{\r
// make a note of the name and description\r
autoAnnots\r
- .put(aa[aai].graph\r
- + "\t"\r
- + aa[aai].label\r
- + "\t"\r
- + aa[aai].description\r
- + "\t"\r
- + (aa[aai].sequenceRef != null ? aa[aai].sequenceRef\r
- .getDisplayId(true) : ""),\r
+ .put(autoAnnotsKey(aa[aai], aa[aai].sequenceRef, (aa[aai].groupRef==null ? null : aa[aai].groupRef.getName())\r
+ ),\r
new Integer(1));\r
}\r
}\r
annotation.score = score;\r
if (!overrideAutoAnnot\r
&& autoAnnots\r
- .containsKey(annotation.graph\r
- + "\t"\r
- + annotation.label\r
- + "\t"\r
- + annotation.description\r
- + "\t"\r
- + (refSeq != null ? refSeq\r
- .getDisplayId(true) : "")))\r
+ .containsKey(autoAnnotsKey(annotation, refSeq, groupRef)))\r
{\r
// skip - we've already got an automatic annotation of this type.\r
continue;\r
return true;\r
}\r
\r
+ private Object autoAnnotsKey(AlignmentAnnotation annotation, SequenceI refSeq, String groupRef)\r
+ {\r
+ return annotation.graph\r
+ + "\t"\r
+ + annotation.label\r
+ + "\t"\r
+ + annotation.description\r
+ + "\t"\r
+ + (refSeq != null ? refSeq\r
+ .getDisplayId(true) : "");\r
+ }\r
+\r
Annotation parseAnnotation(String string, int graphStyle)\r
{\r
boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH); // don't\r