Package	Files	Average Method Complexity	TOTAL Coverage
jalview.analysis jalview.analysis	34.0 34	4.5088105 4.51	0.5910555 0.591055559.1%

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%
PCA PCA	17.0 17	1.2352941 1.24	0.0 0.00%
PaSiMap PaSiMap	22.0 22	1.3181819 1.32	0.0 0.00%
ParseProperties ParseProperties	4.0 4	4.0 4	0.0 0.00%
SecStrConsensus SecStrConsensus	6.0 6	4.1666665 4.17	0.0 0.00%
StructureFrequency StructureFrequency	4.0 4	14.5 14.5	0.0 0.00%
TreeBuilder TreeBuilder	10.0 10	1.6 1.6	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	2.6153846 2.62	0.27952754 0.2795275428%
CrossRef CrossRef	16.0 16	8.5625 8.56	0.40778688 0.4077868840.8%
SeqsetUtils SeqsetUtils	7.0 7	5.571429 5.57	0.45890412 0.4589041245.9%
AlignmentSorter AlignmentSorter	17.0 17	5.882353 5.88	0.465 0.46546.5%
SecStrConsensus.SimpleBP SecStrConsensus.SimpleBP	7.0 7	1.0 1	0.5 0.550%
Rna Rna	13.0 13	5.230769 5.23	0.565 0.56556.5%
Dna Dna	16.0 16	8.625 8.62	0.6368715 0.636871563.7%
AlignSeq AlignSeq	46.0 46	3.8913043 3.89	0.64871794 0.6487179464.9%
SequenceIdMatcher SequenceIdMatcher	12.0 12	2.75 2.75	0.65789473 0.6578947365.8%
SequenceIdMatcher.SeqIdName SequenceIdMatcher.SeqIdName	5.0 5	2.8 2.8	0.65789473 0.6578947365.8%
WUSSParseException WUSSParseException	3.0 3	1.0 1	0.71428573 0.7142857371.4%
AlignmentGenerator AlignmentGenerator	8.0 8	3.5 3.5	0.72307694 0.7230769472.3%
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%
AlignmentUtils AlignmentUtils	60.0 60	6.1833334 6.18	0.7852922 0.785292278.5%
AlignmentAnnotationUtils AlignmentAnnotationUtils	4.0 4	10.0 10	0.8103448 0.810344881%
AAFrequency AAFrequency	18.0 18	6.2222223 6.22	0.85040987 0.8504098785%
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%
AverageDistanceEngine AverageDistanceEngine	10.0 10	4.4 4.4	0.94505495 0.9450549594.5%
Conservation Conservation	19.0 19	5.5263157 5.53	0.9546539 0.954653995.5%
Finder Finder	20.0 20	3.65 3.65	0.96363634 0.9636363496.4%
CodonComparator CodonComparator	1.0 1	15.0 15	1.0 1.0100%