@Override public String getHeaderName() { return ofEv.getId()+"?"; } }
/** * Returns a JLabel for the evidence type */ @Override public Object getElementAt(int index) { JLabel label = null; if (index > -1) { EvidenceType et = al.get(index); String name = et.getFullname(); if (name.trim().length() == 0) name = et.getId(); label = new JLabel(name); label.setName(et.getId()); label.setToolTipText("(" + et.getId() + ") " + et.getDescription()); } return label; }
for (EvidenceType et : experiment.getEvidence()) { if (!et.getId().equals("IMPD")) { String etName = et.getFullname(); if (etName == null || etName.length() == 0) etName = et.getId();
/** * Generate metadata for Evidence Type. * @param et * Evidence Type (from the Ondex API). * @return String * String containing information about the Evidence Type. */ private String/*JSONObject*/ buildEvidenceType(EvidenceType et) { /* JSONObject evidenceJson= new JSONObject(); evidenceJson.put(JSONAttributeNames.ID, et.getId()); evidenceJson.put(JSONAttributeNames.FULLNAME, et.getFullname()); evidenceJson.put(JSONAttributeNames.DESCRIPTION, et.getDescription()); */ String evidenceName= et.getFullname().trim(); if(evidenceName.equals("")) { evidenceName= et.toString().trim(); } return evidenceName/*evidenceJson*/; }
/** * Generate metadata for Evidence Type. * @param et * Evidence Type (from the Ondex API). * @return JSONObject * JSONObject containing information about the Evidence Type. */ private String/*JSONObject*/ buildEvidenceType(EvidenceType et) { /* JSONObject evidenceJson= new JSONObject(); evidenceJson.put(JSONAttributeNames.ID, et.getId().trim()); evidenceJson.put(JSONAttributeNames.FULLNAME, et.getFullname().trim()); evidenceJson.put(JSONAttributeNames.DESCRIPTION, et.getDescription().trim()); */ String evidenceName= et.getFullname().trim(); if(evidenceName.equals("")) { evidenceName= et.toString().trim(); } return evidenceName/*evidenceJson*/; }
/** * Constructs user input to add a EvidenceType. * * @param aog * AbstractONDEXGraph to add to * @param et * EvidenceType to use */ public DialogEvidenceType(ONDEXGraph aog, EvidenceType et) { super("Dialog.EvidenceType.Title", "Properties16.gif"); this.aog = aog; // set existing information id.setText(et.getId()); fullname.setText(et.getFullname()); description.setText(et.getDescription()); // set everything to disabled id.setEditable(false); fullname.setEditable(false); description.setEnabled(false); this.getContentPane().setLayout(new BorderLayout()); this.getContentPane().add(makeProperties(), BorderLayout.CENTER); this.getContentPane().add(makeButtonsPanel(null, "Dialog.EvidenceType.Cancel"), BorderLayout.SOUTH); this.pack(); }
public String getValue(ONDEXEntity cOrr) throws InvalidOndexEntityException { for (EvidenceType et : cOrr.getEvidence()){ if(et.equals(ofEv))return ofEv.getId(); } return ""; }
/** * Writes evidence tag in a xml stream writer. * * @param xmlw * xml stream to write in * @param et * EvidenceType object * @throws XMLStreamException * if xml writing fails */ protected void buildEvidenceType(XMLStreamWriter2 xmlw, EvidenceType et, RefOrVal rov) throws XMLStreamException { xmlw.writeStartElement(XMLTagNames.EVIDENCE); switch (rov) { case REF: buildIdRef(xmlw, et); break; case VAL: xmlw.writeStartElement(XMLTagNames.ID); xmlw.writeCharacters(et.getId()); xmlw.writeEndElement(); xmlw.writeStartElement(XMLTagNames.FULLNAME); xmlw.writeCharacters(et.getFullname()); xmlw.writeEndElement(); xmlw.writeStartElement(XMLTagNames.DESCRIPTION); xmlw.writeCharacters(et.getDescription()); xmlw.writeEndElement(); } xmlw.writeEndElement(); // end tag evidence type }
/** * Formats evidence into a series of comma seperated EvidenceType metadata * html links * * @param evidence The evidence to convert * @param metadatadir the dir to link to * @return A series of EvidenceType metadata html links */ private String formatEvidence(Set<EvidenceType> evidence, String metadatadir) { StringBuilder evidenceLinks = new StringBuilder(); for (EvidenceType evidenceType : evidence) { if (evidenceLinks.length() > 0) { evidenceLinks.append(", "); } evidenceLinks.append("<a href=\"" + metadatadir + File.separator + "ets.html#" + evidenceType.getId() + "\" onclick=\"popup(this.href);return false;\" >" + evidenceType.getId() + "</a>"); } return evidenceLinks.toString(); }
if (!nomd.checkEvidenceType(et.getId())) nomd.createEvidenceType(et.getId(), et.getFullname(), et .getDescription());
public String getValue(ONDEXEntity cOrr) throws InvalidOndexEntityException { StringBuilder sb = new StringBuilder(); boolean first = true; for (EvidenceType evidence : cOrr.getEvidence()) { if (!first) sb.append(", "); sb.append(evidence.getId()); first = false; } return sb.toString(); }
/** * Returns node and edge color for a given EvidenceType. * * @param et * EvidenceType * @return Color */ public static Color getColorForEvidenceType(EvidenceType et) { String key = "EvidenceType.Color." + et.getId(); if (visual.getProperty(key) != null) { return convertToColor(visual.getProperty(key)); } return defaultColor; }
public static String etToUri(String graphUri, EvidenceType et) { return toUri(graphUri, "evidenceType", et.getId()); }
@Override public void addEvidenceType(EvidenceType evidencetype) { try { PreparedStatement createRowItem = sg.getConnection().prepareStatement("insert into evidence (sid, id, elementType, evidence_id) values (?,?,?,?)"); createRowItem.setLong(1, sg.getSID()); createRowItem.setInt(2, id); createRowItem.setString(3, tableName); createRowItem.setString(4, evidencetype.getId()); createRowItem.execute(); createRowItem.close(); } catch (SQLException e) { // TODO Auto-generated catch block e.printStackTrace(); } }
@Override public Set<ONDEXConcept> getConceptsOfEvidenceType(EvidenceType et) { Set<Integer> is = new HashSet<Integer>(); try { PreparedStatement getCsofET = conn .prepareStatement("select distinct id from evidence where sid = ? and elementType = ? and evidence_id = ?"); getCsofET.setLong(1, sid); getCsofET.setString(2, "concept"); getCsofET.setString(3, et.getId()); ResultSet rs = getCsofET.executeQuery(); while (rs.next()) { is.add(rs.getInt(1)); } rs.close(); getCsofET.close(); } catch (SQLException e) { // TODO Auto-generated catch block e.printStackTrace(); } return BitSetFunctions.create(this, ONDEXConcept.class, is); }
@Override public Set<ONDEXRelation> getRelationsOfEvidenceType(EvidenceType et) { Set<Integer> is = new HashSet<Integer>(); try { PreparedStatement getRsofET = conn .prepareStatement("select distinct id from evidence where sid = ? and elementType = ? and evidence_id = ?"); getRsofET.setLong(1, sid); getRsofET.setString(2, "relation"); getRsofET.setString(3, et.getId()); ResultSet rs = getRsofET.executeQuery(); while (rs.next()) { is.add(rs.getInt(1)); } rs.close(); getRsofET.close(); } catch (SQLException e) { // TODO Auto-generated catch block e.printStackTrace(); } return BitSetFunctions.create(this, ONDEXRelation.class, is); }
@Override public boolean removeEvidenceType(EvidenceType evidencetype) { try { PreparedStatement deleteEvidenceType = sg.getConnection().prepareStatement("delete from evidence where (sid, id, elementType, evidence_id) = (?,?,?,?)"); deleteEvidenceType.setLong(1, sg.getSID()); deleteEvidenceType.setInt(2, id); deleteEvidenceType.setString(3, tableName); deleteEvidenceType.setString(4, evidencetype.getId()); deleteEvidenceType.execute(); deleteEvidenceType.close(); return true; } catch (SQLException e) { // TODO Auto-generated catch block e.printStackTrace(); } return false; }
/** * Loads available EvidenceTypes into ComboBox. * */ protected void initEvidenceTypes(String selected) { // get list of available evidence types Vector<String> evidenceTypes = new Vector<String>(); evidenceTypes.add(""); evidenceTypes.add(Config.language.getProperty("Dialog.Relation.CreateEvidenceType")); EvidenceType[] sorted = graph.getMetaData().getEvidenceTypes().toArray(new EvidenceType[0]); Arrays.sort(sorted, new CaseInsensitiveMetaDataComparator()); for (EvidenceType et : sorted) { evidenceTypes.add(et.getId()); } evidences.removeAllItems(); for (String et : evidenceTypes) { evidences.addItem(et); } if (selected != null) evidences.setSelectedItem(selected); evidences.revalidate(); }
/** * Loads available EvidenceTypes into ComboBox. * */ protected void initEvidenceType(String selected) { // get list of available evidence types Vector<String> evidenceTypes = new Vector<String>(); evidenceTypes.add(""); evidenceTypes.add(Config.language.getProperty("Dialog.Concept.CreateEvidenceType")); // sort meta data evidence types EvidenceType[] sorted = graph.getMetaData().getEvidenceTypes().toArray(new EvidenceType[0]); Arrays.sort(sorted, new CaseInsensitiveMetaDataComparator()); for (EvidenceType et : sorted) { evidenceTypes.add(et.getId()); } evidences.removeAllItems(); for (String et : evidenceTypes) { evidences.addItem(et); } if (selected != null) evidences.setSelectedItem(selected); evidences.revalidate(); }