Java tutorial
/* * Utils.java * * Copyright (c) 2002-2015 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.bss; import java.awt.Desktop; import java.awt.Frame; import java.io.BufferedInputStream; import java.io.BufferedReader; import java.io.File; import java.io.FileInputStream; import java.io.FileReader; import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; import java.net.URL; import java.nio.charset.Charset; import java.text.NumberFormat; import java.util.ArrayList; import java.util.Iterator; import java.util.LinkedHashMap; import java.util.List; import java.util.Locale; import java.util.Map; import java.util.Map.Entry; import java.util.concurrent.ConcurrentHashMap; import javax.swing.ImageIcon; import javax.swing.JOptionPane; import javax.swing.JTabbedPane; import javax.swing.SwingUtilities; import dr.evolution.tree.TreeUtils; import org.apache.commons.math.random.MersenneTwister; import dr.app.bss.test.AncestralSequenceTrait; import dr.evolution.datatype.Codons; import dr.evolution.datatype.DataType; import dr.evolution.io.Importer.ImportException; import dr.evolution.io.NewickImporter; import dr.evolution.io.NexusImporter; import dr.evolution.sequence.Sequence; import dr.evolution.tree.NodeRef; import dr.evolution.tree.Tree; import dr.evolution.tree.TreeTraitProvider; import dr.evolution.util.MutableTaxonList; import dr.evolution.util.Taxa; import dr.evolution.util.Taxon; import dr.evomodel.tree.TreeModel; import dr.inference.model.Parameter; import dr.math.MathUtils; /** * @author Filip Bielejec * @version $Id$ */ public class Utils { // //////////////////// // ---THREAD UTILS---// // //////////////////// public static void sleep(int seconds) { try { Thread.sleep(seconds * 1000); } catch (InterruptedException e) { e.printStackTrace(); } }// END: sleep // //////////////////////////////// // ---RANDOM NUMB3R GENERATION---// // //////////////////////////////// private static MersenneTwister random = new MersenneTwister(MathUtils.nextLong()); public static double rLogNormal(double stdev, double mean) { double rNorm = random.nextGaussian() * stdev + mean; double rLognormal = Math.exp(rNorm); return rLognormal; }// END: drawRandom public static int rMultinom(double[] probabilities) { int range = probabilities.length + 1; double[] distribution = new double[range]; double sumProb = 0; for (double value : probabilities) { sumProb += value; } // END: probabilities loop distribution[0] = 0; for (int i = 1; i < range; ++i) { distribution[i] = distribution[i - 1] + (probabilities[i - 1] / sumProb); } // END: i loop distribution[range - 1] = 1.0; double key = random.nextDouble(); int mindex = 1; int maxdex = range - 1; int midpoint = mindex + (maxdex - mindex) / 2; while (mindex <= maxdex) { if (key < distribution[midpoint - 1]) { maxdex = midpoint - 1; } else if (key > distribution[midpoint]) { mindex = midpoint + 1; } else { return midpoint - 1; } midpoint = mindex + (int) Math.ceil((maxdex - mindex) / 2); } //END: mindex loop System.out.println("Error in rMultinom!"); return range - 1; }//END: rMultinom // //////////// // ---MATH---// // //////////// public static int sample(double[] probabilities) { int samplePos = -Integer.MAX_VALUE; double cumProb = 0.0; double u = random.nextDouble(); for (int i = 0; i < probabilities.length; i++) { cumProb += probabilities[i]; if (u <= cumProb) { samplePos = i; break; } } return samplePos; }// END: randomChoicePDF public static void rescale(double[] logX) { double max = max(logX); for (int i = 0; i < logX.length; i++) { logX[i] -= max; } }// END: rescale public double getParameterVariance(Parameter param) { int n = param.getSize(); double mean = getParameterMean(param); double var = 0; for (int i = 0; i < n; i++) { var += Math.pow((param.getValue(i) - mean), 2); } var /= (n - 1); return var; }// END: getParameterVariance public double getParameterMean(Parameter param) { double mean = 0; int n = param.getSize(); for (int i = 0; i < n; i++) { mean += param.getValue(i); } mean /= n; return mean; }// END: getParameterMean public static double getNorm(double[] vector) { double norm = 0; for (int i = 0; i < vector.length; i++) { norm += Math.pow(vector[i], 2); } return Math.sqrt(norm); }// END: getNorm public static void normalize(double[] vector) { double norm = getNorm(vector); for (int i = 0; i < vector.length; i++) { vector[i] = vector[i] / norm; } }// END: normalize // //////////////////// // ---ARRAYS UTILS---// // //////////////////// public static void exponentiate(double[] array) { for (int i = 0; i < array.length; i++) { array[i] = Math.exp(array[i]); } }// END: exponentiate public static int max(int[] array) { int max = -Integer.MAX_VALUE; for (int i = 0; i < array.length; i++) { if (array[i] > max) { max = (int) array[i]; } // END: if check } // END: i loop return max; }// END: findMaximum public static int max(double[] array) { int max = -Integer.MAX_VALUE; for (int i = 0; i < array.length; i++) { if (array[i] > max) { max = (int) array[i]; } // END: if check } // END: i loop return max; }// END: findMaximum public static int max(ArrayList<Integer> array) { int max = -Integer.MAX_VALUE; for (Integer element : array) { if (element > max) { max = element; } // END: if check } // END: i loop return max; }// END: findMaximum public static double sumArray(int[] array) { double sum = 0.0; for (int i = 0; i < array.length; i++) { sum += array[i]; } return sum; }// END: sumArray public static double sumArray(double[] array) { double sum = 0.0; for (int i = 0; i < array.length; i++) { sum += array[i]; } return sum; }// END: sumArray // ///////////////// // ---CONSTANTS---// // ///////////////// // public static final int TREE_MODEL_ELEMENT = 0; public static final int BRANCH_MODEL_ELEMENT = 1; public static final int SITE_RATE_MODEL_ELEMENT = 2; public static final int BRANCH_RATE_MODEL_ELEMENT = 3; public static final int FREQUENCY_MODEL_ELEMENT = 4; public static final int DEMOGRAPHIC_MODEL_ELEMENT = 5; public static final String TOPOLOGY = "topology"; public static final String ABSOLUTE_HEIGHT = "absoluteHeight"; public static final String TREE_FILENAME = "treeFilename"; public static final String SUBSTITUTION_MODEL = "substitutionModel"; public static final String DEMOGRAPHIC_MODEL = "demographicModel"; public static final String FREQUENCY_MODEL = "frequencyModel"; public static final String CODON_UNIVERSAL = "codon-universal"; public static final String CHOOSE_FILE = "Choose file..."; public static final String EDIT_TAXA_SET = "Edit taxa set..."; public static final String ANCESTRAL_SEQUENCE = "ancestralSequence"; public static final String BSS_ICON = "icons/bss.png"; public static final String CHECK_ICON = "icons/check.png"; public static final String ERROR_ICON = "icons/error.png"; public static final String HAMMER_ICON = "icons/hammer.png"; public static final String CLOSE_ICON = "icons/close.png"; public static final String BIOHAZARD_ICON = "icons/biohazard.png"; public static final String BUBBLE_BLUE_ICON = "icons/bubble-blue.png"; public static final String SAVE_ICON = "icons/save.png"; public static final String TEXT_FILE_ICON = "icons/file.png"; public static final double[] UNIFORM_CODON_FREQUENCIES = new double[] { 0.0163936, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344, 0.01639344 }; public static final String STOP_CODONS[] = new String[] { "TAA", "TAG", "TGA" }; // /////////////////////////////// // ---GENERAL UTILITY METHODS---// // /////////////////////////////// public static double logfactor(int n) { double logfactor = 0.0; for (int i = 1; i <= n; i++) { logfactor += Math.log(i); } return logfactor; } public static double map(double value, double low1, double high1, double low2, double high2) { /** * maps a single value from its range into another interval * * @param low1 * , high1 - range of value; low2, high2 - interval * @return the mapped value */ return (value - low1) / (high1 - low1) * (high2 - low2) + low2; }// END: map public static String[] loadStrings(String filename) throws IOException { int linesCount = countLines(filename); String[] lines = new String[linesCount]; FileInputStream inputStream; BufferedReader reader; String line; inputStream = new FileInputStream(filename); reader = new BufferedReader(new InputStreamReader(inputStream, Charset.forName("UTF-8"))); int i = 0; while ((line = reader.readLine()) != null) { lines[i] = line; i++; } // Clean up reader.close(); reader = null; inputStream = null; return lines; }// END: loadStrings public static int countLines(String filename) throws IOException { InputStream is = new BufferedInputStream(new FileInputStream(filename)); byte[] c = new byte[1024]; int count = 0; int readChars = 0; boolean empty = true; while ((readChars = is.read(c)) != -1) { empty = false; for (int i = 0; i < readChars; ++i) { if (c[i] == '\n') { ++count; } } } is.close(); return (count == 0 && !empty) ? 1 : count; }// END: countLines public static Taxa importTaxaFromFile(File file) throws IOException { Taxa taxa = new Taxa(); Taxon taxon; String[] lines = Utils.loadStrings(file.getAbsolutePath()); for (int i = 0; i < lines.length; i++) { String[] line = lines[i].split("\\s+"); taxon = new Taxon(line[TaxaEditorTableModel.NAME_INDEX]); taxon.setAttribute(Utils.ABSOLUTE_HEIGHT, Double.valueOf(line[TaxaEditorTableModel.HEIGHT_INDEX])); taxa.addTaxon(taxon); } // END: i loop return taxa; }// END: importTaxaFromFile public static Tree importTreeFromFile(File file) throws IOException, ImportException { Tree tree = null; BufferedReader reader = new BufferedReader(new FileReader(file)); String line = reader.readLine(); if (line.toUpperCase().startsWith("#NEXUS")) { NexusImporter importer = new NexusImporter(reader); tree = importer.importTree(null); } else { NewickImporter importer = new NewickImporter(reader); tree = importer.importTree(null); } reader.close(); return tree; }// END: importTreeFromFile public static void removeTaxaWithAttributeValue(PartitionDataList dataList, String attribute, String value) { for (int i = 0; i < dataList.allTaxa.getTaxonCount(); i++) { Taxon taxon = dataList.allTaxa.getTaxon(i); if (taxon.getAttribute(attribute).toString().equalsIgnoreCase(value)) { dataList.allTaxa.removeTaxon(taxon); i--; } } }// END: removeTaxaWithAttributeValue public static void centreLine(String line, int pageWidth) { int n = pageWidth - line.length(); int n1 = n / 2; for (int i = 0; i < n1; i++) { System.out.print(" "); } System.out.println(line); } public static int getSiteCount(PartitionDataList dataList) { int siteCount = 0; int to = 0; for (PartitionData data : dataList) { // siteCount += data.createPartitionSiteCount(); to = data.to; if (to > siteCount) { siteCount = to; } } return siteCount;// + 1; }// END: getSiteCount public static int arrayIndex(String[] array, String element) { List<String> vector = new ArrayList<String>(); for (int i = 0; i < array.length; i++) { vector.add(array[i]); } return vector.indexOf(element); }// END: arrayIndex public static ArrayList<TreeModel> treesToList(PartitionDataList dataList) { ArrayList<TreeModel> treeModelsList = new ArrayList<TreeModel>(); for (PartitionData data : dataList) { treeModelsList.add(data.createTreeModel()); } return treeModelsList; }// END: treesToList public static boolean taxonExists(Taxon taxon, MutableTaxonList taxonList) { boolean exists = false; for (Taxon taxon2 : taxonList) { if (taxon.equals(taxon2) // && // taxon.getAttribute(Utils.TREE_FILENAME).toString().equalsIgnoreCase(taxon2.getAttribute(Utils.TREE_FILENAME).toString()) ) { exists = true; break; } } return exists; }// END: taxonExists // private boolean isFileInList(File file) { // boolean exists = false; // // for (File file2 : dataList.treesList) { // // if (file.getName().equalsIgnoreCase(file2.getName())) { // exists = true; // break; // } // // } // // return exists; // }// END: isFileInList public static double getAbsoluteTaxonHeight(Taxon taxon, Tree tree) { double height = 0.0; for (int i = 0; i < tree.getExternalNodeCount(); i++) { NodeRef externalNode = tree.getExternalNode(i); Taxon externalNodeTaxon = tree.getNodeTaxon(externalNode); if (externalNodeTaxon.equals(taxon)) { height = tree.getNodeHeight(externalNode); } } // END: external node loop return height; }// END: getAbsoluteTaxonHeight public static boolean isRecordInList(TreesTableRecord record, ArrayList<TreesTableRecord> recordsList) { boolean exists = false; for (TreesTableRecord record2 : recordsList) { if (record.getName().equalsIgnoreCase(record2.getName())) { exists = true; break; } } return exists; }// END: isRecordInList public static boolean isTaxaInList(Taxa taxa, ArrayList<Taxa> taxaList) { boolean exists = false; for (Taxa taxa2 : taxaList) { if (taxaToString(taxa, true).equalsIgnoreCase(taxaToString(taxa2, true))) { exists = true; break; } } return exists; }// END: isTaxaInList public static int taxaIsIdenticalWith(Taxa taxa, ArrayList<Taxa> taxaList) { int index = -Integer.MAX_VALUE; for (Taxa taxa2 : taxaList) { if (taxaToString(taxa, true).equalsIgnoreCase(taxaToString(taxa2, true))) { index = taxaList.indexOf(taxa2); break; } } return index; }// END: treeModelIsIdenticalWith public static boolean isTreeModelInList(TreeModel treeModel, ArrayList<TreeModel> treeModelList) { boolean exists = false; for (TreeModel treeModel2 : treeModelList) { if (treeModel.getNewick().equalsIgnoreCase(treeModel2.getNewick())) { exists = true; break; } } return exists; }// END: isTreeModelInList public static int treeModelIsIdenticalWith(TreeModel treeModel, ArrayList<TreeModel> treeModelList) { int index = -Integer.MAX_VALUE; for (TreeModel treeModel2 : treeModelList) { if (treeModel.getNewick().equalsIgnoreCase(treeModel2.getNewick())) { index = treeModelList.indexOf(treeModel2); break; } } return index; }// END: treeModelIsIdenticalWith public static boolean isElementInList(PartitionData data, ArrayList<PartitionData> partitionList, int elementIndex) { boolean exists = false; switch (elementIndex) { case DEMOGRAPHIC_MODEL_ELEMENT: for (PartitionData data2 : partitionList) { if (demographicModelToString(data).equalsIgnoreCase(demographicModelToString(data2))) { exists = true; break; } } break; case BRANCH_RATE_MODEL_ELEMENT: for (PartitionData data2 : partitionList) { if (clockRateModelToString(data).equalsIgnoreCase(clockRateModelToString(data2))) { exists = true; break; } } break; case FREQUENCY_MODEL_ELEMENT: for (PartitionData data2 : partitionList) { if (frequencyModelToString(data).equalsIgnoreCase(frequencyModelToString(data2))) { exists = true; break; } } break; case BRANCH_MODEL_ELEMENT: for (PartitionData data2 : partitionList) { if (branchSubstitutionModelToString(data) .equalsIgnoreCase(branchSubstitutionModelToString(data2))) { exists = true; break; } } break; case SITE_RATE_MODEL_ELEMENT: for (PartitionData data2 : partitionList) { if (siteRateModelToString(data).equalsIgnoreCase(siteRateModelToString(data2))) { exists = true; break; } } break; default: throw new RuntimeException("Unknown element"); }// END: switch return exists; }// END: isModelInList public static int isIdenticalWith(PartitionData data, ArrayList<PartitionData> partitionList, int elementIndex) { int index = -Integer.MAX_VALUE; switch (elementIndex) { case DEMOGRAPHIC_MODEL_ELEMENT: for (PartitionData data2 : partitionList) { if (demographicModelToString(data).equalsIgnoreCase(demographicModelToString(data2))) { index = partitionList.indexOf(data2); break; } } break; case BRANCH_RATE_MODEL_ELEMENT: for (PartitionData data2 : partitionList) { if (clockRateModelToString(data).equalsIgnoreCase(clockRateModelToString(data2))) { index = partitionList.indexOf(data2); break; } } break; case FREQUENCY_MODEL_ELEMENT: for (PartitionData data2 : partitionList) { if (frequencyModelToString(data).equalsIgnoreCase(frequencyModelToString(data2))) { index = partitionList.indexOf(data2); break; } } break; case BRANCH_MODEL_ELEMENT: for (PartitionData data2 : partitionList) { if (branchSubstitutionModelToString(data) .equalsIgnoreCase(branchSubstitutionModelToString(data2))) { index = partitionList.indexOf(data2); break; } } break; case SITE_RATE_MODEL_ELEMENT: for (PartitionData data2 : partitionList) { if (siteRateModelToString(data).equalsIgnoreCase(siteRateModelToString(data2))) { index = partitionList.indexOf(data2); break; } } break; default: throw new RuntimeException("Unknown element"); }// END: switch return index; }// END: isIdenticalWith // ///////////////// // ---GUI UTILS---// // ///////////////// public static ImageIcon createImageIcon(String path) { ImageIcon icon = null; URL imgURL = BeagleSequenceSimulatorApp.class.getResource(path); if (imgURL != null) { icon = new ImageIcon(imgURL); } else { System.err.println("Couldn't find file: " + path + "\n"); } return icon; }// END: CreateImageIcon public static boolean isBrowsingSupported() { if (!Desktop.isDesktopSupported()) { return false; } boolean result = false; Desktop desktop = java.awt.Desktop.getDesktop(); if (desktop.isSupported(Desktop.Action.BROWSE)) { result = true; } return result; }// END: isBrowsingSupported public static int getTabbedPaneComponentIndex(JTabbedPane tabbedPane, String title) { int index = -Integer.MAX_VALUE; int count = tabbedPane.getTabCount(); for (int i = 0; i < count; i++) { if (tabbedPane.getTitleAt(i).toString().equalsIgnoreCase(title)) { index = i; break; } // END: title check } // END: i loop return index; }// END: getComponentIndex public static Frame getActiveFrame() { Frame result = null; Frame[] frames = Frame.getFrames(); for (int i = 0; i < frames.length; i++) { Frame frame = frames[i]; if (frame.isVisible()) { result = frame; break; } } return result; } public static String getMultipleWritePath(File outFile, String defaultExtension, int i) { String path = outFile.getParent(); String[] nameArray = outFile.getName().split("\\.", 2); String name = ((i == 0) ? nameArray[0] : nameArray[0] + i); String extension = (nameArray.length == 1) ? (defaultExtension) : (nameArray[1]); String fullPath = path + System.getProperty("file.separator") + name + "." + extension; return fullPath; }// END: getMultipleWritePath public static String getWritePath(File outFile, String defaultExtension) { String path = outFile.getParent(); String[] nameArray = outFile.getName().split("\\.", 2); String name = nameArray[0]; String extension = (nameArray.length == 1) ? (defaultExtension) : (nameArray[1]); String fullPath = path + System.getProperty("file.separator") + name + "." + extension; return fullPath; }// END: getWritePath public static void showDialog(final String message) { if (SwingUtilities.isEventDispatchThread()) { JOptionPane.showMessageDialog(getActiveFrame(), message, "Message", JOptionPane.ERROR_MESSAGE, Utils.createImageIcon(Utils.BUBBLE_BLUE_ICON)); } else { SwingUtilities.invokeLater(new Runnable() { public void run() { JOptionPane.showMessageDialog(getActiveFrame(), message, "Message", JOptionPane.ERROR_MESSAGE, Utils.createImageIcon(Utils.BUBBLE_BLUE_ICON)); } }); } // END: edt check }// END: showDialog // //////////////////////////////// // ---EXCEPTION HANDLING UTILS---// // //////////////////////////////// public static void handleException(final Throwable e, final String message) { final Thread t = Thread.currentThread(); if (SwingUtilities.isEventDispatchThread()) { showExceptionDialog(t, e, message); } else { SwingUtilities.invokeLater(new Runnable() { public void run() { showExceptionDialog(t, e, message); } }); } // END: edt check }// END: uncaughtException public static void handleException(final Throwable e) { final Thread t = Thread.currentThread(); if (SwingUtilities.isEventDispatchThread()) { showExceptionDialog(t, e); } else { SwingUtilities.invokeLater(new Runnable() { public void run() { showExceptionDialog(t, e); } }); } // END: edt check }// END: handleException private static void showExceptionDialog(Thread t, Throwable e) { String msg = String.format("Unexpected problem on thread %s: %s", t.getName(), e.getMessage()); logException(t, e); JOptionPane.showMessageDialog(Utils.getActiveFrame(), // msg, // "Error", // JOptionPane.ERROR_MESSAGE, // Utils.createImageIcon(Utils.ERROR_ICON)); }// END: showExceptionDialog private static void showExceptionDialog(Thread t, Throwable e, String message) { String msg = String.format("Unexpected problem on thread %s: %s" + "\n" + message, t.getName(), e.getMessage()); logException(t, e); JOptionPane.showMessageDialog(Utils.getActiveFrame(), // msg, // "Error", // JOptionPane.ERROR_MESSAGE, // Utils.createImageIcon(Utils.ERROR_ICON)); }// END: showExceptionDialog private static void logException(Thread t, Throwable e) { e.printStackTrace(); }// END: logException // /////////////////// // ---PRINT UTILS---// // /////////////////// public static void printMap(Map<?, ?> mp) { Iterator<?> it = mp.entrySet().iterator(); while (it.hasNext()) { Entry<?, ?> pairs = (Entry<?, ?>) it.next(); Object obj = pairs.getValue(); if (obj instanceof int[]) { int[] seq = (int[]) obj; System.out.print(pairs.getKey() + " ="); for (int i = 0; i < seq.length; ++i) { System.out.print(" " + seq[i]); } System.out.println(); } else if (obj instanceof double[]) { double[] seq = (double[]) obj; System.out.print(pairs.getKey() + " ="); for (int i = 0; i < seq.length; ++i) { System.out.print(" " + seq[i]); } System.out.println(); } else { System.out.println(pairs.getKey() + " = " + pairs.getValue()); } // END: obj class check } }// END: printMap public static void printHashMap(ConcurrentHashMap<?, ?> hashMap) { Iterator<?> iterator = hashMap.entrySet().iterator(); while (iterator.hasNext()) { Entry<?, ?> pairs = (Entry<?, ?>) iterator.next(); Taxon taxon = (Taxon) pairs.getKey(); int[] sequence = (int[]) pairs.getValue(); System.out.println(taxon.toString()); Utils.printArray(sequence); } // END: while has next }// END: printHashMap public static void printArray(Object[] x) { for (int i = 0; i < x.length; i++) { System.out.print(x[i] + " "); } System.out.println(); }// END: printArray public static void printArray(int[] x) { for (int i = 0; i < x.length; i++) { System.out.print(x[i] + " "); } System.out.println(); }// END: printArray public static void printArray(double[] x) { for (int i = 0; i < x.length; i++) { System.out.print(x[i] + " "); } System.out.println(); }// END: printArray public static void printArray(boolean[] x) { for (int i = 0; i < x.length; i++) { System.out.print(x[i] + " "); } System.out.println(); } public static void printArray(String[] x) { for (int i = 0; i < x.length; i++) { System.out.println(x[i]); } }// END: printArray public static void print2DArray(double[][] array) { for (int row = 0; row < array.length; row++) { for (int col = 0; col < array[row].length; col++) { System.out.print(array[row][col] + " "); } System.out.print("\n"); } }// END: print2DArray public static void print2DArray(int[][] array) { for (int row = 0; row < array.length; row++) { for (int col = 0; col < array[row].length; col++) { System.out.print(array[row][col] + " "); } System.out.print("\n"); } }// END: print2DArray public static void print2Arrays(int[] array1, double[] array2, int nrow) { for (int row = 0; row < nrow; row++) { System.out.print(array1[row] + " " + array2[row] + " "); System.out.print("\n"); } }// END: print2DArray public static void print2DArray(double[][] array, int formatEvery) { int i = 0; for (int row = 0; row < array.length; row++) { for (int col = 0; col < array[row].length; col++) { if (i == formatEvery) { System.out.print("\n"); i = 0; } System.out.print(array[row][col] + " "); i++; } System.out.print("\n"); } }// END: print2DArray public static void printBranchSubstitutionModel(PartitionData data) { System.out.print("\tBranch Substitution model: "); System.out.print(branchSubstitutionModelToString(data)); System.out.print("\n"); }// END: printBranchSubstitutionModel public static void printClockRateModel(PartitionData data) { System.out.print("\tClock rate model: "); System.out.print(clockRateModelToString(data)); System.out.print("\n"); }// END: printClockRateModel public static void printFrequencyModel(PartitionData data) { System.out.print("\tFrequency model: "); System.out.print(frequencyModelToString(data)); System.out.print("\n"); }// END: printFrequencyModel public static void printSiteRateModel(PartitionData data) { System.out.print("\tSite rate model: "); System.out.print(siteRateModelToString(data)); System.out.print("\n"); }// END: printFrequencyModel public static void printDemographicModel(PartitionData data) { System.out.print("\tDemographic model: "); System.out.print(demographicModelToString(data)); System.out.print("\n"); }// END: printFrequencyModel private static void printDataType(PartitionData data) { System.out.print("\tData type: "); System.out.print(dataTypeToString(data)); System.out.print("\n"); }// END: printDataType public static void printTaxaSet(Taxa taxa) { for (int i = 0; i < taxa.getTaxonCount(); i++) { Taxon taxon = taxa.getTaxon(i); System.out.print("\t\t " + taxonToString(taxon, false) + ("\n")); } }// END: printTaxaSet public static void printTree(TreesTableRecord record) { System.out.print(record.getTree().toString()); System.out.print("\n"); }// END: printTree public static void printRecord(TreesTableRecord record) { if (record == null) { System.out.println("\tRecord: NOT SET"); } else if (record.isTreeSet()) { System.out.print("\t" + record.getName() + ": "); printTree(record); } else if (record.isTaxaSet()) { System.out.println("\t" + record.getName() + ":"); printTaxaSet(record.getTaxa()); } else { // } }// END: printRecord public static void printRecords(PartitionDataList dataList) { for (TreesTableRecord record : dataList.recordsList) { printRecord(record); } // END: record loop }// END: printRecords public static void printPartitionData(PartitionData data) { printRecord(data.record); printDataType(data); printDemographicModel(data); System.out.println("\tFrom: " + data.from); System.out.println("\tTo: " + data.to); System.out.println("\tEvery: " + data.every); printBranchSubstitutionModel(data); printSiteRateModel(data); printClockRateModel(data); printFrequencyModel(data); }// END: printPartitionData public static void printPartitionDataList(PartitionDataList dataList) { // System.out.println(dataList.get(0).from + " " + // dataList.get(1).from); if (BeagleSequenceSimulatorApp.DEBUG) { System.out.println("Possible records: "); printRecords(dataList); } System.out.println("\tSite count: " + getSiteCount(dataList)); System.out.println("\tOutput type: " + dataList.outputFormat); if (dataList.setSeed) { System.out.println("\tStarting seed: " + dataList.startingSeed); } int row = 1; for (PartitionData data : dataList) { System.out.println("Partition: " + row); printPartitionData(data); row++; } // END: data list loop }// END: printDataList public static void printTaxonList(PartitionDataList dataList) { System.out.println(taxaToString(dataList.allTaxa, true)); }// END: printTaxonList public static Sequence intArray2Sequence(Taxon taxon, int[] seq, int gapFlag, DataType dataType) { StringBuilder sSeq = new StringBuilder(); int partitionSiteCount = seq.length; if (dataType instanceof Codons) { for (int i = 0; i < partitionSiteCount; i++) { int state = seq[i]; if (state == gapFlag) { sSeq.append(dataType.getTriplet(dataType.getGapState())); } else { sSeq.append(dataType.getTriplet(seq[i])); } // END: gap check } // END: replications loop } else { for (int i = 0; i < partitionSiteCount; i++) { int state = seq[i]; if (state == gapFlag) { sSeq.append(dataType.getCode(dataType.getGapState())); } else { sSeq.append(dataType.getCode(seq[i])); } // END: gap check } // END: replications loop } // END: dataType check return new Sequence(taxon, sSeq.toString()); }// END: intArray2Sequence // ////////////////////// // ---TOSTRING UTILS---// // ////////////////////// public static String taxonToString(Taxon taxon, boolean printNames) { String string = null; if (printNames) { string = taxon.getId() + " (" + taxon.getAttribute(Utils.ABSOLUTE_HEIGHT) + "," + taxon.getAttribute(Utils.TREE_FILENAME) + ")"; } else { string = taxon.getId() + " (" + taxon.getAttribute(Utils.ABSOLUTE_HEIGHT) + ")"; } return string; }// END: taxonToString public static String taxaToString(Taxa taxa, boolean printNames) { String string = ""; for (int i = 0; i < taxa.getTaxonCount(); i++) { Taxon taxon = taxa.getTaxon(i); string += taxonToString(taxon, printNames) + ("\n"); } return string; }// END: taxaToString public static String partitionDataToString(PartitionData data, TreeModel simulatedTreeModel // , LinkedHashMap<NodeRef, int[]> sequencesMap ) { String string = ""; // if (data.record.isTreeSet()) { // // string += ("Tree: " + data.record.getTree().toString())+ ("\n"); // // } else if (data.record.isTaxaSet()) { // // string += ("Taxa Set: \n" + taxaToString(data.record.getTaxa(), // false));//+ ("\n"); // // } else { // // // } string += ("Tree model: " + simulatedTreeModel.toString()) + ("\n"); // string += ("Tree model: " // +annotatedTreeModelToString(simulatedTreeModel, sequencesMap, // data.createDataType()) ) + ("\n"); string += ("From: " + data.from) + ("\n"); string += ("To: " + data.to) + ("\n"); string += ("Every: " + data.every) + ("\n"); string += ("Data type: ") + dataTypeToString(data) + ("\n"); string += ("Demographic model: ") + demographicModelToString(data) + ("\n"); string += ("Branch Substitution model: ") + branchSubstitutionModelToString(data) + ("\n"); string += ("Frequency model: ") + frequencyModelToString(data) + ("\n"); string += ("Site Rate model: ") + siteRateModelToString(data) + ("\n"); string += ("Clock Rate model: ") + clockRateModelToString(data) + ("\n"); return string; }// END: partitionDataToString public static String partitionDataListToString(PartitionDataList dataList, // ArrayList<TreeModel> simulatedTreeModelList // ,LinkedHashMap<Integer,LinkedHashMap<NodeRef, int[]>> // partitionSequencesMap ) { String string = ""; TreeModel simulatedTreeModel; // LinkedHashMap<NodeRef, int[]> sequencesMap; string += ("Site count: " + getSiteCount(dataList)) + ("\n"); if (dataList.setSeed) { string += ("Starting seed: " + dataList.startingSeed) + ("\n"); } int row = 0; for (PartitionData data : dataList) { simulatedTreeModel = simulatedTreeModelList.get(row); // sequencesMap = partitionSequencesMap.get(row); string += ("Partition: " + (row + 1)) + ("\n"); string += partitionDataToString(data, simulatedTreeModel // , sequencesMap ); string += ("\n"); row++; } // END: data list loop return string; }// END: partitionDataListToString // TODO: doesn't work public static String annotatedTreeModelToString(TreeModel treeModel, LinkedHashMap<NodeRef, int[]> sequencesMap, DataType dataType) { StringBuffer buffer = new StringBuffer(); NumberFormat format = NumberFormat.getNumberInstance(Locale.ENGLISH); boolean useTipLabels = true; AncestralSequenceTrait ancestralSequence = new AncestralSequenceTrait(sequencesMap, dataType); TreeTraitProvider[] treeTraitProviders = new TreeTraitProvider[] { ancestralSequence }; TreeUtils.newick(treeModel, // treeModel.getRoot(), // useTipLabels, // TreeUtils.BranchLengthType.LENGTHS_AS_TIME, // format, // null, // treeTraitProviders, // null, buffer); return buffer.toString(); } private static String dataTypeToString(PartitionData data) { String string = PartitionData.dataTypes[data.dataTypeIndex]; return string; } public static String demographicModelToString(PartitionData data) { String string = PartitionData.demographicModels[data.demographicModelIndex]; string += (" ( "); for (int i = 0; i < PartitionData.demographicParameterIndices[data.demographicModelIndex].length; i++) { string += data.demographicParameterValues[PartitionData.demographicParameterIndices[data.demographicModelIndex][i]]; string += " "; } // END: indices loop string += ")"; return string; } public static String clockRateModelToString(PartitionData data) { String string = PartitionData.clockModels[data.clockModelIndex]; string += (" ( "); for (int i = 0; i < PartitionData.clockParameterIndices[data.clockModelIndex].length; i++) { string += data.clockParameterValues[PartitionData.clockParameterIndices[data.clockModelIndex][i]]; string += " "; } // END: indices loop string += ")"; if (data.clockModelIndex == data.LRC_INDEX) { String space = (data.lrcParametersInRealSpace == true ? "real" : "log"); string += " ( " + "Parameters in " + space + " space )"; } return string; } public static String frequencyModelToString(PartitionData data) { String string = PartitionData.frequencyModels[data.frequencyModelIndex]; string += (" ( "); for (int i = 0; i < data.frequencyParameterIndices[data.frequencyModelIndex].length; i++) { string += data.frequencyParameterValues[data.frequencyParameterIndices[data.frequencyModelIndex][i]]; string += " "; } // END: indices loop string += ")"; return string; } public static String branchSubstitutionModelToString(PartitionData data) { String string = PartitionData.substitutionModels[data.substitutionModelIndex]; string += (" ( "); for (int i = 0; i < PartitionData.substitutionParameterIndices[data.substitutionModelIndex].length; i++) { string += data.substitutionParameterValues[PartitionData.substitutionParameterIndices[data.substitutionModelIndex][i]]; string += " "; } // END: indices loop string += ")"; return string; } public static String siteRateModelToString(PartitionData data) { String string = PartitionData.siteRateModels[data.siteRateModelIndex]; string += (" ( "); for (int i = 0; i < PartitionData.siteRateModelParameterIndices[data.siteRateModelIndex].length; i++) { string += data.siteRateModelParameterValues[PartitionData.siteRateModelParameterIndices[data.siteRateModelIndex][i]]; string += " "; } // END: indices loop string += ")"; return string; } public static String demographyModelToString(PartitionData data) { String string = PartitionData.demographicModels[data.demographicModelIndex]; string += (" ( "); for (int i = 0; i < PartitionData.demographicParameterIndices[data.demographicModelIndex].length; i++) { string += data.demographicParameterValues[PartitionData.demographicParameterIndices[data.demographicModelIndex][i]]; string += " "; } // END: indices loop string += ")"; return string; } }// END: class