*/
public class SequenceAnnotationReport
{
+ private static final int MAX_DESCRIPTION_LENGTH = 40;
+
private static final String COMMA = ",";
private static final String ELLIPSIS = "...";
* Comparator to order DBRefEntry by Source + accession id (case-insensitive),
* with 'Primary' sources placed before others, and 'chromosome' first of all
*/
- private static Comparator<DBRefEntry> comparator = new Comparator<DBRefEntry>()
+ private static Comparator<DBRefEntry> comparator = new Comparator<>()
{
@Override
if (description != null && !description.equals(feature.getType()))
{
description = StringUtils.stripHtmlTags(description);
+
+ /*
+ * truncate overlong descriptions unless they contain an href
+ * (as truncation could leave corrupted html)
+ */
+ boolean hasLink = description.indexOf("a href") > -1;
+ if (description.length() > MAX_DESCRIPTION_LENGTH && !hasLink)
+ {
+ description = description.substring(0, MAX_DESCRIPTION_LENGTH)
+ + ELLIPSIS;
+ }
sb.append("; ").append(description);
}
if (sequence.getDescription() != null)
{
tmp = sequence.getDescription();
- sb.append("<br>").append(tmp);
+ sb.append(tmp);
maxWidth = Math.max(maxWidth, tmp.length());
}
SequenceI ds = sequence;