+ private static final String COMMA = ",";
+
+ private static final String ELLIPSIS = "...";
+
+ private static final int MAX_REFS_PER_SOURCE = 4;
+
+ private static final int MAX_SOURCES = 40;
+
+ private static String linkImageURL;
+
+ // public static final String[][] PRIMARY_SOURCES moved to DBRefSource.java
+
+ /*
+ * 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>()
+ {
+
+ @Override
+ public int compare(DBRefEntry ref1, DBRefEntry ref2)
+ {
+ if (ref1 instanceof GeneLociI)
+ {
+ return -1;
+ }
+ if (ref2 instanceof GeneLociI)
+ {
+ return 1;
+ }
+ String s1 = ref1.getSource();
+ String s2 = ref2.getSource();
+ boolean s1Primary = DBRefSource.isPrimarySource(s1);
+ boolean s2Primary = DBRefSource.isPrimarySource(s2);
+ if (s1Primary && !s2Primary)
+ {
+ return -1;
+ }
+ if (!s1Primary && s2Primary)
+ {
+ return 1;
+ }
+ int comp = s1 == null ? -1 : (s2 == null ? 1 : s1
+ .compareToIgnoreCase(s2));
+ if (comp == 0)
+ {
+ String a1 = ref1.getAccessionId();
+ String a2 = ref2.getAccessionId();
+ comp = a1 == null ? -1 : (a2 == null ? 1 : a1
+ .compareToIgnoreCase(a2));
+ }
+ return comp;
+ }
+
+// private boolean isPrimarySource(String source)
+// {
+// for (String[] primary : DBRefSource.PRIMARY_SOURCES)
+// {
+// for (String s : primary)
+// {
+// if (source.equals(s))
+// {
+// return true;
+// }
+// }
+// }
+// return false;
+// }
+ };
+
+ private boolean forTooltip;
+
+ /**
+ * Constructor given a flag which affects behaviour
+ * <ul>
+ * <li>if true, generates feature details suitable to show in a tooltip</li>
+ * <li>if false, generates feature details in a form suitable for the sequence
+ * details report</li>
+ * </ul>
+ *
+ * @param isForTooltip
+ */
+ public SequenceAnnotationReport(boolean isForTooltip)