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| /* | ||
| * TaxonMarkovJumpHistory.java | ||
| * | ||
| * Copyright (c) 2002-2020 Alexei Drummond, Andrew Rambaut and Marc Suchard | ||
| * | ||
| * This file is part of BEAST. | ||
| * See the NOTICE file distributed with this work for additional | ||
| * information regarding copyright ownership and licensing. | ||
| * | ||
| * BEAST is free software; you can redistribute it and/or modify | ||
| * it under the terms of the GNU Lesser General Public License as | ||
| * published by the Free Software Foundation; either version 2 | ||
| * of the License, or (at your option) any later version. | ||
| * | ||
| * BEAST is distributed in the hope that it will be useful, | ||
| * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| * GNU Lesser General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU Lesser General Public | ||
| * License along with BEAST; if not, write to the | ||
| * Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, | ||
| * Boston, MA 02110-1301 USA | ||
| */ | ||
|
|
||
| package dr.app.tools; | ||
|
|
||
| import dr.app.beast.BeastVersion; | ||
| import dr.app.util.Arguments; | ||
| import dr.evolution.tree.NodeRef; | ||
| import dr.evolution.tree.Tree; | ||
| import dr.evolution.tree.TreeUtils; | ||
| import dr.util.Version; | ||
|
|
||
| import java.io.*; | ||
| import java.util.ArrayList; | ||
| import java.util.HashSet; | ||
| import java.util.List; | ||
| import java.util.Set; | ||
|
|
||
| /** | ||
| * @author Philippe Lemey | ||
| * @author Marc Suchard | ||
| */ | ||
| public class TreeMarkovJumpHistoryAnalyzer extends BaseTreeTool { | ||
|
|
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| private final static Version version = new BeastVersion(); | ||
|
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| private static final String HISTORY = "history"; | ||
| private static final String BURN_IN = "burnIn"; | ||
| private static final String[] falseTrue = {"false", "true"}; | ||
|
|
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| // private static final boolean NEW_OUTPUT = true; | ||
|
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| private TreeMarkovJumpHistoryAnalyzer(String inputFileName, | ||
| String outputFileName, | ||
| int burnIn, | ||
| String[] taxaToIgnore, | ||
| boolean basedOnNameContent, | ||
| double mrsd | ||
| ) throws IOException { | ||
|
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| List<Tree> trees = new ArrayList<>(); | ||
|
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| readTrees(trees, inputFileName, burnIn); | ||
|
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| Set taxa = getTaxaToIgnore(trees.get(0), taxaToIgnore, basedOnNameContent); | ||
|
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| this.mrsd = mrsd; | ||
|
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| this.ps = openOutputFile(outputFileName); | ||
| processTrees(trees, burnIn, taxa); | ||
| closeOutputFile(ps); | ||
| } | ||
|
|
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| private Set getTaxaToIgnore(Tree tree, String[] taxaToProcess, boolean basedOnContent) { | ||
| Set taxa = new HashSet(); | ||
| getTaxaToFromName(tree, taxa, taxaToProcess, basedOnContent); | ||
| return taxa; | ||
| } | ||
|
|
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| private void processTrees(List<Tree> trees, int burnIn, Set taxa) { | ||
| if (burnIn < 0) { | ||
| burnIn = 0; | ||
| } | ||
| for (int i = burnIn; i < trees.size(); ++i) { | ||
| Tree tree = trees.get(i); | ||
| processOneTree(tree, taxa); | ||
| } | ||
| } | ||
|
|
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| private void processOneTree(Tree tree, Set taxa) { | ||
|
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| String treeId = tree.getId(); | ||
| if (treeId.startsWith("STATE_")) { | ||
| treeId = treeId.replaceFirst("STATE_", ""); | ||
| } | ||
| // System.out.println(treeId); | ||
|
|
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| for (int i = 0; i < tree.getNodeCount(); ++i) { | ||
| NodeRef node = tree.getNode(i); | ||
| if (nodeToConsider(tree, node, taxa)){ | ||
| Object[] jumps = readCJH(node, tree); | ||
| if (jumps != null) { | ||
| for (int j = jumps.length - 1; j >= 0; j--) { | ||
| Object[] jump = (Object[]) jumps[j]; | ||
| Row row = new Row(treeId, (String) jump[1], (String) jump[2], adjust((Double) jump[0])); | ||
| ps.println(row); | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
|
|
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| private boolean nodeToConsider(Tree tree, NodeRef node, Set taxa){ | ||
| boolean consider = true; | ||
| Set descendants = TreeUtils.getDescendantLeaves(tree,node); | ||
| descendants.removeAll(taxa); | ||
| if (descendants.isEmpty()){ | ||
| consider = false; | ||
| } | ||
| return consider; | ||
| } | ||
|
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| private class Row { | ||
| String treeId; | ||
| String startLocation; | ||
| String endLocation; | ||
| double time; | ||
|
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| private static final String DELIMITER = ","; | ||
|
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| private Row(String treeId, | ||
| String startLocation, String endLocation, | ||
| double time) { | ||
| this.treeId = treeId; | ||
| this.startLocation = startLocation; this.endLocation = endLocation; | ||
| this.time = time; | ||
| } | ||
|
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| public String toString() { | ||
| return treeId + DELIMITER | ||
| + startLocation + DELIMITER + endLocation + DELIMITER | ||
| + time; | ||
| } | ||
| } | ||
|
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|
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| private double adjust(double time) { | ||
| if (mrsd < Double.MAX_VALUE) { | ||
| time = mrsd - time; | ||
| } | ||
| return time; | ||
| } | ||
|
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|
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| private static Object[] readCJH(NodeRef node, Tree treeTime) { | ||
| if (treeTime.getNodeAttribute(node, HISTORY) != null) { | ||
| return (Object[]) treeTime.getNodeAttribute(node, HISTORY); | ||
| } else { | ||
| return null; | ||
| } | ||
| } | ||
|
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| protected PrintStream openOutputFile(String outputFileName) { | ||
|
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| PrintStream ps = super.openOutputFile(outputFileName); | ||
| ps.println("treeId,startLocation,endLocation,time"); | ||
| return ps; | ||
| } | ||
|
|
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| private void closeOutputFile(PrintStream ps) { | ||
| if (ps != null) { | ||
| ps.close(); | ||
| } | ||
| } | ||
|
|
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| private double mrsd; | ||
|
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| private PrintStream ps; | ||
|
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| public static void printTitle() { | ||
| progressStream.println(); | ||
| centreLine("TreeMarkovJumpHistory " + version.getVersionString() + ", " + version.getDateString(), 60); | ||
| centreLine("tool to get a Markov Jump History for a tree", 60); | ||
| centreLine("by", 60); | ||
| centreLine("Philippe Lemey and Marc Suchard", 60); | ||
| progressStream.println(); | ||
| progressStream.println(); | ||
| } | ||
|
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| public static void printUsage(Arguments arguments) { | ||
|
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| arguments.printUsage("TaxonMarkovJumpHistory", "<input-file-name> [<output-file-name>]"); | ||
| progressStream.println(); | ||
| progressStream.println(" Example: taxonMarkovJumpHistory -taxaToProcess taxon1,taxon2 input.trees output.trees"); | ||
| progressStream.println(); | ||
| } | ||
|
|
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| //Main method | ||
| public static void main(String[] args) throws IOException { | ||
|
|
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| String[] taxaToIgnore = null; | ||
| double mrsd = Double.MAX_VALUE; | ||
| int burnIn = -1; | ||
|
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| printTitle(); | ||
|
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| Arguments arguments = new Arguments( | ||
| new Arguments.Option[]{ | ||
| new Arguments.IntegerOption(BURN_IN, "the number of states to be considered as 'burn-in' [default = 0]"), | ||
| new Arguments.StringOption("taxaToIgnore", "list", "a list of taxon names that defines parts of trees to ignore in MJH processing"), | ||
| new Arguments.RealOption("mrsd", "The most recent sampling time to convert heights to times [default=MAX_VALUE]"), | ||
| new Arguments.StringOption(NAME_CONTENT, falseTrue, false, | ||
| "add true noise [default = true])"), | ||
| new Arguments.Option("help", "option to print this message"), | ||
| }); | ||
|
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|
|
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| handleHelp(arguments, args, TaxaMarkovJumpHistoryAnalyzer::printUsage); | ||
|
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| if (arguments.hasOption("taxaToIgnore")) { | ||
| taxaToIgnore = Branch2dRateToGrid.parseVariableLengthStringArray(arguments.getStringOption("taxaToIgnore")); | ||
| } | ||
|
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|
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| if (arguments.hasOption("mrsd")) { | ||
| mrsd = arguments.getRealOption("mrsd"); | ||
| } | ||
|
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| if (arguments.hasOption(BURN_IN)) { | ||
| burnIn = arguments.getIntegerOption(BURN_IN); | ||
| System.err.println("Ignoring a burn-in of " + burnIn + " trees."); | ||
| } | ||
|
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| boolean basedOnNameContent = parseBasedOnNameContent(arguments); | ||
|
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| String[] fileNames = getInputOutputFileNames(arguments, TaxaMarkovJumpHistoryAnalyzer::printUsage); | ||
|
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| new TreeMarkovJumpHistoryAnalyzer(fileNames[0], fileNames[1], burnIn, | ||
| taxaToIgnore, | ||
| basedOnNameContent, | ||
| mrsd | ||
| ); | ||
|
|
||
| System.exit(0); | ||
| } | ||
| } |
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