1 files changed, 0 insertions, 252 deletions
diff --git a/src/de/lmu/ifi/dbs/elki/distance/distancefunction/external/NumberDistanceParser.java b/src/de/lmu/ifi/dbs/elki/distance/distancefunction/external/NumberDistanceParser.java
deleted file mode 100644
index b8e720ab..00000000
--- a/src/de/lmu/ifi/dbs/elki/distance/distancefunction/external/NumberDistanceParser.java
+++ /dev/null
@@ -1,252 +0,0 @@
-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) 2013
- 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.HashMap;
-import java.util.Map;
-import java.util.regex.Pattern;
-
-import de.lmu.ifi.dbs.elki.database.ids.DBID;
-import de.lmu.ifi.dbs.elki.database.ids.DBIDIter;
-import de.lmu.ifi.dbs.elki.database.ids.DBIDPair;
-import de.lmu.ifi.dbs.elki.database.ids.DBIDRef;
-import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil;
-import de.lmu.ifi.dbs.elki.database.ids.ModifiableDBIDs;
-import de.lmu.ifi.dbs.elki.datasource.parser.AbstractParser;
-import de.lmu.ifi.dbs.elki.distance.distancevalue.Distance;
-import de.lmu.ifi.dbs.elki.distance.distancevalue.DoubleDistance;
-import de.lmu.ifi.dbs.elki.distance.distancevalue.NumberDistance;
-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;
-import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter;
-
-/**
- * Provides a parser for parsing one distance value per line.
- * <p/>
- * A line must have the following format: 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
- * 
- * @apiviz.has NumberDistance
- * 
- * @param <D> distance type
- */
-@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 NumberDistanceParser<D extends NumberDistance<D, ?>> extends AbstractParser implements DistanceParser<D> {
-  /**
-   * The logger for this class.
-   */
-  private static final Logging LOG = Logging.getLogger(NumberDistanceParser.class);
-
-  /**
-   * The distance function.
-   */
-  private final D distanceFactory;
-
-  /**
-   * Constructor.
-   * 
-   * @param colSep Column separator pattern
-   * @param quoteChars Quote characters
-   * @param comment Comment pattern
-   * @param distanceFactory Distance factory to use
-   */
-  public NumberDistanceParser(Pattern colSep, String quoteChars, Pattern comment, D distanceFactory) {
-    super(colSep, quoteChars, comment);
-    this.distanceFactory = distanceFactory;
-  }
-
-  @Override
-  public DistanceParsingResult<D> parse(InputStream in) {
-    BufferedReader reader = new BufferedReader(new InputStreamReader(in));
-    int lineNumber = 0;
-
-    IndefiniteProgress prog = LOG.isVerbose() ? new IndefiniteProgress("Parsing distance matrix", LOG) : null;
-    ModifiableDBIDs ids = DBIDUtil.newHashSet();
-    Map<DBIDPair, D> distanceCache = new HashMap<>();
-    try {
-      for(String line; (line = reader.readLine()) != null; lineNumber++) {
-        if(prog != null) {
-          prog.incrementProcessed(LOG);
-        }
-        // Skip empty lines and comments
-        if(line.length() <= 0 || (comment != null && comment.matcher(line).matches())) {
-          continue;
-        }
-        tokenizer.initialize(line, 0, lengthWithoutLinefeed(line));
-
-        if(!tokenizer.valid()) {
-          throw new IllegalArgumentException("Less than three values in line " + lineNumber);
-        }
-        DBID id1, id2;
-        try {
-          id1 = DBIDUtil.importInteger((int) tokenizer.getLongBase10());
-          tokenizer.advance();
-        }
-        catch(NumberFormatException e) {
-          throw new IllegalArgumentException("Error in line " + lineNumber + ": id1 is no integer!");
-        }
-        if(!tokenizer.valid()) {
-          throw new IllegalArgumentException("Less than three values in line " + lineNumber);
-        }
-
-        try {
-          id2 = DBIDUtil.importInteger((int) tokenizer.getLongBase10());
-          tokenizer.advance();
-        }
-        catch(NumberFormatException e) {
-          throw new IllegalArgumentException("Error in line " + lineNumber + ": id2 is no integer!");
-        }
-        if(!tokenizer.valid()) {
-          throw new IllegalArgumentException("Less than three values in line " + lineNumber);
-        }
-
-        try {
-          final D distance;
-          if(distanceFactory == DoubleDistance.FACTORY) {
-            @SuppressWarnings("unchecked")
-            D dist = (D) DoubleDistance.FACTORY.fromDouble(tokenizer.getDouble());
-            distance = dist;
-          }
-          else {
-            distance = distanceFactory.parseString(tokenizer.getSubstring());
-          }
-          tokenizer.advance();
-          put(id1, id2, distance, distanceCache);
-          ids.add(id1);
-          ids.add(id2);
-        }
-        catch(IllegalArgumentException e) {
-          throw new IllegalArgumentException("Error in line " + lineNumber + ":" + e.getMessage(), e);
-        }
-        if(tokenizer.valid()) {
-          throw new IllegalArgumentException("More than three values in line " + lineNumber);
-        }
-      }
-    }
-    catch(IOException e) {
-      throw new IllegalArgumentException("Error while parsing line " + lineNumber + ".");
-    }
-
-    if(prog != null) {
-      prog.setCompleted(LOG);
-    }
-
-    // check if all distance values are specified
-    for(DBIDIter iter = ids.iter(); iter.valid(); iter.advance()) {
-      for(DBIDIter iter2 = ids.iter(); iter2.valid(); iter2.advance()) {
-        if(DBIDUtil.compare(iter2, iter) <= 0) {
-          continue;
-        }
-        if(!containsKey(iter, iter2, distanceCache)) {
-          throw new IllegalArgumentException("Distance value for " + DBIDUtil.toString(iter) + " - " + DBIDUtil.toString(iter2) + " is missing!");
-        }
-      }
-    }
-    return new DistanceParsingResult<>(distanceCache);
-  }
-
-  /**
-   * Puts the specified distance value for the given ids to the distance cache.
-   * 
-   * @param id1 the first id
-   * @param id2 the second id
-   * @param distance the distance value
-   * @param cache the distance cache
-   */
-  private void put(DBID id1, DBID id2, D distance, Map<DBIDPair, D> cache) {
-    // the smaller id is the first key
-    if(DBIDUtil.compare(id1, id2) > 0) {
-      put(id2, id1, distance, cache);
-      return;
-    }
-
-    D oldDistance = cache.put(DBIDUtil.newPair(id1, id2), distance);
-
-    if(oldDistance != null) {
-      throw new IllegalArgumentException("Distance value for specified ids is already assigned!");
-    }
-  }
-
-  /**
-   * Returns <tt>true</tt> if the specified distance cache contains a distance
-   * value for the specified ids.
-   * 
-   * @param id1 the first id
-   * @param id2 the second id
-   * @param cache the distance cache
-   * @return <tt>true</tt> if this cache contains a distance value for the
-   *         specified ids, false otherwise
-   */
-  public boolean containsKey(DBIDRef id1, DBIDRef id2, Map<DBIDPair, D> cache) {
-    if(DBIDUtil.compare(id1, id2) > 0) {
-      return containsKey(id2, id1, cache);
-    }
-
-    return cache.containsKey(DBIDUtil.newPair(id1, id2));
-  }
-
-  @Override
-  protected Logging getLogger() {
-    return LOG;
-  }
-
-  /**
-   * Parameterization class.
-   * 
-   * @author Erich Schubert
-   * 
-   * @apiviz.exclude
-   */
-  public static class Parameterizer<D extends NumberDistance<D, ?>> extends AbstractParser.Parameterizer {
-    /**
-     * The distance function.
-     */
-    protected D distanceFactory;
-
-    @Override
-    protected void makeOptions(Parameterization config) {
-      super.makeOptions(config);
-      ObjectParameter<D> distFuncP = new ObjectParameter<>(DISTANCE_ID, Distance.class);
-      if(config.grab(distFuncP)) {
-        distanceFactory = distFuncP.instantiateClass(config);
-      }
-    }
-
-    @Override
-    protected NumberDistanceParser<D> makeInstance() {
-      return new NumberDistanceParser<>(colSep, quoteChars, comment, distanceFactory);
-    }
-  }
-}