Build files

Jalview Builds - Gradle Develop Build - bug-JAL-4559_old_cli_args_in_JVL_docs - Clover and Tests / src / jalview / analysis

	File	Size	Date
	scoremodels		09 Dec 2025, 4:53:18 PM
	AAFrequency.java	30 kB	09 Dec 2025, 4:53:18 PM
	AlignSeq.java	37 kB	09 Dec 2025, 4:53:18 PM
	AlignmentAnnotationUtils.java	16 kB	09 Dec 2025, 4:53:18 PM
	AlignmentSorter.java	24 kB	09 Dec 2025, 4:53:18 PM
	AlignmentUtils.java	101 kB	09 Dec 2025, 4:53:18 PM
	AnnotationSorter.java	16 kB	09 Dec 2025, 4:53:18 PM
	AverageDistanceEngine.java	9 kB	09 Dec 2025, 4:53:18 PM
	AverageDistanceTree.java	3 kB	09 Dec 2025, 4:53:18 PM
	CodingUtils.java	4 kB	09 Dec 2025, 4:53:18 PM
	CodonComparator.java	3 kB	09 Dec 2025, 4:53:18 PM
	Connectivity.java	4 kB	09 Dec 2025, 4:53:18 PM
	ConnectivityException.java	2 kB	09 Dec 2025, 4:53:18 PM
	Conservation.java	23 kB	09 Dec 2025, 4:53:18 PM
	CrossRef.java	37 kB	09 Dec 2025, 4:53:18 PM
	Dna.java	29 kB	09 Dec 2025, 4:53:18 PM
	Finder.java	20 kB	09 Dec 2025, 4:53:18 PM
	GeneticCodeI.java	2 kB	09 Dec 2025, 4:53:18 PM
	GeneticCodes.java	12 kB	09 Dec 2025, 4:53:18 PM
	Grouping.java	11 kB	09 Dec 2025, 4:53:18 PM
	NJTree.java	3 kB	09 Dec 2025, 4:53:18 PM
	PCA.java	6 kB	09 Dec 2025, 4:53:18 PM
	PaSiMap.java	9 kB	09 Dec 2025, 4:53:18 PM
	ParseProperties.java	5 kB	09 Dec 2025, 4:53:18 PM
	Rna.java	12 kB	09 Dec 2025, 4:53:18 PM
	SecStrConsensus.java	6 kB	09 Dec 2025, 4:53:18 PM
	SeqsetUtils.java	9 kB	09 Dec 2025, 4:53:18 PM
	SequenceIdMatcher.java	9 kB	09 Dec 2025, 4:53:18 PM
	StructureFrequency.java	13 kB	09 Dec 2025, 4:53:18 PM
	TreeBuilder.java	6 kB	09 Dec 2025, 4:53:18 PM
	TreeEngine.java	6 kB	09 Dec 2025, 4:53:18 PM
	TreeModel.java	16 kB	09 Dec 2025, 4:53:18 PM
	WUSSParseException.java	1 kB	09 Dec 2025, 4:53:18 PM
	ccAnalysis.java	29 kB	09 Dec 2025, 4:53:18 PM