/** Evaluates the current alignment using the reference alignment */
public void evaluate() {
boolean gui = userInterface != null;
int[] eval = a.evaluate(ref);
int found = a.size() - eval[1];
int correct = eval[0];
int total = ref.size() - ref.countConflicts();
precision = 1.0 * correct / found;
String prc = Math.round(precision * 1000) / 10.0 + "%";
recall = 1.0 * correct / total;
String rec = Math.round(recall * 1000) / 10.0 + "%";
fMeasure = 2 * precision * recall / (precision + recall);
String fms = Math.round(fMeasure * 1000) / 10.0 + "%";
if (gui) {
evaluation = "Precision: " + prc + "; Recall: " + rec + "; F-measure: " + fms;
userInterface.refresh();
} else
evaluation =
"Precision\tRecall\tF-measure\tFound\tCorrect\tReference\n"
+ prc
+ "\t"
+ rec
+ "\t"
+ fms
+ "\t"
+ found
+ "\t"
+ correct
+ "\t"
+ total;
}
public SearchAlignment() {
super();
this.setTitle("Search Alignment");
this.setModalityType(Dialog.ModalityType.APPLICATION_MODAL);
this.setPreferredSize(new Dimension(700, 140));
AML aml = AML.getInstance();
// The containing panel
dialogPanel = new JPanel();
cl = new CardLayout();
dialogPanel.setLayout(cl);
// The search panel
JLabel desc = new JLabel("Enter Search Term: (min 3 characters)");
Font font = desc.getFont();
boldFont = new Font(font.getFontName(), Font.BOLD, font.getSize());
desc.setFont(boldFont);
JPanel labelPanel = new JPanel();
labelPanel.add(desc);
Alignment a = AML.getInstance().getAlignment();
int total = a.size();
mappings = new ArrayList<String>(total);
for (int i = 0; i < total; i++) {
Mapping m = a.get(i);
String map = aml.getSource().getName(m.getSourceId());
map += " = ";
map += aml.getTarget().getName(m.getTargetId());
mappings.add(map);
}
searchField = new JTextArea(1, 60);
searchField.setEditable(true);
AutoCompleteDecorator.decorate(searchField, mappings, false);
JPanel selectionPanel = new JPanel();
selectionPanel.add(searchField);
cancel = new JButton("Cancel");
cancel.setPreferredSize(new Dimension(70, 28));
cancel.addActionListener(this);
find = new JButton("Find");
find.setPreferredSize(new Dimension(70, 28));
find.addActionListener(this);
JPanel buttonPanel = new JPanel();
buttonPanel.add(cancel);
buttonPanel.add(find);
searchPanel = new JPanel();
searchPanel.setLayout(new BoxLayout(searchPanel, BoxLayout.PAGE_AXIS));
searchPanel.add(labelPanel);
searchPanel.add(selectionPanel);
searchPanel.add(buttonPanel);
dialogPanel.add(searchPanel, "Search");
cl.show(dialogPanel, "Search");
this.add(dialogPanel);
this.pack();
this.setVisible(true);
}
public void removeIncorrect() {
Alignment reviewed = new Alignment();
for (Mapping m : a) if (!m.getStatus().equals(MappingStatus.INCORRECT)) reviewed.add(m);
if (a.size() > reviewed.size()) {
aml.setAlignment(reviewed);
if (a.size() > 0) activeMapping = 0;
if (userInterface != null) userInterface.refresh();
needSave = true;
}
}
public static Alignment tfIdfMainParse(String sourcePath, String targetPath)
throws OWLOntologyCreationException {
double sim = 0.0d;
csMaps = new Alignment();
source = new Ontology2Match(sourcePath);
target = new Ontology2Match(targetPath);
String sName, tName;
List<double[]> docsrcVector, doctgtVector = new ArrayList<double[]>();
// Get class Names of the source and target
Set<Integer> sourceKeys = source.getClasses();
Set<Integer> targetKeys = target.getClasses();
// Parse Class Names of Source and Target
for (Integer i : sourceKeys) {
for (Integer j : targetKeys) {
sName = source.getName(i);
tName = target.getName(j);
sim = calcCosSim(sName, tName);
csMaps.add(new Mapping(i, j, sim));
}
}
// Get Data Properties of the source and target
Set<Integer> sDProp = source.getDataProperties();
Set<Integer> tDProp = target.getDataProperties();
// Parse Data Properties of Source and Target
for (Integer i : sDProp) {
for (Integer j : tDProp) {
sName = source.getName(i);
tName = target.getName(j);
sim = calcCosSim(sName, tName);
csMaps.add(new Mapping(i, j, sim));
}
}
// Get Object Properties of the source and target
Set<Integer> sOProp = source.getObjectProperties();
Set<Integer> tOProp = target.getObjectProperties();
// Parse Object Properties of Source and Target
for (Integer i : sOProp) {
for (Integer j : tOProp) {
sName = source.getName(i);
tName = target.getName(j);
sim = calcCosSim(sName, tName);
csMaps.add(new Mapping(i, j, sim));
}
}
return csMaps;
}
/**
* Opens an alignment from a file as the active alignment
*
* @param path: the path to the alignment file
* @throws Exception if the alignment file can't be read or interpreted
*/
public void openAlignment(String path) throws Exception {
a = new Alignment(path);
evaluation = null;
if (a.size() > 0) activeMapping = 0;
if (userInterface != null) userInterface.refresh();
needSave = false;
}
public void setAlignment(Alignment maps) {
a = maps;
if (a.size() > 0) activeMapping = 0;
qf = null;
evaluation = null;
rep = null;
needSave = false;
}
/** Matches the active ontologies using manual configurations */
public void matchManual() {
im = new InteractionManager();
ManualMatcher.match();
evaluation = null;
rep = null;
if (a.size() > 0) activeMapping = 0;
if (userInterface != null) userInterface.refresh();
needSave = true;
}
/** Matches the active ontologies using the default configuration */
public void matchAuto() {
defaultConfig();
im = new InteractionManager();
AutomaticMatcher.match();
evaluation = null;
rep = null;
if (a.size() > 0) activeMapping = 0;
if (userInterface != null) userInterface.refresh();
needSave = true;
}
public void sortDescending() {
a.sortDescending();
if (a.size() > 0) activeMapping = 0;
if (userInterface != null) userInterface.refresh();
}
public void saveAlignmentTSV(String file) throws Exception {
a.saveTSV(file);
needSave = false;
}
/** @return whether there is a non-empty active alignment */
public boolean hasAlignment() {
return a != null && a.size() > 0;
}