Package	Files	Average Method Complexity	TOTAL Coverage
jalview.analysis jalview.analysis	28.0 28	4.791304 4.79	0.6895856 0.689585669%

Class	Methods	Average Method Complexity	TOTAL Coverage
AlignmentUtils.DnaVariant AlignmentUtils.DnaVariant	4.0 4	1.5 1.5	0.0 0.00%
AverageDistanceTree AverageDistanceTree	4.0 4	3.75 3.75	0.0 0.00%
NJTree NJTree	4.0 4	3.75 3.75	0.0 0.00%
SecStrConsensus SecStrConsensus	6.0 6	4.1666665 4.17	0.0 0.00%
TreeBuilder TreeBuilder	17.0 17	2.3529413 2.35	0.0 0.00%
AnnotationSorter.SequenceAnnotationOrder AnnotationSorter.SequenceAnnotationOrder	3.0 3	1.3333334 1.33	0.18181819 0.1818181918.2%
TreeModel TreeModel	26.0 26	2.5769231 2.58	0.4183267 0.418326741.8%
CrossRef CrossRef	16.0 16	8.5625 8.56	0.46311477 0.4631147746.3%
AlignmentSorter AlignmentSorter	17.0 17	5.8235292 5.82	0.465 0.46546.5%
SecStrConsensus.SimpleBP SecStrConsensus.SimpleBP	7.0 7	1.0 1	0.5 0.550%
PCA PCA	17.0 17	1.2352941 1.24	0.5316456 0.531645653.2%
StructureFrequency StructureFrequency	4.0 4	14.5 14.5	0.5805243 0.580524358.1%
SeqsetUtils SeqsetUtils	7.0 7	5.571429 5.57	0.6232877 0.623287762.3%
Dna Dna	16.0 16	8.625 8.62	0.6499069 0.649906965%
SequenceIdMatcher SequenceIdMatcher	12.0 12	2.75 2.75	0.68421054 0.6842105468.4%
WUSSParseException WUSSParseException	3.0 3	1.0 1	0.71428573 0.7142857371.4%
AlignmentGenerator AlignmentGenerator	8.0 8	3.5 3.5	0.7307692 0.730769273.1%
AnnotationSorter AnnotationSorter	12.0 12	5.3333335 5.33	0.7326203 0.732620373.3%
AlignSeq AlignSeq	30.0 30	4.0666666 4.07	0.7338262 0.733826273.4%
AlignmentUtils AlignmentUtils	40.0 40	7.1 7.1	0.84085315 0.8408531584.1%
SequenceIdMatcher.SeqIdName SequenceIdMatcher.SeqIdName	5.0 5	2.8 2.8	0.84210527 0.8421052784.2%
AAFrequency AAFrequency	13.0 13	5.923077 5.92	0.875 0.87587.5%
GeneticCodes GeneticCodes	15.0 15	3.1333334 3.13	0.89440995 0.8944099589.4%
CodingUtils CodingUtils	5.0 5	4.0 4	0.8965517 0.896551789.7%
Grouping Grouping	3.0 3	4.6666665 4.67	0.92045456 0.9204545692%
ParseProperties ParseProperties	4.0 4	4.0 4	0.9411765 0.941176594.1%
Conservation Conservation	16.0 16	6.1875 6.19	0.95566505 0.9556650595.6%
AlignmentAnnotationUtils AlignmentAnnotationUtils	3.0 3	9.0 9	0.95604396 0.9560439695.6%
Rna Rna	13.0 13	5.230769 5.23	0.97 0.9797%
Finder Finder	14.0 14	3.642857 3.64	0.9883041 0.988304198.8%
CodonComparator CodonComparator	1.0 1	15.0 15	1.0 1.0100%