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readTree function requires jebl3 to export jebl.evolution.trees.Tree #…
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| ψ = newick(tree="((A:1,B:1):1,(C:0.5, D:0.5):1.5):0.0;"); |
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lphy-base/src/main/java/lphy/base/function/io/ReadTrees.java
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| //package lphy.base.function.io; | ||
| // | ||
| //import jebl.evolution.io.ImportException; | ||
| //import jebl.evolution.io.NewickImporter; | ||
| //import jebl.evolution.io.NexusImporter; | ||
| //import jebl.evolution.io.TreeImporter; | ||
| //import jebl.evolution.trees.Tree; | ||
| //import lphy.base.evolution.alignment.MetaDataAlignment; | ||
| //import lphy.base.evolution.tree.TimeTree; | ||
| //import lphy.base.function.alignment.MetaDataOptions; | ||
| //import lphy.base.parser.NexusParser; | ||
| //import lphy.core.io.UserDir; | ||
| //import lphy.core.logger.LoggerUtils; | ||
| //import lphy.core.model.DeterministicFunction; | ||
| //import lphy.core.model.Value; | ||
| //import lphy.core.model.annotation.GeneratorCategory; | ||
| //import lphy.core.model.annotation.GeneratorInfo; | ||
| //import lphy.core.model.annotation.ParameterInfo; | ||
| // | ||
| //import java.io.BufferedReader; | ||
| //import java.io.FileNotFoundException; | ||
| //import java.io.IOException; | ||
| //import java.nio.charset.StandardCharsets; | ||
| //import java.nio.file.Files; | ||
| //import java.nio.file.Path; | ||
| //import java.util.*; | ||
| // | ||
| ///** TODO It requires jebl3 to export jebl.evolution.trees.Tree | ||
| // * Newick or Nexus | ||
| // * @see lphy.base.function.tree.Newick | ||
| // */ | ||
| //public class ReadTrees extends DeterministicFunction<TimeTree[]> { | ||
| // | ||
| // public ReadTrees(@ParameterInfo(name = ReaderConst.FILE, narrativeName = "file name", description = "the name of Nexus/Newick file including path.") Value<String> filePath, | ||
| // @ParameterInfo(name = ReaderConst.FORMAT, description = "Nexus or Newick (case-insesitive), default to Nexus.", | ||
| // optional=true) Value<String> format ) { | ||
| // setParam(ReaderConst.FILE, filePath); | ||
| // // default to true | ||
| // if (format != null) | ||
| // setParam(ReaderConst.FORMAT, format); | ||
| // else setParam(ReaderConst.FORMAT, new Value<>(null, "nexus")); | ||
| // } | ||
| // | ||
| // @GeneratorInfo(name="readTrees", category = GeneratorCategory.TREE, examples = {"readTrees.lphy"}, | ||
| // description = "A function that parses trees from either a Nexus (default) or Newick file.") | ||
| // public Value<TimeTree[]> apply() { | ||
| // String filePath = ((Value<String>) getParams().get(ReaderConst.FILE)).value(); | ||
| // Path path = UserDir.getUserPath(filePath); | ||
| // | ||
| // String format = ((Value<String>) getParams().get(ReaderConst.FORMAT)).value(); | ||
| // if (format == null || | ||
| // !(format.equalsIgnoreCase("Nexus") || format.equalsIgnoreCase("Newick")) ) | ||
| // throw new IllegalArgumentException("The argument value of " + ReaderConst.FORMAT + | ||
| // " must be either Nexus or Newick ! But get " + format); | ||
| // | ||
| // try (BufferedReader reader = Files.newBufferedReader(path, StandardCharsets.UTF_8)) { | ||
| // //*** parsing ***// | ||
| // TreeImporter treeImporter; | ||
| // if (format.equalsIgnoreCase("Newick")) { | ||
| // boolean unquotedLabels = false; | ||
| // treeImporter = new NewickImporter(reader, unquotedLabels); | ||
| // } else { | ||
| // boolean compactTrees = false; | ||
| // treeImporter = new NexusImporter(reader, compactTrees, 0); | ||
| // } | ||
| // | ||
| // treeImporter.importTrees(); | ||
| // | ||
| // List<jebl.evolution.trees.Tree> | ||
| // | ||
| // | ||
| // } catch (FileNotFoundException e) { | ||
| // LoggerUtils.log.severe("File " + Path.of(filePath).toAbsolutePath() + " is not found !\n" + | ||
| // "The current working dir = " + UserDir.getUserDir()); | ||
| // } catch (IOException e) { | ||
| // LoggerUtils.logStackTrace(e); | ||
| // } | ||
| // | ||
| // | ||
| // | ||
| // //*** parsing ***// | ||
| // NexusImporter nexusImporter = new NexusImporter(path.toString()); | ||
| // | ||
| // MetaDataAlignment nexusData = null; | ||
| // try { | ||
| // // if ageDirectionStr = null, then assume forward | ||
| // nexusData = nexusParser.importNexus(ageDirectionStr); | ||
| // } catch (IOException | ImportException e) { | ||
| // LoggerUtils.logStackTrace(e); | ||
| // } | ||
| // // set age to Taxon | ||
| // if (ageRegxStr != null) { | ||
| // if (! Objects.requireNonNull(nexusData).isUltrametric()) | ||
| // LoggerUtils.log.severe("Taxa ages had been imported from the nexus file ! " + | ||
| // "It would be problematic to overwrite taxa ages from the command line !"); | ||
| // | ||
| // nexusData.setAgesParsedFromTaxaName(ageRegxStr, ageDirectionStr); | ||
| // } | ||
| // | ||
| // // set species to Taxon | ||
| // if (spRegxStr != null) | ||
| // Objects.requireNonNull(nexusData).setSpeciesParsedFromTaxaName(spRegxStr); | ||
| // | ||
| // return new Value<>(null, nexusData, this); | ||
| // | ||
| // } | ||
| // | ||
| //} |
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