Package	Files	Average Method Complexity	TOTAL Coverage
jalview.analysis jalview.analysis	35.0 35	4.444196 4.44	0.0 0.00%

Class	Methods	Average Method Complexity	TOTAL Coverage
AAFrequency AAFrequency	18.0 18	6.0555553 6.06	0.0 0.00%
AlignSeq AlignSeq	46.0 46	3.8913043 3.89	0.0 0.00%
AlignmentAnnotationUtils AlignmentAnnotationUtils	3.0 3	9.0 9	0.0 0.00%
AlignmentGenerator AlignmentGenerator	8.0 8	3.5 3.5	0.0 0.00%
AlignmentSorter AlignmentSorter	17.0 17	5.882353 5.88	0.0 0.00%
AlignmentUtils AlignmentUtils	50.0 50	6.52 6.52	0.0 0.00%
AlignmentUtils.DnaVariant AlignmentUtils.DnaVariant	4.0 4	1.5 1.5	0.0 0.00%
AnnotationSorter AnnotationSorter	14.0 14	4.928571 4.93	0.0 0.00%
AnnotationSorter.SequenceAnnotationOrder AnnotationSorter.SequenceAnnotationOrder	3.0 3	1.3333334 1.33	0.0 0.00%
AverageDistanceEngine AverageDistanceEngine	10.0 10	4.4 4.4	0.0 0.00%
AverageDistanceTree AverageDistanceTree	4.0 4	3.75 3.75	0.0 0.00%
CodingUtils CodingUtils	5.0 5	4.0 4	0.0 0.00%
CodonComparator CodonComparator	1.0 1	15.0 15	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%
Conservation Conservation	16.0 16	6.1875 6.19	0.0 0.00%
CrossRef CrossRef	16.0 16	8.5625 8.56	0.0 0.00%
Dna Dna	16.0 16	8.625 8.62	0.0 0.00%
Finder Finder	20.0 20	3.65 3.65	0.0 0.00%
GeneticCodes GeneticCodes	15.0 15	3.1333334 3.13	0.0 0.00%
Grouping Grouping	3.0 3	4.6666665 4.67	0.0 0.00%
NJTree NJTree	4.0 4	3.75 3.75	0.0 0.00%
PCA PCA	25.0 25	1.36 1.36	0.0 0.00%
PaSiMap PaSiMap	23.0 23	1.3043479 1.3	0.0 0.00%
ParseProperties ParseProperties	4.0 4	4.0 4	0.0 0.00%
Rna Rna	13.0 13	5.230769 5.23	0.0 0.00%
SecStrConsensus SecStrConsensus	6.0 6	4.1666665 4.17	0.0 0.00%
SecStrConsensus.SimpleBP SecStrConsensus.SimpleBP	7.0 7	1.0 1	0.0 0.00%
SeqsetUtils SeqsetUtils	7.0 7	5.571429 5.57	0.0 0.00%
SequenceIdMatcher SequenceIdMatcher	12.0 12	2.75 2.75	0.0 0.00%
SequenceIdMatcher.SeqIdName SequenceIdMatcher.SeqIdName	5.0 5	2.8 2.8	0.0 0.00%
StructureFrequency StructureFrequency	4.0 4	14.5 14.5	0.0 0.00%
TreeBuilder TreeBuilder	9.0 9	1.5555556 1.56	0.0 0.00%
TreeEngine TreeEngine	8.0 8	3.25 3.25	0.0 0.00%
TreeModel TreeModel	26.0 26	2.5769231 2.58	0.0 0.00%
WUSSParseException WUSSParseException	3.0 3	1.0 1	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%