Import Debian changes 0.6.0-1

elki (0.6.0-1) unstable; urgency=low

  * New upstream final.
  * 3DPC extension is not included, but may be uploaded as a separate
    package when there is actual need (it is a demo software, not meant
    for use outside of research, so just get the source code!)
  * Upgrade to policy 3.9.5.0 (no changes)

1 files changed, 27 insertions, 124 deletions

diff --git a/src/de/lmu/ifi/dbs/elki/datasource/parser/AbstractParser.java b/src/de/lmu/ifi/dbs/elki/datasource/parser/AbstractParser.java
index 1e689638..e8201db1 100644
--- a/src/de/lmu/ifi/dbs/elki/datasource/parser/AbstractParser.java
+++ b/src/de/lmu/ifi/dbs/elki/datasource/parser/AbstractParser.java
@@ -23,15 +23,11 @@ package de.lmu.ifi.dbs.elki.datasource.parser;
  along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-import java.util.ArrayList;
-import java.util.List;
-import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
 import de.lmu.ifi.dbs.elki.logging.Logging;
 import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer;
 import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID;
-import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.StringLengthConstraint;
 import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization;
 import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.PatternParameter;
 import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.StringParameter;
@@ -41,6 +37,9 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.StringParameter;
  * options.
  * 
  * @author Arthur Zimek
+ * @author Erich Schubert
+ * 
+ * @apiviz.composedOf Tokenizer
  */
 public abstract class AbstractParser {
   /**
@@ -51,7 +50,7 @@ public abstract class AbstractParser {
   /**
    * A quote pattern
    */
-  public static final char QUOTE_CHAR = '\"';
+  public static final String QUOTE_CHARS = "\"'";
 
   /**
    * A pattern catching most numbers that can be parsed using
@@ -73,96 +72,38 @@ public abstract class AbstractParser {
   public static final String ATTRIBUTE_CONCATENATION = " ";
 
   /**
-   * Stores the column separator pattern
-   */
-  private Pattern colSep = null;
-
-  /**
-   * Stores the quotation character
+   * Comment pattern.
    */
-  protected char quoteChar = QUOTE_CHAR;
+  protected Pattern comment = null;
 
   /**
-   * Comment pattern.
+   * String tokenizer.
    */
-  protected Pattern comment = null;
+  protected Tokenizer tokenizer;
 
   /**
    * Constructor.
    * 
    * @param colSep Column separator
-   * @param quoteChar Quote character
+   * @param quoteChars Quote character
    * @param comment Comment pattern
    */
-  public AbstractParser(Pattern colSep, char quoteChar, Pattern comment) {
+  public AbstractParser(Pattern colSep, String quoteChars, Pattern comment) {
     super();
-    this.colSep = colSep;
-    this.quoteChar = quoteChar;
+    this.tokenizer = new Tokenizer(colSep, quoteChars);
     this.comment = comment;
   }
 
-  /**
-   * Tokenize a string. Works much like colSep.split() except it honors
-   * quotation characters.
-   * 
-   * @param input Input string
-   * @return Tokenized string
-   */
-  protected List<String> tokenize(String input) {
-    ArrayList<String> matchList = new ArrayList<>();
-    Matcher m = colSep.matcher(input);
-
-    int index = 0;
-    boolean inquote = (input.length() > 0) && (input.charAt(0) == quoteChar);
-    while (m.find()) {
-      // Quoted code path vs. regular code path
-      if (inquote && m.start() > 0) {
-        // Closing quote found?
-        if (m.start() > index + 1 && input.charAt(m.start() - 1) == quoteChar) {
-          // Strip quote characters
-          if (index + 1 < m.start() - 1) {
-            matchList.add(input.substring(index + 1, m.start() - 1));
-          }
-          // Seek past
-          index = m.end();
-          // new quote?
-          inquote = (index < input.length()) && (input.charAt(index) == quoteChar);
-        }
-      } else {
-        // Add match before separator
-        if (index < m.start()) {
-          matchList.add(input.substring(index, m.start()));
-        }
-        // Seek past separator
-        index = m.end();
-        // new quote?
-        inquote = (index < input.length()) && (input.charAt(index) == quoteChar);
+  public static int lengthWithoutLinefeed(String line) {
+    int length = line.length();
+    while(length > 0) {
+      char last = line.charAt(length - 1);
+      if(last != '\n' && last != '\r') {
+        break;
       }
+      --length;
     }
-    // Nothing found - return original string.
-    if (index == 0) {
-      matchList.add(input);
-      return matchList;
-    }
-    // Add tail after last separator.
-    if (inquote) {
-      if (input.charAt(input.length() - 1) == quoteChar) {
-        if (index + 1 < input.length() - 1) {
-          matchList.add(input.substring(index + 1, input.length() - 1));
-        }
-      } else {
-        getLogger().warning("Invalid quoted line in input: no closing quote found in: " + input);
-        if (index < input.length()) {
-          matchList.add(input.substring(index, input.length()));
-        }
-      }
-    } else {
-      if (index < input.length()) {
-        matchList.add(input.substring(index, input.length()));
-      }
-    }
-    // Return
-    return matchList;
+    return length;
   }
 
   /**
@@ -183,43 +124,6 @@ public abstract class AbstractParser {
   }
 
   /**
-   * Utility function, which is a bit more robust wrt. parsing double values. In
-   * particular: infinite values, and creates fewer objects.
-   * 
-   * @param s String s
-   * @return parsed value
-   * @throws NumberFormatException
-   */
-  public static double parseDouble(String s) throws NumberFormatException {
-    try {
-      return Double.parseDouble(s);
-    } catch (NumberFormatException e) {
-      int len = s.length();
-      if (len > 0) {
-        int p = 0;
-        char cur = s.charAt(p);
-        boolean isNegative = cur == '-';
-        if (isNegative && ++p < len) {
-          cur = s.charAt(p);
-        }
-        if (cur == '∞') {
-          return isNegative ? Double.NEGATIVE_INFINITY : Double.POSITIVE_INFINITY;
-        }
-        if (len - p == 3 && "Inf".regionMatches(true, 0, s, p, 3)) {
-          return isNegative ? Double.NEGATIVE_INFINITY : Double.POSITIVE_INFINITY;
-        }
-        if (len - p == 8 && "Infinity".regionMatches(true, 0, s, p, 8)) {
-          return isNegative ? Double.NEGATIVE_INFINITY : Double.POSITIVE_INFINITY;
-        }
-        if (len == 3 && "NaN".equalsIgnoreCase(s)) {
-          return Double.NaN;
-        }
-      }
-      throw e;
-    }
-  }
-
-  /**
    * Parameterization class.
    * 
    * @author Erich Schubert
@@ -235,9 +139,9 @@ public abstract class AbstractParser {
 
     /**
      * OptionID for the quote character parameter (defaults to a double
-     * quotation mark as in {@link #QUOTE_CHAR}.
+     * quotation mark as in {@link AbstractParser#QUOTE_CHARS}.
      */
-    public static final OptionID QUOTE_ID = new OptionID("parser.quote", "Quotation character. The default is to use a double quote.");
+    public static final OptionID QUOTE_ID = new OptionID("parser.quote", "Quotation characters. By default, both double and single ASCII quotes are accepted.");
 
     /**
      * Comment pattern.
@@ -252,7 +156,7 @@ public abstract class AbstractParser {
     /**
      * Stores the quotation character
      */
-    protected char quoteChar = QUOTE_CHAR;
+    protected String quoteChars = QUOTE_CHARS;
 
     /**
      * Comment pattern.
@@ -263,16 +167,15 @@ public abstract class AbstractParser {
     protected void makeOptions(Parameterization config) {
       super.makeOptions(config);
       PatternParameter colParam = new PatternParameter(COLUMN_SEPARATOR_ID, DEFAULT_SEPARATOR);
-      if (config.grab(colParam)) {
+      if(config.grab(colParam)) {
         colSep = colParam.getValue();
       }
-      StringParameter quoteParam = new StringParameter(QUOTE_ID, String.valueOf(QUOTE_CHAR));
-      quoteParam.addConstraint(new StringLengthConstraint(1, 1));
-      if (config.grab(quoteParam)) {
-        quoteChar = quoteParam.getValue().charAt(0);
+      StringParameter quoteParam = new StringParameter(QUOTE_ID, QUOTE_CHARS);
+      if(config.grab(quoteParam)) {
+        quoteChars = quoteParam.getValue();
       }
       PatternParameter commentP = new PatternParameter(COMMENT_ID, COMMENT_PATTERN);
-      if (config.grab(commentP)) {
+      if(config.grab(commentP)) {
         comment = commentP.getValue();
       }
     }