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diff --git a/src/de/lmu/ifi/dbs/elki/distance/distancefunction/external/AsciiDistanceParser.java b/src/de/lmu/ifi/dbs/elki/distance/distancefunction/external/AsciiDistanceParser.java
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+package de.lmu.ifi.dbs.elki.distance.distancefunction.external;
+
+/*
+ This file is part of ELKI:
+ Environment for Developing KDD-Applications Supported by Index-Structures
+
+ Copyright (C) 2014
+ Ludwig-Maximilians-Universität München
+ Lehr- und Forschungseinheit für Datenbanksysteme
+ ELKI Development Team
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Affero General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program 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 Affero General Public License for more details.
+
+ You should have received a copy of the GNU Affero General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.regex.Pattern;
+
+import de.lmu.ifi.dbs.elki.datasource.parser.AbstractParser;
+import de.lmu.ifi.dbs.elki.logging.Logging;
+import de.lmu.ifi.dbs.elki.logging.progress.IndefiniteProgress;
+import de.lmu.ifi.dbs.elki.utilities.documentation.Description;
+import de.lmu.ifi.dbs.elki.utilities.documentation.Title;
+import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization;
+
+/**
+ * Parser for parsing one distance value per line.
+ *
+ * A line must have the following format: {@code id1 id2 distanceValue}, where
+ * id1 and id2 are integers representing the two ids belonging to the distance
+ * value. Lines starting with &quot;#&quot; will be ignored.
+ *
+ * @author Elke Achtert
+ * @author Erich Schubert
+ */
+@Title("Number Distance Parser")
+@Description("Parser for the following line format:\n" //
+ + "id1 id2 distanceValue, where id1 and is2 are integers representing the two ids belonging to the distance value.\n" //
+ + "The ids and the distance value are separated by whitespace. Empty lines and lines beginning with \"#\" will be ignored.")
+public class AsciiDistanceParser extends AbstractParser implements DistanceParser {
+ /**
+ * The logger for this class.
+ */
+ private static final Logging LOG = Logging.getLogger(AsciiDistanceParser.class);
+
+ /**
+ * Constructor.
+ *
+ * @param colSep Column separator pattern
+ * @param quoteChars Quote characters
+ * @param comment Comment pattern
+ */
+ public AsciiDistanceParser(Pattern colSep, String quoteChars, Pattern comment) {
+ super(colSep, quoteChars, comment);
+ }
+
+ @Override
+ public void parse(InputStream in, DistanceCacheWriter cache) {
+ BufferedReader reader = new BufferedReader(new InputStreamReader(in));
+ int lineNumber = 1;
+
+ int min = Integer.MAX_VALUE, max = Integer.MIN_VALUE;
+ IndefiniteProgress prog = LOG.isVerbose() ? new IndefiniteProgress("Parsing distance matrix", LOG) : null;
+ try {
+ for(String line; (line = reader.readLine()) != null; lineNumber++) {
+ LOG.incrementProcessed(prog);
+ // Skip empty lines and comments
+ if(line.length() <= 0 || isComment(line)) {
+ continue;
+ }
+ tokenizer.initialize(line, 0, lengthWithoutLinefeed(line));
+
+ if(!tokenizer.valid()) {
+ throw new IllegalArgumentException("Less than three values in line " + lineNumber);
+ }
+ int id1, id2;
+ try {
+ id1 = (int) tokenizer.getLongBase10();
+ tokenizer.advance();
+ }
+ catch(NumberFormatException e) {
+ throw new IllegalArgumentException("Error in line " + lineNumber + ": id1 is not an integer!");
+ }
+ if(!tokenizer.valid()) {
+ throw new IllegalArgumentException("Less than three values in line " + lineNumber);
+ }
+
+ try {
+ id2 = (int) tokenizer.getLongBase10();
+ tokenizer.advance();
+ }
+ catch(NumberFormatException e) {
+ throw new IllegalArgumentException("Error in line " + lineNumber + ": id2 is not an integer!");
+ }
+ if(!tokenizer.valid()) {
+ throw new IllegalArgumentException("Less than three values in line " + lineNumber);
+ }
+
+ // Track minimum and maximum
+ if(id1 < id2) {
+ min = (id1 < min) ? id1 : min;
+ max = (id2 > min) ? id2 : max;
+ }
+ else {
+ min = (id2 < min) ? id2 : min;
+ max = (id1 > min) ? id1 : max;
+ }
+
+ try {
+ double distance = tokenizer.getDouble();
+ cache.put(id1, id2, distance);
+ }
+ catch(IllegalArgumentException e) {
+ throw new IllegalArgumentException("Error in line " + lineNumber + ":" + e.getMessage(), e);
+ }
+ tokenizer.advance();
+ if(tokenizer.valid()) {
+ throw new IllegalArgumentException("More than three values in line " + lineNumber);
+ }
+ }
+ }
+ catch(IOException e) {
+ throw new IllegalArgumentException("Error while parsing line " + lineNumber + ".");
+ }
+
+ LOG.setCompleted(prog);
+
+ // check if all distance values are specified
+ for(int i1 = min; i1 <= max; i1++) {
+ for(int i2 = i1 + 1; i2 <= max; i2++) {
+ if(!cache.containsKey(i1, i2)) {
+ throw new IllegalArgumentException("Distance value for " + i1 + " to " + i2 + " is missing!");
+ }
+ }
+ }
+ }
+
+ @Override
+ protected Logging getLogger() {
+ return LOG;
+ }
+
+ /**
+ * Parameterization class.
+ *
+ * @author Erich Schubert
+ *
+ * @apiviz.exclude
+ */
+ public static class Parameterizer extends AbstractParser.Parameterizer {
+ @Override
+ protected void makeOptions(Parameterization config) {
+ super.makeOptions(config);
+ }
+
+ @Override
+ protected AsciiDistanceParser makeInstance() {
+ return new AsciiDistanceParser(colSep, quoteChars, comment);
+ }
+ }
+}