+ public boolean parse(AlignmentI align, \r
+ Map colours, boolean removeHTML, boolean relaxedIdMatching)\r
+ {\r
+ return parse(align, colours, null, removeHTML, relaxedIdMatching);\r
+ }\r
+\r
+ /**\r
+ * Parse GFF or sequence features file optionally using case-independent matching\r
+ * @param align - alignment/dataset containing sequences that are to be annotated\r
+ * @param colours - hashtable to store feature colour definitions\r
+ * @param featureLink - hashtable to store associated URLs \r
+ * @param removeHTML - process html strings into plain text\r
+ * @return true if features were added\r
+ */\r
+ public boolean parse(AlignmentI align, Map colours,\r
+ Map featureLink, boolean removeHTML)\r
+ {\r
+ return parse(align, colours, featureLink, removeHTML, false);\r
+ }\r
+\r
+ /**\r
+ /**\r
+ * Parse GFF or sequence features file \r
+ * @param align - alignment/dataset containing sequences that are to be annotated\r
+ * @param colours - hashtable to store feature colour definitions\r
+ * @param featureLink - hashtable to store associated URLs \r
+ * @param removeHTML - process html strings into plain text\r
+ * @param relaxedIdmatching - when true, ID matches to compound sequence IDs are allowed\r
+ * @return true if features were added\r
+ */\r
+ public boolean parse(AlignmentI align,\r
+ Map colours, Map featureLink, boolean removeHTML, boolean relaxedIdmatching)\r