- else if (!(this._alignmentSequenceAnnotationList.equals(temp._alignmentSequenceAnnotationList)))
- return false;
- }
- else if (temp._alignmentSequenceAnnotationList != null)
+ if (this._alignmentSequenceAnnotationList != temp._alignmentSequenceAnnotationList) {
+ thcycle=org.castor.util.CycleBreaker.startingToCycle(this._alignmentSequenceAnnotationList);
+ tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._alignmentSequenceAnnotationList);
+ if (thcycle!=tmcycle) {
+ if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._alignmentSequenceAnnotationList); };
+ if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._alignmentSequenceAnnotationList); };
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._alignmentSequenceAnnotationList.equals(temp._alignmentSequenceAnnotationList)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._alignmentSequenceAnnotationList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._alignmentSequenceAnnotationList);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._alignmentSequenceAnnotationList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._alignmentSequenceAnnotationList);
+ }
+ }
+ } else if (temp._alignmentSequenceAnnotationList != null)