* Sorts the alignment by size of group. <br>
* Maintains the order of sequences in each group by order in given alignment
* object.
* Sorts the alignment by size of group. <br>
* Maintains the order of sequences in each group by order in given alignment
* object.
/**
* Select sequences in order from tmp that is present in mask, and any
* remaining seqeunces in mask not in tmp
/**
* Select sequences in order from tmp that is present in mask, and any
* remaining seqeunces in mask not in tmp
* @return intersect(tmp,mask)+intersect(complement(tmp),mask)
*/
private static SequenceI[] vectorSubsetToArray(List<SequenceI> tmp,
* @return intersect(tmp,mask)+intersect(complement(tmp),mask)
*/
private static SequenceI[] vectorSubsetToArray(List<SequenceI> tmp,
/**
* Sort sequence in order of increasing score attribute for annotation with a
* particular scoreLabel. Or reverse if same label was used previously
/**
* Sort sequence in order of increasing score attribute for annotation with a
* particular scoreLabel. Or reverse if same label was used previously
/**
* sort the alignment using the features on each sequence found between start
* and stop with the given featureLabel (and optional group qualifier)
/**
* sort the alignment using the features on each sequence found between start
* and stop with the given featureLabel (and optional group qualifier)