/**
* Verify that the list has an appropriate unbroken chain of back links.
*
* @param list the list of splices to validate
* @return true if the list has an unbroken chain of back links
*/
boolean spliceListIsValid(final ObjectArrayList<GobyAlignment> list) {
if (list != null && list.size() > 1) {
Alignments.AlignmentEntry prevEntry = list.get(0).entry;
for (int i = 1; i < list.size(); i++) {
Alignments.AlignmentEntry currentEntry = list.get(i).entry;
if (!currentEntry.hasSplicedBackwardAlignmentLink()) return false;
else {
Alignments.RelatedAlignmentEntry currentBackwardLink =
currentEntry.getSplicedBackwardAlignmentLink();
if ((prevEntry.getQueryIndex() != currentEntry.getQueryIndex())
|| (prevEntry.getFragmentIndex() != currentBackwardLink.getFragmentIndex())
|| (prevEntry.getPosition() != currentBackwardLink.getPosition())
|| (prevEntry.getTargetIndex() != currentBackwardLink.getTargetIndex())) {
return false;
}
}
prevEntry = currentEntry;
}
}
return true;
}
