├── .editorconfig ├── .gitignore ├── CREDITS ├── LICENSE.txt ├── README.md ├── RELEASE-HOWTO.md ├── changelog.txt ├── collatex-core ├── pom.xml └── src │ ├── main │ ├── java │ │ └── eu │ │ │ └── interedition │ │ │ └── collatex │ │ │ ├── CollationAlgorithm.java │ │ │ ├── CollationAlgorithmFactory.java │ │ │ ├── Token.java │ │ │ ├── VariantGraph.java │ │ │ ├── Witness.java │ │ │ ├── dekker │ │ │ ├── DekkerAlgorithm.kt │ │ │ ├── InspectableCollationAlgorithm.java │ │ │ ├── Match.kt │ │ │ ├── PhraseMatchDetector.kt │ │ │ ├── TranspositionDetector.kt │ │ │ ├── Tuple.java │ │ │ ├── astar │ │ │ │ ├── AstarAlgorithm.java │ │ │ │ └── Cost.java │ │ │ ├── editgraphaligner │ │ │ │ ├── EditGraphAligner.java │ │ │ │ └── MatchCube.java │ │ │ ├── island │ │ │ │ ├── Archipelago.java │ │ │ │ ├── Coordinate.java │ │ │ │ ├── Island.kt │ │ │ │ ├── IslandCollection.java │ │ │ │ ├── IslandCompetition.java │ │ │ │ ├── IslandConflictResolver.java │ │ │ │ ├── IslandDepthAndSizeComparator.java │ │ │ │ ├── IslandSelection.java │ │ │ │ ├── IslandSizeComparator.java │ │ │ │ └── package-info.java │ │ │ ├── legacy │ │ │ │ ├── IslandPositionComparator.java │ │ │ │ ├── MatchTable.java │ │ │ │ ├── MatchTableImpl.java │ │ │ │ ├── MatchTableLinker.java │ │ │ │ ├── MatchTableSelection.java │ │ │ │ └── MatchTableSerializer.java │ │ │ ├── package-info.java │ │ │ └── token_index │ │ │ │ ├── Block.kt │ │ │ │ ├── TokenIndex.kt │ │ │ │ └── TokenIndexToMatches.kt │ │ │ ├── matching │ │ │ ├── EditDistance.java │ │ │ ├── EditDistanceTokenComparator.java │ │ │ ├── EqualityTokenComparator.java │ │ │ ├── Matches.java │ │ │ ├── StrictEqualityTokenComparator.java │ │ │ └── package-info.java │ │ │ ├── medite │ │ │ ├── AlignmentDecisionGraph.java │ │ │ ├── Matches.java │ │ │ ├── MediteAlgorithm.java │ │ │ ├── SuffixTree.java │ │ │ └── package-info.java │ │ │ ├── needlemanwunsch │ │ │ ├── NeedlemanWunschAlgorithm.java │ │ │ ├── NeedlemanWunschScorer.java │ │ │ └── package-info.java │ │ │ ├── package-info.java │ │ │ ├── simple │ │ │ ├── SimpleCollation.java │ │ │ ├── SimplePatternTokenizer.java │ │ │ ├── SimpleToken.java │ │ │ ├── SimpleTokenNormalizers.java │ │ │ ├── SimpleVariantGraphSerializer.java │ │ │ ├── SimpleWitness.java │ │ │ ├── SimpleWitnessTeiBuilder.java │ │ │ └── package-info.java │ │ │ ├── suffixarray │ │ │ ├── Algorithm.java │ │ │ ├── BPR.java │ │ │ ├── CharSequenceAdapter.java │ │ │ ├── DeepShallow.java │ │ │ ├── DensePositiveDecorator.java │ │ │ ├── DensePositiveMapper.java │ │ │ ├── DivSufSort.java │ │ │ ├── ExtraTrailingCellsDecorator.java │ │ │ ├── GenericArrayAdapter.java │ │ │ ├── ISuffixArrayBuilder.java │ │ │ ├── ISymbolMapper.java │ │ │ ├── MinMax.java │ │ │ ├── QSufSort.java │ │ │ ├── SAIS.java │ │ │ ├── Skew.java │ │ │ ├── SuffixArrays.java │ │ │ ├── SuffixData.java │ │ │ ├── Tools.java │ │ │ └── Traversals.java │ │ │ ├── suffixtree │ │ │ ├── ActivePoint.java │ │ │ ├── Cursor.java │ │ │ ├── Edge.java │ │ │ ├── Node.java │ │ │ ├── Sequence.java │ │ │ ├── SequenceTerminal.java │ │ │ ├── Suffix.java │ │ │ ├── SuffixTree.java │ │ │ └── Utils.java │ │ │ └── util │ │ │ ├── GreedyStringTilingAlgorithm.java │ │ │ ├── ParallelSegmentationApparatus.java │ │ │ ├── StreamUtil.java │ │ │ ├── VariantGraphRanking.java │ │ │ ├── VariantGraphTraversal.kt │ │ │ ├── VertexMatch.java │ │ │ └── package-info.java │ └── javadoc │ │ └── overview.html │ └── test │ └── java │ └── eu │ └── interedition │ └── collatex │ ├── AbstractTest.java │ ├── ScriptEngineTest.java │ ├── VariantGraphTest.java │ ├── dekker │ ├── AlignmentTest.java │ ├── BeckettTest.java │ ├── DarwinTest.java │ ├── DekkerAlgorithmTest.java │ ├── SpencerHoweTest.java │ ├── TranspositionGraphTest.java │ ├── TranspositionRenderingTest.java │ ├── VariantGraphRankerTest.java │ ├── VariantGraphTest.java │ ├── editgraphaligner │ │ └── EditGraphMultiWitnessAlignerTest.java │ ├── island │ │ └── IslandTest.java │ ├── legacy │ │ ├── HermansTest.java │ │ ├── IslandConflictResolverTest.java │ │ ├── MatchTableLinkerTest.java │ │ └── MatchTableTest.java │ └── token_index │ │ ├── TokenComparatorTest.java │ │ ├── TokenIndexTest.java │ │ └── VariantGraphMatcher.java │ ├── lab │ ├── CollateXLaboratory.java │ ├── MatchMatrixCellStatus.java │ ├── MatchMatrixTableModel.java │ ├── MatchTableCell.java │ └── WitnessPanel.java │ ├── matching │ ├── MatchesTest.java │ └── NearMatcherTest.java │ ├── medite │ ├── MediteTest.java │ └── SuffixTreeTest.java │ ├── needlemanwunsch │ └── NeedlemanWunschTest.java │ ├── output │ └── AlignmentTableTest.java │ └── simple │ ├── SimpleWitnessTeiBuilderTest.java │ └── SimpleWitnessTest.java ├── collatex-pythonport ├── .gitignore ├── .pydevproject ├── AUTHORS.rst ├── CONTRIBUTING.rst ├── ClusterShell │ ├── RangeSet.py │ └── __init__.py ├── HISTORY.rst ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.rst ├── RELEASE.txt ├── TODO.txt ├── collatex │ ├── HTML.py │ ├── __init__.py │ ├── astar.py │ ├── block.py │ ├── core_classes.py │ ├── core_functions.py │ ├── display_module.py │ ├── edit_graph_aligner.py │ ├── exceptions.py │ ├── experimental_astar_aligner.py │ ├── extended_suffix_array.py │ ├── linsuffarr.py │ ├── near_matching.py │ ├── suffix_based_scorer.py │ ├── tokenindex.py │ └── transposition_handling.py ├── docs │ ├── Makefile │ ├── authors.rst │ ├── conf.py │ ├── contributing.rst │ ├── history.rst │ ├── index.rst │ ├── installation.rst │ ├── make.bat │ ├── readme.rst │ └── usage.rst ├── installing_pygraphviz.txt ├── near_matching_analysis.ipynb ├── old_readme ├── requirements.txt ├── setup.cfg ├── setup.py ├── tests │ ├── __init__.py │ ├── test_alignment.py │ ├── test_alignment_table_rendering.py │ ├── test_astar_edit_graph_aligner.py │ ├── test_beckett.py │ ├── test_collatex.py │ ├── test_collatex_block_witnesses.py │ ├── test_collatex_dekker_algorithm.py │ ├── test_collatex_linsuffarr.py │ ├── test_collatex_simple.py │ ├── test_decision_tree_aligner.py │ ├── test_edit_graph_aligner.py │ ├── test_export_alignment_table_as_tei.py │ ├── test_export_alignment_table_as_xml.py │ ├── test_near_matching.py │ ├── test_near_matching_pretokenized.py │ ├── test_suffix_based_scorer.py │ ├── test_suffix_edit_graph_aligner.py │ ├── test_tokenindex.py │ ├── test_tokenized_json.py │ ├── test_variant_graph.py │ └── test_witness_tokens.py ├── tox.ini └── use_cases │ ├── darwin.py │ └── darwin_chapter1_para1.json ├── collatex-servlet ├── .gitignore ├── pom.xml └── src │ └── main │ ├── java │ └── eu │ │ └── interedition │ │ └── collatex │ │ ├── http │ │ ├── CollateApplication.java │ │ └── CollateResource.java │ │ └── io │ │ ├── IOExceptionMapper.java │ │ ├── SimpleCollationJSONMessageBodyReader.java │ │ ├── VariantGraphDotMessageBodyWriter.java │ │ ├── VariantGraphGraphMLMessageBodyWriter.java │ │ ├── VariantGraphJSONMessageBodyWriter.java │ │ ├── VariantGraphSVGMessageBodyWriter.java │ │ └── VariantGraphTEIMessageBodyWriter.java │ ├── resources │ └── static │ │ ├── collatex-console.js │ │ ├── collatex.css │ │ ├── collatex.js │ │ ├── collatex.png │ │ ├── darwin.html │ │ ├── favicon.ico │ │ ├── index.html │ │ ├── yui-3.8.1-head.html │ │ ├── yui-3.8.1-modules.css │ │ └── yui-3.8.1-modules.js │ └── webapp │ └── WEB-INF │ └── web.xml ├── collatex-tools ├── pom.xml └── src │ ├── main │ ├── java │ │ └── eu │ │ │ └── interedition │ │ │ └── collatex │ │ │ └── tools │ │ │ ├── CollateX.java │ │ │ ├── CollationPipe.java │ │ │ ├── CollationServer.java │ │ │ ├── JsonProcessor.java │ │ │ └── PluginScript.java │ └── resources │ │ └── static │ │ ├── collatex-console.js │ │ ├── collatex.css │ │ ├── collatex.js │ │ ├── collatex.png │ │ ├── darwin.html │ │ ├── favicon.ico │ │ ├── index.html │ │ ├── yui-3.8.1-head.html │ │ ├── yui-3.8.1-modules.css │ │ └── yui-3.8.1-modules.js │ └── test │ ├── fixtures │ ├── base-2w.json │ └── base-4w.json │ └── java │ └── eu │ └── interedition │ └── collatex │ └── tools │ └── CollectionPipeTest.java ├── docs ├── _layouts │ └── default.html ├── images │ ├── html2_output.png │ ├── svg_output.png │ └── svg_simple_output.png ├── pythonport.md └── style.css ├── logging.properties ├── pom.xml ├── site ├── Gruntfile.js ├── collatex.js ├── collatex.less ├── google-code-prettify │ ├── prettify-sunburst-theme.less │ ├── prettify.js │ └── prettify.less ├── grunt │ ├── aliases.yaml │ ├── browserify.js │ ├── clean.js │ ├── connect.js │ ├── cssmin.js │ ├── jade.js │ ├── less.js │ ├── uglify.js │ └── watch.js ├── htdocs │ ├── about │ │ └── index.html │ ├── collatex.css │ ├── collatex.js │ ├── doc │ │ └── index.html │ ├── download │ │ └── index.html │ ├── favicon.ico │ ├── images │ │ ├── aligner.png │ │ ├── analyzer.png │ │ ├── tokenizer.png │ │ ├── variant-graph-collatex.png │ │ ├── variant-graph-schmidt.png │ │ └── variant-graph-snippet.png │ └── index.html ├── package.json └── templates │ ├── about │ └── index.jade │ ├── doc │ ├── index.jade │ └── usage-instructions.txt │ ├── download │ └── index.jade │ ├── index.jade │ └── page.jade └── tmp └── .gitignore /.editorconfig: 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