Package	Files	Average Method Complexity	TOTAL Coverage
jalview.analysis jalview.analysis	34.0 34	4.5956044 4.6	0.6764094 0.676409467.6%

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%
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%
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%
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%
TreeModel TreeModel	28.0 28	2.5 2.5	0.5116279 0.511627951.2%
AlignmentSorter AlignmentSorter	18.0 18	5.7777777 5.78	0.52870816 0.5287081652.9%
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%
AnnotationSorter AnnotationSorter	16.0 16	5.375 5.38	0.58984375 0.5898437559%
SeqsetUtils SeqsetUtils	7.0 7	5.571429 5.57	0.6232877 0.623287762.3%
Dna Dna	16.0 16	8.6875 8.69	0.64935064 0.6493506464.9%
AlignSeq AlignSeq	46.0 46	3.9130435 3.91	0.6530612 0.653061265.3%
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%
TreeBuilder TreeBuilder	10.0 10	2.1 2.1	0.79518074 0.7951807479.5%
SequenceIdMatcher.SeqIdName SequenceIdMatcher.SeqIdName	5.0 5	2.8 2.8	0.84210527 0.8421052784.2%
AlignmentUtils AlignmentUtils	56.0 56	6.196429 6.2	0.8443662 0.844366284.4%
AlignmentAnnotationUtils AlignmentAnnotationUtils	6.0 6	12.166667 12.17	0.8490566 0.849056684.9%
AAFrequency AAFrequency	19.0 19	6.368421 6.37	0.86939573 0.8693957386.9%
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%
NJTree NJTree	4.0 4	3.75 3.75	0.9166667 0.916666791.7%
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%
TreeEngine TreeEngine	8.0 8	3.25 3.25	0.94285715 0.9428571594.3%
AverageDistanceEngine AverageDistanceEngine	10.0 10	4.4 4.4	0.94505495 0.9450549594.5%
Conservation Conservation	16.0 16	6.3125 6.31	0.9541063 0.954106395.4%
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%