Package	Files	Average Method Complexity	TOTAL Coverage
jalview.analysis jalview.analysis	34.0 34	4.503417 4.5	0.64663184 0.6466318464.7%

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%
Connectivity Connectivity	2.0 2	3.5 3.5	0.0 0.00%
ConnectivityException ConnectivityException	5.0 5	1.0 1	0.0 0.00%
NJTree NJTree	4.0 4	3.75 3.75	0.0 0.00%
PaSiMap PaSiMap	22.0 22	1.3181819 1.32	0.0 0.00%
SecStrConsensus SecStrConsensus	6.0 6	4.1666665 4.17	0.0 0.00%
TreeBuilder TreeBuilder	9.0 9	1.5555556 1.56	0.0 0.00%
ccAnalysis ccAnalysis	12.0 12	6.3333335 6.33	0.0 0.00%
ccAnalysis.TrustRegion ccAnalysis.TrustRegion	4.0 4	1.0 1	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%
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%
AlignmentSorter AlignmentSorter	17.0 17	5.882353 5.88	0.5525 0.552555.3%
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%
AlignSeq AlignSeq	46.0 46	3.8913043 3.89	0.65 0.6565%
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%
TreeEngine TreeEngine	8.0 8	3.25 3.25	0.74285716 0.7428571674.3%
AnnotationSorter AnnotationSorter	14.0 14	4.928571 4.93	0.74384236 0.7438423674.4%
AAFrequency AAFrequency	18.0 18	6.0555553 6.06	0.7489452 0.748945274.9%
AlignmentUtils AlignmentUtils	50.0 50	6.52 6.52	0.8048246 0.804824680.5%
SequenceIdMatcher.SeqIdName SequenceIdMatcher.SeqIdName	5.0 5	2.8 2.8	0.84210527 0.8421052784.2%
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%
AverageDistanceEngine AverageDistanceEngine	10.0 10	4.4 4.4	0.94505495 0.9450549594.5%
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%
Finder Finder	20.0 20	3.65 3.65	0.96363634 0.9636363496.4%
Rna Rna	13.0 13	5.230769 5.23	0.97 0.9797%
CodonComparator CodonComparator	1.0 1	15.0 15	1.0 1.0100%