public ArrayList getAnswerArray() {
ArrayList list = new ArrayList();
Iterator iter = answerSet.iterator();
while (iter.hasNext()) {
list.add(iter.next());
}
return list;
}
/**
* Builds a SgrScoreCalculator object
*
* @param data - name of file containing sgr data
* @param winSize - size of display window
* @throws IOException - if the file cannot be accessed
*/
public SgrScoreCalculator(String data, int winSize, CurationSet curation) throws IOException {
super(winSize);
BufferedReader br = new BufferedReader(new FileReader(data));
String line;
double minAbsScore = Double.POSITIVE_INFINITY;
Set<String> unmatchedIds = new HashSet<String>();
while ((line = br.readLine()) != null) {
String[] tokens = line.split("\t");
String refId = curation.getRefSequence().getName();
if (!tokens[0].equals(refId)) {
if (!unmatchedIds.contains(tokens[0])) {
logger.warn(
"Score id "
+ tokens[0]
+ " does not match main sequence id "
+ refId
+ ". Skipping score.");
unmatchedIds.add(tokens[0]);
}
continue;
}
Double score = new Double(Double.parseDouble(tokens[2]));
// chuck out scores outside of the given range
int pos = Integer.parseInt(tokens[1]);
if (pos >= curation.getLow() && pos <= curation.getHigh()) {
scoreMap.put(pos, score);
}
if (Math.abs(score) < minAbsScore) {
minAbsScore = Math.abs(score);
}
if (score.doubleValue() < minScore) {
minScore = score;
}
if (score.doubleValue() > maxScore) {
maxScore = score;
}
}
while (minAbsScore * factor < 1) {
factor *= 10;
}
}
// for EMI - Attachments at Answer Level
public boolean getHasAttachment() {
if (itemTextAttachmentSet != null && itemTextAttachmentSet.size() > 0) return true;
else return false;
}
/** Sherpa romeo submission support */
public void make_sherpaRomeo_submission(Item item, Division divIn) throws WingException {
if (ConfigurationManager.getBooleanProperty(
"webui.submission.sherparomeo-policy-enabled", true)) {
SHERPASubmitService sherpaSubmitService =
new DSpace().getSingletonService(SHERPASubmitService.class);
if (sherpaSubmitService.hasISSNs(context, item)) {
List div = divIn.addList("submit-upload-new", List.TYPE_FORM);
div.setHead(T_sherpa_title);
// Since sherpa web service doesn't work reliable with more than 1 issn, perform the service
// for each issn
Set<String> issns = sherpaSubmitService.getISSNs(context, item);
Iterator<String> issnsIterator = issns.iterator();
int i = 0;
while (issnsIterator.hasNext()) {
SHERPAResponse shresp =
sherpaSubmitService.searchRelatedJournalsByISSN(issnsIterator.next());
java.util.List<SHERPAJournal> journals = shresp.getJournals();
java.util.List<SHERPAPublisher> publishers = shresp.getPublishers();
if (CollectionUtils.isNotEmpty(journals)) {
for (SHERPAJournal journ : journals) {
SHERPAPublisher pub = publishers.get(0);
List sherpaList = div.addList("sherpaList" + (i + 1), "simple", "sherpaList");
sherpaList
.addItem()
.addFigure(
contextPath + "/static/images/" + (i == 0 ? "romeosmall" : "clear") + ".gif",
"http://www.sherpa.ac.uk/romeo/",
"sherpaLogo");
sherpaList.addItem().addHighlight("sherpaBold").addContent(T_sherpa_journal);
sherpaList.addItem(journ.getTitle() + " (" + journ.getIssn() + ")");
sherpaList.addItem().addHighlight("sherpaBold").addContent(T_sherpa_publisher);
sherpaList.addItemXref(pub.getHomeurl(), pub.getName());
sherpaList.addItem().addHighlight("sherpaBold").addContent(T_sherpa_colour);
sherpaList
.addItem()
.addHighlight("sherpaStyle " + pub.getRomeocolour())
.addContent(message("xmlui.aspect.sherpa.submission." + pub.getRomeocolour()));
sherpaList
.addItem()
.addXref(
"http://www.sherpa.ac.uk/romeo/search.php?issn=" + journ.getIssn(),
T_sherpa_more,
"sherpaMoreInfo");
i = i + 1;
}
}
}
List sherpaList = div.addList("sherpaListEnd", "simple", "sherpaList");
sherpaList.addItem(T_sherpa_consult);
}
}
}
