Package	Files	Average Method Complexity	Uncovered Elements	TOTAL Coverage
jalview.analysis jalview.analysis	26.0 26	4.8802395 4.88	2117.0 2,117	0.66864926 0.6686492666.9%

Class	Methods	Average Method Complexity	Uncovered Elements	TOTAL Coverage
AverageDistanceTree AverageDistanceTree	4.0 4	3.75 3.75	54.0 54	0.0 0.00%
NJTree NJTree	4.0 4	3.75 3.75	48.0 48	0.0 0.00%
PCA PCA	10.0 10	1.4 1.4	62.0 62	0.0 0.00%
SecStrConsensus SecStrConsensus	6.0 6	4.1666665 4.17	112.0 112	0.0 0.00%
TreeBuilder TreeBuilder	17.0 17	2.3529413 2.35	168.0 168	0.0 0.00%
AnnotationSorter.SequenceAnnotationOrder AnnotationSorter.SequenceAnnotationOrder	3.0 3	1.3333334 1.33	9.0 9	0.18181819 0.1818181918.2%
CrossRef CrossRef	16.0 16	8.3125 8.31	275.0 275	0.4234801 0.423480142.3%
TreeModel TreeModel	26.0 26	2.5769231 2.58	144.0 144	0.42629483 0.4262948342.6%
AlignmentSorter AlignmentSorter	17.0 17	5.8235292 5.82	214.0 214	0.465 0.46546.5%
SecStrConsensus.SimpleBP SecStrConsensus.SimpleBP	7.0 7	1.0 1	7.0 7	0.5 0.550%
StructureFrequency StructureFrequency	5.0 5	11.8 11.8	122.0 122	0.5595668 0.559566856%
SeqsetUtils SeqsetUtils	7.0 7	5.571429 5.57	55.0 55	0.6232877 0.623287762.3%
Dna Dna	16.0 16	8.8125 8.81	199.0 199	0.63619745 0.6361974563.6%
AlignmentUtils.DnaVariant AlignmentUtils.DnaVariant	4.0 4	1.5 1.5	5.0 5	0.64285713 0.6428571364.3%
SequenceIdMatcher SequenceIdMatcher	12.0 12	2.75 2.75	36.0 36	0.68421054 0.6842105468.4%
WUSSParseException WUSSParseException	3.0 3	1.0 1	2.0 2	0.71428573 0.7142857371.4%
AlignmentGenerator AlignmentGenerator	8.0 8	3.5 3.5	35.0 35	0.7307692 0.730769273.1%
AnnotationSorter AnnotationSorter	12.0 12	5.3333335 5.33	50.0 50	0.7326203 0.732620373.3%
AlignSeq AlignSeq	30.0 30	4.0666666 4.07	144.0 144	0.7338262 0.733826273.4%
Finder Finder	20.0 20	2.8 2.8	38.0 38	0.75949365 0.7594936575.9%
AAFrequency AAFrequency	13.0 13	5.6923075 5.69	74.0 74	0.775076 0.77507677.5%
SequenceIdMatcher.SeqIdName SequenceIdMatcher.SeqIdName	5.0 5	2.8 2.8	7.0 7	0.81578946 0.8157894681.6%
AlignmentUtils AlignmentUtils	44.0 44	7.1136365 7.11	214.0 214	0.84276265 0.8427626584.3%
CodingUtils CodingUtils	5.0 5	4.0 4	6.0 6	0.8965517 0.896551789.7%
Grouping Grouping	3.0 3	4.6666665 4.67	7.0 7	0.92045456 0.9204545692%
ParseProperties ParseProperties	4.0 4	4.0 4	4.0 4	0.9411765 0.941176594.1%
AlignmentAnnotationUtils AlignmentAnnotationUtils	3.0 3	9.0 9	4.0 4	0.95604396 0.9560439695.6%
Conservation Conservation	16.0 16	6.1875 6.19	16.0 16	0.96059114 0.9605911496.1%
Rna Rna	13.0 13	5.230769 5.23	6.0 6	0.9701493 0.970149397%
CodonComparator CodonComparator	1.0 1	15.0 15	0.0 0	1.0 1.0100%