/**
* This method adds a new Mention and associated concepts to a SofaText, there can be overlap
* between concept names and multiple concepts can match a string, instead of choosing one
* concept, we record them all.
*
* @param m
* @param concepts
*/
public void addMentionAndConcepts(Mention m, List<Concept> concepts) {
// System.out.println("Mention Text: " + m.getText());
ArrayList<SofaTextMention> toRemove = new ArrayList<SofaTextMention>();
// check all SofaTextMentions
for (SofaTextMention stm : sofaTextMention) {
// if new mention is subsumed by existing mention, add associated concepts to subsuming
// mention
// and then return
// test for overlap
if (isOverlapping(stm, m)) { // there is overlap, keep the larger of the two mentions
if (stm.getMentionEnd() - stm.getMentionStart()
< m.getEnd() - m.getStart()) // mention is larger
{
System.out.println("1");
concepts.addAll(stm.getConcepts());
toRemove.add(stm);
} else {
System.out.println("2");
stm.addConcepts(concepts);
return;
}
}
}
// remove mentions from remove list
sofaTextMention.removeAll(toRemove);
// add new mention to sofatext
sofaTextMention.add(new SofaTextMention(this, m, concepts));
}
private boolean isOverlapping(SofaTextMention stm, Mention m) {
if (stm.getMentionStart() == m.getStart() // same start token
|| stm.getMentionEnd() == m.getEnd() // same end token
|| (stm.getMentionStart() <= m.getStart() && stm.getMentionEnd() >= m.getStart())
|| (stm.getMentionStart() >= m.getStart() && stm.getMentionStart() <= m.getEnd())) {
return true;
}
return false;
}
/**
* returns all SofaTextMention objects with type "treatment" in this SofaText object
*
* @return
*/
public Collection<? extends SofaTextMention> getTreatments() {
List<SofaTextMention> treatments = new ArrayList<SofaTextMention>();
for (SofaTextMention stm : sofaTextMention) {
if (stm.getMentionType().equals("treatment")) treatments.add(stm);
}
return treatments;
}
/**
* returns all SofaTextMention objects with type "problem" in this SofaText object
*
* @return
*/
public Collection<? extends SofaTextMention> getProblems() {
List<SofaTextMention> problems = new ArrayList<SofaTextMention>();
for (SofaTextMention stm : sofaTextMention) {
if (stm.getMentionType().equals("problem")) problems.add(stm);
}
return problems;
}
/**
* Helper method to generate HTML, will be moved to controller in future, the html contains the
* text of the SofaText object with each mention wrapped in a span tag
*
* @return
*/
public String getAnnotatedHTML() {
String html = new String(text);
String tagged;
for (SofaTextMention m : sofaTextMention) {
tagged = wrapInMentionTypeTag(m.getMentionText(), m.getMentionType());
// System.out.println(tagged);
if (!m.getSofaTextMentionConcept().isEmpty()) tagged = wrapInConceptTag(tagged, m);
html = html.replace(m.getMentionText(), tagged);
// html = html.replaceAll("\\n", "<br/>");
}
return html;
}
private String wrapInConceptTag(String tagged, SofaTextMention m) {
SofaTextMentionConcept c = (SofaTextMentionConcept) m.getSofaTextMentionConcept().toArray()[0];
return String.format(
"<a href=/openmrs/dictionary/concept.htm?conceptId=%d>%s</a>",
c.getConcept().getConceptId(), tagged);
}
