTR_TOOL_ARGUMENTS"/>
+<booleanAttribute key="org.eclipse.ui.externaltools.ATTR_TRIGGERS_CONFIGURED" value="true"/>
+</launchConfiguration>

.project

@@ -33,13 +33,17 @@
  </arguments>
  </buildCommand>
  <buildCommand>
- <name>org.eclipse.m2e.core.maven2Builder</name>
+ <name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
+ <triggers>full,incremental,</triggers>
  <arguments>
+ <dictionary>
+ <key>LaunchConfigHandle</key>
+ <value>&lt;project&gt;/.externalToolBuilders/org.eclipse.m2e.core.maven2Builder.launch</value>
+ </dictionary>
  </arguments>
  </buildCommand>
  </buildSpec>
  <natures>
- <nature>org.eclipse.m2e.core.maven2Nature</nature>
  <nature>org.eclipse.jem.workbench.JavaEMFNature</nature>
  <nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
  <nature>org.eclipse.wst.common.project.facet.core.nature</nature>

.settings/com.vaadin.integration.eclipse.prefs

@@ -1,6 +1,7 @@
+com.vaadin.integration.eclipse.mavenAutoCompileWidgetset=true
 com.vaadin.integration.eclipse.mavenLatestVersionsUpgrade=["7.6.8","7.7.3"]
 com.vaadin.integration.eclipse.previousCompileAction=both
 com.vaadin.integration.eclipse.useLatestNightly=false
-com.vaadin.integration.eclipse.widgetsetCompilationEta=35476
+com.vaadin.integration.eclipse.widgetsetCompilationEta=34834
 com.vaadin.integration.eclipse.widgetsetDirty=false
 eclipse.preferences.version=1

WebContent/.gitignore

@@ -0,0 +1,2 @@
+/data/
+/WEB-INF/

build/classes/hpoweb/widgetset/HpowebWidgetset.gwt.xml

@@ -2,7 +2,5 @@
 <!DOCTYPE module PUBLIC "-//Google Inc.//DTD Google Web Toolkit 2.5.1//EN" "http:https://google-web-toolkit.googlecode.com/svn/tags/2.5.1/distro-source/core/src/gwt-module.dtd">
 <module>
  <inherits name="com.vaadin.graph.GraphExplorerWidgetset" /> 
-
-
  <inherits name="com.vaadin.DefaultWidgetSet" />
 </module>

ivy.xml

@@ -36,7 +36,7 @@
  <dependency org="com.vaadin" name="vaadin-client-compiler" rev="&vaadin.version;" conf="widgetset-compile->default" />
  <dependency org="org.vaadin" name="viritin" rev="1.34" /> 
  <dependency org="org.vaadin.addons" name="graph-explorer" rev="0.7.0" />
- <dependency org="org.vaadin.addon" name="tableexport-for-vaadin" rev="1.5.1.5" />
+ <dependency org="org.vaadin.addon" name="tableexport-for-vaadin" rev="1.6.0" />
  <dependency org="org.vaadin.addons" name="googleanalyticstracker" rev="2.1.0" />
  <dependency org="com.github.vaadin4qbanos" name="jsclipboard" rev="1.0.2" />
  <dependency org="com.sebworks" name="vaadstrap" rev="0.1.2" /> 

src/hpoweb/data/HpData.java

@@ -1,17 +1,21 @@
 package hpoweb.data;
 
 import java.util.HashSet;
+import java.util.List;
 import java.util.Set;
 
 import org.semanticweb.owlapi.model.IRI;
 import org.semanticweb.owlapi.model.OWLClass;
 
+import com.google.common.collect.HashMultimap;
+import com.google.common.collect.ImmutableSet;
 import com.vaadin.server.VaadinService;
 
 import de.charite.phenowl.annotations.AnnotationUtils;
 import de.charite.phenowl.hpowl.util.ExtendedOwlOntology;
 import de.charite.phenowl.hpowl.util.OwlAxiomClass;
 import hpo.DiseaseGeneMapper;
+import hpoweb.uicontent.table.HpoClassTableEntry;
 
 public class HpData {
 
@@ -57,4 +61,27 @@ public AnnotationUtils getAnnotationUtils() {
  public ExtendedOwlOntology getExtOwlOntologyWithLogicalDefs() {
  return extOwlOntologyWithLogicalDefs;
  }
+
+ /**
+ * @param tableContent
+ * @return
+ */
+ public HashMultimap<OWLClass, OWLClass> getLevelOneBins(List<HpoClassTableEntry> tableContent) {
+
+ HashMultimap<OWLClass, OWLClass> ret = HashMultimap.create();
+
+ ImmutableSet<OWLClass> targets = extOwlOntology.getChildrenAsserted(extOwlOntology.getClassForId("HP:0000118"));
+
+ for (HpoClassTableEntry hpoCTE : tableContent) {
+ OWLClass cls = extOwlOntology.getClassForId(hpoCTE.getHpoId());
+ ImmutableSet<OWLClass> anc = extOwlOntology.getAncestorsAsserted(cls);
+ for (OWLClass a : anc) {
+ if (targets.contains(a)) {
+ ret.put(a, cls);
+ }
+ }
+ }
+ return ret;
+ }
+
 }

src/hpoweb/data/dataprovider/IDiseaseDataProvider.java

@@ -1,11 +1,11 @@
 package hpoweb.data.dataprovider;
 
-import hpoweb.data.entities.DiseaseGene;
-import hpoweb.uicontent.table.HpoClassTableEntry;
-
 import java.util.Collection;
 import java.util.List;
 
+import hpoweb.data.entities.DiseaseGene;
+import hpoweb.uicontent.table.HpoClassTableEntry;
+
 public interface IDiseaseDataProvider extends IEntityDataProvider {
 
  Collection<String> getAlternativeNames();

src/hpoweb/data/dataprovider/IEntityDataProvider.java

@@ -1,5 +1,7 @@
 package hpoweb.data.dataprovider;
 
+import hpoweb.data.HpData;
+
 /**
  * Provide data for an entity like an HPO class or a gene
  * 
@@ -14,4 +16,6 @@ public interface IEntityDataProvider {
 
  public String getTypeOfEntityString();
 
+ public HpData getHpData();
+
 }

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

@@ -108,8 +108,7 @@ private String generateAnnotationDescription(Set<HPOAnnotation> annotations) {
 
  if (multipleAnnotations) {
  buffer.append(" Meta data for annotation " + i + ":<br>");
- }
- else {
+ } else {
  buffer.append(" Meta data for this annotation:<br>");
  }
 
@@ -133,4 +132,14 @@ private String generateAnnotationDescription(Set<HPOAnnotation> annotations) {
  public Collection<DiseaseGene> getAssociatedGenes() {
  return diseaseGenes;
  }
+
+ /*
+ * (non-Javadoc)
+ * 
+ * @see hpoweb.data.dataprovider.IEntityDataProvider#getHpData()
+ */
+ @Override
+ public HpData getHpData() {
+ return hpData;
+ }
 }

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

@@ -1,9 +1,5 @@
 package hpoweb.data.dataprovider.impl;
 
-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;
@@ -13,6 +9,11 @@
 
 import com.google.common.collect.ImmutableSet;
 
+import hpoweb.data.HpData;
+import hpoweb.data.dataprovider.IDiseaseDataProvider;
+import hpoweb.data.entities.DiseaseGene;
+import hpoweb.uicontent.table.HpoClassTableEntry;
+
 public class FakeDiseaseDataProvider implements IDiseaseDataProvider {
 
  public FakeDiseaseDataProvider() {
@@ -38,8 +39,10 @@ public String getTypeOfEntityString() {
  public Collection<String> getAlternativeNames() {
  double rand = Math.random();
  if (rand > 0.3) {
- return ImmutableSet.of(RandomStringUtils.randomAlphabetic(10).toUpperCase(), RandomStringUtils.randomAlphabetic(7).toUpperCase(),
- RandomStringUtils.randomAlphabetic(9).toUpperCase(), RandomStringUtils.randomAlphabetic(15).toUpperCase(),
+ return ImmutableSet.of(RandomStringUtils.randomAlphabetic(10).toUpperCase(),
+ RandomStringUtils.randomAlphabetic(7).toUpperCase(),
+ RandomStringUtils.randomAlphabetic(9).toUpperCase(),
+ RandomStringUtils.randomAlphabetic(15).toUpperCase(),
  "ghfsadgfibba gfisbafkba hfjksbfkjsabf hfjksdhfsaf hflhsa fhsdahfa hfldshflsad hflsahfkldsaf");
  } else {
  return ImmutableSet.of();
@@ -52,7 +55,8 @@ public List<HpoClassTableEntry> getAnnotatedHpoClasses() {
  for (int i = 0; i < 50; i++) {
 
  String hpoId = "HP:" + RandomStringUtils.randomNumeric(7);
- String hpoLab = "Abnormality of " + RandomStringUtils.randomAlphabetic(4) + " " + RandomStringUtils.randomAlphabetic(8);
+ String hpoLab = "Abnormality of " + RandomStringUtils.randomAlphabetic(4) + " "
+ + RandomStringUtils.randomAlphabetic(8);
  HpoClassTableEntry entry = new HpoClassTableEntry(hpoId, hpoLab, "fake description here");
  tableEntries.add(entry);
  }
@@ -76,4 +80,15 @@ public Collection<DiseaseGene> getAssociatedGenes() {
  }
 
  }
+
+ /*
+ * (non-Javadoc)
+ * 
+ * @see hpoweb.data.dataprovider.IEntityDataProvider#getHpData()
+ */
+ @Override
+ public HpData getHpData() {
+ // TODO Auto-generated method stub
+ return null;
+ }
 }

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

@@ -10,6 +10,7 @@
 
 import de.charite.phenowl.annotations.OwlAnnotatedDiseaseEntry;
 import hpo.ItemId;
+import hpoweb.data.HpData;
 import hpoweb.data.dataprovider.IGeneDataProvider;
 import hpoweb.uicontent.table.HpoClassTableEntry;
 
@@ -44,7 +45,8 @@ public List<HpoClassTableEntry> getAssociatedHpoClasses() {
  for (int i = 0; i < 50; i++) {
 
  String hpoId = "HP:" + RandomStringUtils.randomNumeric(7);
- String hpoLab = "Abnormality of " + RandomStringUtils.randomAlphabetic(4) + " " + RandomStringUtils.randomAlphabetic(8);
+ String hpoLab = "Abnormality of " + RandomStringUtils.randomAlphabetic(4) + " "
+ + RandomStringUtils.randomAlphabetic(8);
  HpoClassTableEntry entry = new HpoClassTableEntry(hpoId, hpoLab, "fake description here");
  tableEntries.add(entry);
  }
@@ -56,8 +58,20 @@ public Collection<OwlAnnotatedDiseaseEntry> getAssociatedDiseases() {
 
  ItemId id = new ItemId("OMIM", RandomStringUtils.randomNumeric(6));
  OwlAnnotatedDiseaseEntry entry = new OwlAnnotatedDiseaseEntry(id, null, null);
- entry.setName(RandomStringUtils.randomAlphabetic(8) + " " + RandomStringUtils.randomAlphabetic(4) + " syndrome");
+ entry.setName(
+ RandomStringUtils.randomAlphabetic(8) + " " + RandomStringUtils.randomAlphabetic(4) + " syndrome");
  return Lists.newArrayList(entry);
  }
 
+ /*
+ * (non-Javadoc)
+ * 
+ * @see hpoweb.data.dataprovider.IEntityDataProvider#getHpData()
+ */
+ @Override
+ public HpData getHpData() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
 }