Revision: 17595
          http://sourceforge.net/p/gate/code/17595
Author:   markagreenwood
Date:     2014-03-08 13:05:32 +0000 (Sat, 08 Mar 2014)
Log Message:
-----------
the pre-lunch checkin of generics and serialVersionUID updates

Modified Paths:
--------------
    gate/trunk/src/main/gate/creole/splitter/RegexSentenceSplitter.java
    gate/trunk/src/main/gate/creole/splitter/SentenceSplitter.java
    gate/trunk/src/main/gate/creole/tokeniser/DFSMState.java
    gate/trunk/src/main/gate/creole/tokeniser/DefaultTokeniser.java
    gate/trunk/src/main/gate/creole/tokeniser/FSMState.java
    gate/trunk/src/main/gate/creole/tokeniser/InvalidRuleException.java
    gate/trunk/src/main/gate/creole/tokeniser/SimpleTokeniser.java
    gate/trunk/src/main/gate/creole/tokeniser/TokeniserException.java
    gate/trunk/src/main/gate/creole/tokeniser/UnicodeType.java
    gate/trunk/src/main/gate/email/EmailDocumentHandler.java
    gate/trunk/src/main/gate/event/AnnotationEvent.java
    gate/trunk/src/main/gate/event/AnnotationSetEvent.java
    gate/trunk/src/main/gate/event/ControllerEvent.java
    gate/trunk/src/main/gate/event/CorpusEvent.java
    gate/trunk/src/main/gate/event/CreoleEvent.java
    gate/trunk/src/main/gate/event/DatastoreEvent.java
    gate/trunk/src/main/gate/event/DocumentEvent.java
    gate/trunk/src/main/gate/event/GateEvent.java
    gate/trunk/src/main/gate/event/ObjectModificationEvent.java
    gate/trunk/src/main/gate/event/ProgressListenerAdaptor.java
    gate/trunk/src/main/gate/fsm/FSM.java
    gate/trunk/src/main/gate/fsm/FSMInstance.java
    gate/trunk/src/main/gate/fsm/State.java
    gate/trunk/src/main/gate/fsm/Transition.java
    gate/trunk/src/main/gate/jape/PrioritisedRuleList.java

Modified: gate/trunk/src/main/gate/creole/splitter/RegexSentenceSplitter.java
===================================================================
--- gate/trunk/src/main/gate/creole/splitter/RegexSentenceSplitter.java 
2014-03-08 12:07:09 UTC (rev 17594)
+++ gate/trunk/src/main/gate/creole/splitter/RegexSentenceSplitter.java 
2014-03-08 13:05:32 UTC (rev 17595)
@@ -18,6 +18,8 @@
 import java.util.*;
 import java.util.regex.*;
 
+import org.apache.commons.io.IOUtils;
+
 import gate.*;
 import gate.creole.*;
 import gate.creole.metadata.CreoleParameter;
@@ -101,22 +103,30 @@
   protected Pattern nonSplitsPattern;
 
   protected Pattern compilePattern(URL paternsListUrl, String encoding)
-    throws UnsupportedEncodingException, IOException{
-    BufferedReader reader = new 
BomStrippingInputStreamReader(paternsListUrl.openStream(), encoding);
+          throws UnsupportedEncodingException, IOException {
+    BufferedReader reader = null;
     StringBuffer patternString = new StringBuffer();
+    
+    try {
+      reader =
+              new BomStrippingInputStreamReader(paternsListUrl.openStream(),
+                      encoding);
+      
+      String line = reader.readLine();
+      while(line != null) {
+        line = line.trim();
 
-    String line = reader.readLine();
-    while(line != null){
-      line = line.trim();
-
-      if(line.length() == 0 || line.startsWith("//")){
-        //ignore empty lines and comments
-      }else{
-        if(patternString.length() > 0) patternString.append("|");
-        patternString.append("(?:" + line + ")");
+        if(line.length() == 0 || line.startsWith("//")) {
+          // ignore empty lines and comments
+        } else {
+          if(patternString.length() > 0) patternString.append("|");
+          patternString.append("(?:" + line + ")");
+        }
+        // move to next line
+        line = reader.readLine();
       }
-      //move to next line
-      line = reader.readLine();
+    } finally {
+      IOUtils.closeQuietly(reader);
     }
     return Pattern.compile(patternString.toString());
   }

Modified: gate/trunk/src/main/gate/creole/splitter/SentenceSplitter.java
===================================================================
--- gate/trunk/src/main/gate/creole/splitter/SentenceSplitter.java      
2014-03-08 12:07:09 UTC (rev 17594)
+++ gate/trunk/src/main/gate/creole/splitter/SentenceSplitter.java      
2014-03-08 13:05:32 UTC (rev 17595)
@@ -46,6 +46,8 @@
 @CreoleResource(name="ANNIE Sentence Splitter", comment="ANNIE sentence 
splitter.", helpURL="http://gate.ac.uk/userguide/sec:annie:splitter";, 
icon="sentence-splitter")
 public class SentenceSplitter extends AbstractLanguageAnalyser implements 
Benchmarkable{
 
+  private static final long serialVersionUID = -5335682060379173111L;
+
   public static final String
     SPLIT_DOCUMENT_PARAMETER_NAME = "document";
 
@@ -314,9 +316,6 @@
     this.benchmarkId = benchmarkId;
   }
 
-
-
-  private static final boolean DEBUG = false;
   private String inputASName;
   private String outputASName;
 }//public class SentenceSplitter extends Nerc

Modified: gate/trunk/src/main/gate/creole/tokeniser/DFSMState.java
===================================================================
--- gate/trunk/src/main/gate/creole/tokeniser/DFSMState.java    2014-03-08 
12:07:09 UTC (rev 17594)
+++ gate/trunk/src/main/gate/creole/tokeniser/DFSMState.java    2014-03-08 
13:05:32 UTC (rev 17595)
@@ -33,8 +33,7 @@
   */
 class DFSMState implements java.io.Serializable { //extends FSMState{
 
-  /** Debug flag */
-  private static final boolean DEBUG = false;
+  private static final long serialVersionUID = 7584872407097617987L;
 
   /** Constructs a new DFSMState object and adds it to the list of 
deterministic
     * states of the {@link DefaultTokeniser DefaultTokeniser} provided as 
owner.
@@ -78,8 +77,7 @@
     ///String res = "";
     //OT
     StringBuffer res = new StringBuffer(gate.Gate.STRINGBUFFER_SIZE);
-    Set nextSet;
-    Iterator nextSetIter;
+
     DFSMState nextState;
 
     for(int i = 0; i< transitionFunction.length; i++){
@@ -123,12 +121,11 @@
     StringBuffer prefix = new StringBuffer(gate.Gate.STRINGBUFFER_SIZE);
     StringBuffer read = new StringBuffer(gate.Gate.STRINGBUFFER_SIZE);
 
-    LinkedList attributes = new LinkedList(),
-               values = new LinkedList();
+    LinkedList<String> attributes = new LinkedList<String>(),
+               values = new LinkedList<String>();
     StringTokenizer mainSt =
       new StringTokenizer(rhs, ignorables + "\\\";=", true);
 
-    int descIndex = 0;
     //phase means:
     //0 == looking for type;
     //1 == looking for attribute;
@@ -212,8 +209,8 @@
     tokenDesc = new String[attributes.size()][2];
 
     for(int i = 0; i < attributes.size(); i++) {
-      tokenDesc[i][0] = (String)attributes.get(i);
-      tokenDesc[i][1] = (String)values.get(i);
+      tokenDesc[i][0] = attributes.get(i);
+      tokenDesc[i][1] = values.get(i);
     }
 
     // for(int i = 0; i < attributes.size(); i++){

Modified: gate/trunk/src/main/gate/creole/tokeniser/DefaultTokeniser.java
===================================================================
--- gate/trunk/src/main/gate/creole/tokeniser/DefaultTokeniser.java     
2014-03-08 12:07:09 UTC (rev 17594)
+++ gate/trunk/src/main/gate/creole/tokeniser/DefaultTokeniser.java     
2014-03-08 13:05:32 UTC (rev 17595)
@@ -28,6 +28,8 @@
 @CreoleResource(name = "ANNIE English Tokeniser", comment = "A customisable 
English tokeniser.", helpURL = 
"http://gate.ac.uk/userguide/sec:annie:tokeniser";, icon = "tokeniser")
 public class DefaultTokeniser extends AbstractLanguageAnalyser implements 
Benchmarkable {
 
+  private static final long serialVersionUID = 3860943928124433852L;
+
   public static final String
     DEF_TOK_DOCUMENT_PARAMETER_NAME = "document";
 

Modified: gate/trunk/src/main/gate/creole/tokeniser/FSMState.java
===================================================================
--- gate/trunk/src/main/gate/creole/tokeniser/FSMState.java     2014-03-08 
12:07:09 UTC (rev 17594)
+++ gate/trunk/src/main/gate/creole/tokeniser/FSMState.java     2014-03-08 
13:05:32 UTC (rev 17595)
@@ -22,8 +22,7 @@
     */
 class FSMState implements java.io.Serializable {
 
-  /** Debug flag */
-  private static final boolean DEBUG = false;
+  private static final long serialVersionUID = -8044319707799787043L;
 
   /** Creates a new FSMState belonging to a specified tokeniser
     * @param owner the tokeniser that contains this new state
@@ -38,7 +37,7 @@
     * As this state can belong to a non-deterministic automaton, the result
     * will be a set.
     */
-  Set nextSet(UnicodeType type) {
+  Set<FSMState> nextSet(UnicodeType type) {
     if(null == type) return transitionFunction[SimpleTokeniser.maxTypeId];
     else return transitionFunction[type.type];
   } // nextSet(UnicodeType type)
@@ -48,7 +47,7 @@
     * As this state can belong to a non-deterministic automaton, the result
     * will be a set.
     */
-  Set nextSet(int type) {
+  Set<FSMState> nextSet(int type) {
     return transitionFunction[type];
   } // nextSet(int type)
 
@@ -69,7 +68,7 @@
     */
   void put(int index, FSMState state) {
     if(null == transitionFunction[index])
-      transitionFunction[index] = new HashSet();
+      transitionFunction[index] = new HashSet<FSMState>();
     transitionFunction[index].add(state);
   } // put(int index, FSMState state)
 
@@ -90,8 +89,8 @@
   String getEdgesGML() {
 ///    String res = "";
     StringBuffer res = new StringBuffer(gate.Gate.STRINGBUFFER_SIZE);
-    Set nextSet;
-    Iterator nextSetIter;
+    Set<FSMState> nextSet;
+    Iterator<FSMState> nextSetIter;
     FSMState nextState;
 
     for(int i = 0; i <= SimpleTokeniser.maxTypeId; i++){
@@ -99,7 +98,7 @@
       if(null != nextSet){
         nextSetIter = nextSet.iterator();
         while(nextSetIter.hasNext()){
-          nextState = (FSMState)nextSetIter.next();
+          nextState = nextSetIter.next();
 /*          res += "edge [ source " + myIndex +
           " target " + nextState.getIndex() +
           " label \"";
@@ -127,7 +126,8 @@
     * (the ids used internally by the tokeniser for the Unicode types) to sets
     * of states.
     */
-  Set[] transitionFunction = new Set[SimpleTokeniser.maxTypeId + 1];
+  @SuppressWarnings("unchecked")
+  Set<FSMState>[] transitionFunction = new Set[SimpleTokeniser.maxTypeId + 1];
 
   /** The RHS string value from which the annotation associated to
     * final states is constructed.

Modified: gate/trunk/src/main/gate/creole/tokeniser/InvalidRuleException.java
===================================================================
--- gate/trunk/src/main/gate/creole/tokeniser/InvalidRuleException.java 
2014-03-08 12:07:09 UTC (rev 17594)
+++ gate/trunk/src/main/gate/creole/tokeniser/InvalidRuleException.java 
2014-03-08 13:05:32 UTC (rev 17595)
@@ -19,9 +19,9 @@
 /** Fired when an invalid tokeniser rule is found
   */
 public class InvalidRuleException extends TokeniserException {
-  /** Debug flag */
-  private static final boolean DEBUG = false;
 
+  private static final long serialVersionUID = 171132971054225662L;
+
   public InvalidRuleException(String s) {
     super(s);
   }

Modified: gate/trunk/src/main/gate/creole/tokeniser/SimpleTokeniser.java
===================================================================
--- gate/trunk/src/main/gate/creole/tokeniser/SimpleTokeniser.java      
2014-03-08 12:07:09 UTC (rev 17594)
+++ gate/trunk/src/main/gate/creole/tokeniser/SimpleTokeniser.java      
2014-03-08 13:05:32 UTC (rev 17595)
@@ -16,19 +16,42 @@
 
 package gate.creole.tokeniser;
 
-import java.io.*;
-import java.lang.reflect.Field;
-import java.lang.reflect.Modifier;
-import java.util.*;
-
-import gate.*;
-import gate.creole.*;
+import gate.AnnotationSet;
+import gate.Factory;
+import gate.FeatureMap;
+import gate.Gate;
+import gate.Resource;
+import gate.creole.AbstractLanguageAnalyser;
+import gate.creole.ExecutionException;
+import gate.creole.ExecutionInterruptedException;
+import gate.creole.ResourceInstantiationException;
 import gate.creole.metadata.CreoleParameter;
 import gate.creole.metadata.CreoleResource;
 import gate.creole.metadata.Optional;
 import gate.creole.metadata.RunTime;
-import gate.util.*;
+import gate.util.BomStrippingInputStreamReader;
+import gate.util.Err;
+import gate.util.GateRuntimeException;
+import gate.util.InvalidOffsetException;
+import gate.util.LuckyException;
 
+import java.io.BufferedReader;
+import java.lang.reflect.Field;
+import java.lang.reflect.Modifier;
+import java.util.AbstractSet;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.StringTokenizer;
+
+import org.apache.commons.io.IOUtils;
+
 /** Implementation of a Unicode rule based tokeniser.
  * The tokeniser gets its rules from a file an {@link java.io.InputStream
  * InputStream} or a {@link java.io.Reader Reader} which should be sent to one
@@ -97,6 +120,9 @@
  */
 @CreoleResource(name="GATE Unicode Tokeniser", comment="A customisable Unicode 
tokeniser.", helpURL="http://gate.ac.uk/userguide/sec:annie:tokeniser";, 
icon="tokeniser")
 public class SimpleTokeniser extends AbstractLanguageAnalyser{
+
+  private static final long serialVersionUID = 1411111968361716069L;
+
   public static final String
     SIMP_TOK_DOCUMENT_PARAMETER_NAME = "document";
 
@@ -109,10 +135,6 @@
   public static final String
     SIMP_TOK_ENCODING_PARAMETER_NAME = "encoding";
 
-  /** Debug flag
-   */
-  private static final boolean DEBUG = false;
-
   /**
    * Creates a tokeniser
    */
@@ -127,17 +149,16 @@
    */
   @Override
   public Resource init() throws ResourceInstantiationException{
-    Reader rulesReader;
+    BufferedReader bRulesReader = null;
     try{
       if(rulesURL != null){
-        rulesReader = new BomStrippingInputStreamReader(rulesURL.openStream(), 
encoding);
+        bRulesReader = new BufferedReader(new 
BomStrippingInputStreamReader(rulesURL.openStream(), encoding));
       }else{
         //no init data, Scream!
         throw new ResourceInstantiationException(
           "No URL provided for the rules!");
       }
       initialState = new FSMState(this);
-      BufferedReader bRulesReader = new BufferedReader(rulesReader);
       String line = bRulesReader.readLine();
       ///String toParse = "";
       StringBuffer toParse = new StringBuffer(Gate.STRINGBUFFER_SIZE);
@@ -163,6 +184,9 @@
     }catch(TokeniserException te){
       throw new ResourceInstantiationException(te);
     }
+    finally {
+      IOUtils.closeQuietly(bRulesReader);
+    }
     return this;
   }
 
@@ -376,8 +400,8 @@
 
     FSMState top;
     FSMState currentState;
-    Set nextStates;
-    Iterator statesIter;
+    Set<FSMState> nextStates;
+    Iterator<FSMState> statesIter;
 
     while(!list.isEmpty()) {
       top = list.removeFirst();
@@ -387,7 +411,7 @@
         statesIter = nextStates.iterator();
 
         while(statesIter.hasNext()) {
-          currentState = (FSMState)statesIter.next();
+          currentState = statesIter.next();
           if(!lambdaClosure.contains(currentState)){
             lambdaClosure.add(currentState);
             list.addFirst(currentState);
@@ -406,8 +430,8 @@
 
     //kalina:clear() faster than init() which is called with init()
     newStates.clear();
-    Set<Set> sdStates = new HashSet<Set>();
-    LinkedList<Set> unmarkedDStates = new LinkedList<Set>();
+    Set<Set<FSMState>> sdStates = new HashSet<Set<FSMState>>();
+    LinkedList<Set<FSMState>> unmarkedDStates = new 
LinkedList<Set<FSMState>>();
     DFSMState dCurrentState = new DFSMState(this);
     Set<FSMState> sdCurrentState = new HashSet<FSMState>();
 
@@ -510,9 +534,9 @@
     StringBuffer nodes = new StringBuffer(Gate.STRINGBUFFER_SIZE),
                  edges = new StringBuffer(Gate.STRINGBUFFER_SIZE);
 
-    Iterator fsmStatesIter = fsmStates.iterator();
+    Iterator<FSMState> fsmStatesIter = fsmStates.iterator();
     while (fsmStatesIter.hasNext()){
-      FSMState currentState = (FSMState)fsmStatesIter.next();
+      FSMState currentState = fsmStatesIter.next();
       int stateIndex = currentState.getIndex();
       /*nodes += "node[ id " + stateIndex +
                " label \"" + stateIndex;
@@ -544,9 +568,9 @@
     StringBuffer nodes = new StringBuffer(Gate.STRINGBUFFER_SIZE),
                  edges = new StringBuffer(Gate.STRINGBUFFER_SIZE);
 
-    Iterator dfsmStatesIter = dfsmStates.iterator();
+    Iterator<DFSMState> dfsmStatesIter = dfsmStates.iterator();
     while (dfsmStatesIter.hasNext()) {
-      DFSMState currentState = (DFSMState)dfsmStatesIter.next();
+      DFSMState currentState = dfsmStatesIter.next();
       int stateIndex = currentState.getIndex();
 /*      nodes += "node[ id " + stateIndex +
                " label \"" + stateIndex;
@@ -767,7 +791,7 @@
 
   /** A set containng all the states of the non deterministic machine
    */
-  protected Set fsmStates = new HashSet();
+  protected Set<FSMState> fsmStates = new HashSet<FSMState>();
 
   /** The initial state of the deterministic machine
    */
@@ -775,7 +799,7 @@
 
   /** A set containng all the states of the deterministic machine
    */
-  protected Set dfsmStates = new HashSet();
+  protected Set<DFSMState> dfsmStates = new HashSet<DFSMState>();
 
   /** The separator from LHS to RH
    */
@@ -817,9 +841,9 @@
   private String rulesResourceName;
   private java.net.URL rulesURL;
   private String encoding;
-  private transient Vector progressListeners;
+
   //kalina: added this as method to minimise too many init() calls
-  protected transient Map<Set, DFSMState> newStates = new HashMap<Set, 
DFSMState>();
+  protected transient Map<Set<FSMState>, DFSMState> newStates = new 
HashMap<Set<FSMState>, DFSMState>();
 
 
   /** The static initialiser will inspect the class {@link java.lang.Character}

Modified: gate/trunk/src/main/gate/creole/tokeniser/TokeniserException.java
===================================================================
--- gate/trunk/src/main/gate/creole/tokeniser/TokeniserException.java   
2014-03-08 12:07:09 UTC (rev 17594)
+++ gate/trunk/src/main/gate/creole/tokeniser/TokeniserException.java   
2014-03-08 13:05:32 UTC (rev 17595)
@@ -20,9 +20,9 @@
 
 /** The top level exception for all the exceptions fired by the tokeniser */
 public class TokeniserException extends GateException {
-  /** Debug flag */
-  private static final boolean DEBUG = false;
 
+  private static final long serialVersionUID = 4372777620099537935L;
+
   public TokeniserException(String text){ super(text); }
 
 } // class TokeniserException

Modified: gate/trunk/src/main/gate/creole/tokeniser/UnicodeType.java
===================================================================
--- gate/trunk/src/main/gate/creole/tokeniser/UnicodeType.java  2014-03-08 
12:07:09 UTC (rev 17594)
+++ gate/trunk/src/main/gate/creole/tokeniser/UnicodeType.java  2014-03-08 
13:05:32 UTC (rev 17595)
@@ -20,8 +20,6 @@
   * the static member of java.lang.Character).
   */
 class UnicodeType {
-  /** Debug flag */
-  private static final boolean DEBUG = false;
 
   int type;
   

Modified: gate/trunk/src/main/gate/email/EmailDocumentHandler.java
===================================================================
--- gate/trunk/src/main/gate/email/EmailDocumentHandler.java    2014-03-08 
12:07:09 UTC (rev 17594)
+++ gate/trunk/src/main/gate/email/EmailDocumentHandler.java    2014-03-08 
13:05:32 UTC (rev 17595)
@@ -41,9 +41,6 @@
   */
 public class EmailDocumentHandler {
 
-  /** Debug flag */
-  private static final boolean DEBUG = false;
-
   private String content = null;
   private long documentSize = 0;
 
@@ -130,7 +127,6 @@
 
     boolean insideAnEmail   = false;
     boolean insideHeader    = false;
-    boolean insideBody      = false;
     boolean emailReadBefore = false;
     boolean fieldReadBefore = false;
 
@@ -562,7 +558,7 @@
     * Initialises the collections with data used by method lineBeginsMessage()
     */
   private void setUp(){
-    day = new HashSet();
+    day = new HashSet<String>();
     day.add("Mon");
     day.add("Tue");
     day.add("Wed");
@@ -571,7 +567,7 @@
     day.add("Sat");
     day.add("Sun");
 
-    month = new HashSet();
+    month = new HashSet<String>();
     month.add("Jan");
     month.add("Feb");
     month.add("Mar");
@@ -585,7 +581,7 @@
     month.add("Nov");
     month.add("Dec");
 
-    zone = new HashSet();
+    zone = new HashSet<String>();
     zone.add("UT");
     zone.add("GMT");
     zone.add("EST");
@@ -629,17 +625,13 @@
     * about an event.
     */
   protected void fireStatusChangedEvent(String text){
-    Iterator listenersIter = myStatusListeners.iterator();
+    Iterator<StatusListener> listenersIter = myStatusListeners.iterator();
     while(listenersIter.hasNext())
-      ((StatusListener)listenersIter.next()).statusChanged(text);
+      listenersIter.next().statusChanged(text);
   }
 
   private static final int EMAILS_RATE = 16;
 
-  // the content of the e-mail document, without any tag
-  // for internal use
-  private String tmpDocContent = null;
-
   // a gate document
   private gate.Document gateDocument = null;
 
@@ -653,7 +645,7 @@
   private Map element2StringMap = null;
 
   // listeners for status report
-  protected List myStatusListeners = new LinkedList();
+  protected List<StatusListener> myStatusListeners = new 
LinkedList<StatusListener>();
 
   // this reports the the number of emails that have beed processed so far
   private int emails = 0;
@@ -663,9 +655,9 @@
   // in this member.
   private String fieldName = null;
 
-  private Collection day = null;
-  private Collection month = null;
-  private Collection zone = null;
+  private Collection<String> day = null;
+  private Collection<String> month = null;
+  private Collection<String> zone = null;
 
 
  // TEST SECTION

Modified: gate/trunk/src/main/gate/event/AnnotationEvent.java
===================================================================
--- gate/trunk/src/main/gate/event/AnnotationEvent.java 2014-03-08 12:07:09 UTC 
(rev 17594)
+++ gate/trunk/src/main/gate/event/AnnotationEvent.java 2014-03-08 13:05:32 UTC 
(rev 17595)
@@ -21,6 +21,8 @@
  */
 public class AnnotationEvent extends GateEvent{
 
+  private static final long serialVersionUID = -5794804058531941540L;
+
   /**Event type used for situations when an annotation has been updated*/
   public static final int ANNOTATION_UPDATED = 601;
 

Modified: gate/trunk/src/main/gate/event/AnnotationSetEvent.java
===================================================================
--- gate/trunk/src/main/gate/event/AnnotationSetEvent.java      2014-03-08 
12:07:09 UTC (rev 17594)
+++ gate/trunk/src/main/gate/event/AnnotationSetEvent.java      2014-03-08 
13:05:32 UTC (rev 17595)
@@ -21,6 +21,8 @@
  */
 public class AnnotationSetEvent extends GateEvent{
 
+  private static final long serialVersionUID = 6618095991726447858L;
+
   /**Event type used for situations when a new annotation has been added*/
   public static final int ANNOTATION_ADDED = 201;
 

Modified: gate/trunk/src/main/gate/event/ControllerEvent.java
===================================================================
--- gate/trunk/src/main/gate/event/ControllerEvent.java 2014-03-08 12:07:09 UTC 
(rev 17594)
+++ gate/trunk/src/main/gate/event/ControllerEvent.java 2014-03-08 13:05:32 UTC 
(rev 17595)
@@ -22,6 +22,9 @@
  * Events fired by controllers.
  */
 public class ControllerEvent extends GateEvent{
+
+  private static final long serialVersionUID = 7881276383734235706L;
+
   public ControllerEvent(Object source, int type, ProcessingResource pr){
     super(source, type);
     this.pr = pr;

Modified: gate/trunk/src/main/gate/event/CorpusEvent.java
===================================================================
--- gate/trunk/src/main/gate/event/CorpusEvent.java     2014-03-08 12:07:09 UTC 
(rev 17594)
+++ gate/trunk/src/main/gate/event/CorpusEvent.java     2014-03-08 13:05:32 UTC 
(rev 17595)
@@ -22,6 +22,8 @@
  */
 public class CorpusEvent extends GateEvent {
 
+  private static final long serialVersionUID = -1499954680735513011L;
+
   /**
    * Event type that is fired when a new document is added to a corpus
    */

Modified: gate/trunk/src/main/gate/event/CreoleEvent.java
===================================================================
--- gate/trunk/src/main/gate/event/CreoleEvent.java     2014-03-08 12:07:09 UTC 
(rev 17594)
+++ gate/trunk/src/main/gate/event/CreoleEvent.java     2014-03-08 13:05:32 UTC 
(rev 17595)
@@ -22,6 +22,8 @@
  */
 public class CreoleEvent extends GateEvent {
 
+  private static final long serialVersionUID = -6834347398037784548L;
+
   /**
    * Constructor
    * @param res the {@link gate.Resource} that has been (un)loaded

Modified: gate/trunk/src/main/gate/event/DatastoreEvent.java
===================================================================
--- gate/trunk/src/main/gate/event/DatastoreEvent.java  2014-03-08 12:07:09 UTC 
(rev 17594)
+++ gate/trunk/src/main/gate/event/DatastoreEvent.java  2014-03-08 13:05:32 UTC 
(rev 17595)
@@ -22,6 +22,8 @@
  */
 public class DatastoreEvent extends GateEvent {
 
+  private static final long serialVersionUID = 1807421127920552348L;
+
   /**
    * Constructor.
    * @param source the datastore that originated the event.

Modified: gate/trunk/src/main/gate/event/DocumentEvent.java
===================================================================
--- gate/trunk/src/main/gate/event/DocumentEvent.java   2014-03-08 12:07:09 UTC 
(rev 17594)
+++ gate/trunk/src/main/gate/event/DocumentEvent.java   2014-03-08 13:05:32 UTC 
(rev 17595)
@@ -20,6 +20,8 @@
  */
 public class DocumentEvent extends GateEvent {
 
+  private static final long serialVersionUID = 2315324967342557414L;
+
   /**Event type used to mark the addition of an {@link gate.AnnotationSet}*/
   public static final int ANNOTATION_SET_ADDED = 101;
 

Modified: gate/trunk/src/main/gate/event/GateEvent.java
===================================================================
--- gate/trunk/src/main/gate/event/GateEvent.java       2014-03-08 12:07:09 UTC 
(rev 17594)
+++ gate/trunk/src/main/gate/event/GateEvent.java       2014-03-08 13:05:32 UTC 
(rev 17595)
@@ -20,6 +20,8 @@
  */
 public class GateEvent extends EventObject {
 
+  private static final long serialVersionUID = 7914516539094860389L;
+
   public static final int FEATURES_UPDATED = 701;
 
   /**

Modified: gate/trunk/src/main/gate/event/ObjectModificationEvent.java
===================================================================
--- gate/trunk/src/main/gate/event/ObjectModificationEvent.java 2014-03-08 
12:07:09 UTC (rev 17594)
+++ gate/trunk/src/main/gate/event/ObjectModificationEvent.java 2014-03-08 
13:05:32 UTC (rev 17595)
@@ -18,6 +18,8 @@
 
 public class ObjectModificationEvent extends GateEvent {
 
+  private static final long serialVersionUID = 317108345148607338L;
+
   public static final int OBJECT_CREATED  = 1000;
   public static final int OBJECT_MODIFIED = 1001;
   public static final int OBJECT_DELETED  = 1002;

Modified: gate/trunk/src/main/gate/event/ProgressListenerAdaptor.java
===================================================================
--- gate/trunk/src/main/gate/event/ProgressListenerAdaptor.java 2014-03-08 
12:07:09 UTC (rev 17594)
+++ gate/trunk/src/main/gate/event/ProgressListenerAdaptor.java 2014-03-08 
13:05:32 UTC (rev 17595)
@@ -20,9 +20,6 @@
   */
 public class ProgressListenerAdaptor implements ProgressListener {
 
-  /** Debug flag */
-  private static final boolean DEBUG = false;
-
   @Override
   public void progressChanged(int i){}
 

Modified: gate/trunk/src/main/gate/fsm/FSM.java
===================================================================
--- gate/trunk/src/main/gate/fsm/FSM.java       2014-03-08 12:07:09 UTC (rev 
17594)
+++ gate/trunk/src/main/gate/fsm/FSM.java       2014-03-08 13:05:32 UTC (rev 
17595)
@@ -29,9 +29,11 @@
   */
 public class FSM implements JapeConstants {
   
-  private ArrayList<RuleTime> ruleTimes = new ArrayList<RuleTime>();
+  private static final long serialVersionUID = -7088856970776558801L;
   
-  public ArrayList<RuleTime> getRuleTimes() {
+  private List<RuleTime> ruleTimes = new ArrayList<RuleTime>();
+  
+  public List<RuleTime> getRuleTimes() {
     return ruleTimes;
   }
 
@@ -75,10 +77,10 @@
    * Do the work involved in creating an FSM from a PrioritisedRuleList.
    */
   protected void addRules(PrioritisedRuleList rules) {
-    Iterator rulesEnum = rules.iterator();
+    Iterator<Rule> rulesEnum = rules.iterator();
 
     while(rulesEnum.hasNext()){
-      FSM ruleFSM = spawn((Rule) rulesEnum.next());
+      FSM ruleFSM = spawn(rulesEnum.next());
 
       //added by Karter start -> JapeDebugger
       ruleHash.putAll(ruleFSM.ruleHash);
@@ -343,6 +345,7 @@
   private State generateStates(State startState, ComplexPatternElement cpe,
           LinkedList<String> labels) {
     //create a copy
+    @SuppressWarnings("unchecked")
     LinkedList<String> newBindings = (LinkedList<String>)labels.clone();
     String localLabel = cpe.getBindingName ();
 
@@ -425,8 +428,8 @@
   public void eliminateVoidTransitions() {
 
     dStates.clear(); //kalina: replaced from new HashSet()
-    LinkedList<AbstractSet<State>> unmarkedDStates = new 
LinkedList<AbstractSet<State>>();
-    AbstractSet<State> currentDState = new HashSet<State>();
+    LinkedList<Set<State>> unmarkedDStates = new LinkedList<Set<State>>();
+    Set<State> currentDState = new HashSet<State>();
     //kalina: prefer clear coz faster than init()
     newStates.clear();
 
@@ -441,11 +444,11 @@
     newStates.put(currentDState, initialState);
 
     // find out if the new state is a final one
-    Iterator innerStatesIter = currentDState.iterator();
+    Iterator<State> innerStatesIter = currentDState.iterator();
     RightHandSide action = null;
 
     while(innerStatesIter.hasNext()){
-      State currentInnerState = (State)innerStatesIter.next();
+      State currentInnerState = innerStatesIter.next();
       if(currentInnerState.isFinal()){
         action = currentInnerState.getAction();
         initialState.setAction(action);
@@ -457,18 +460,18 @@
 
     while(!unmarkedDStates.isEmpty()) {
       currentDState = unmarkedDStates.removeFirst();
-      Iterator insideStatesIter = currentDState.iterator();
+      Iterator<State> insideStatesIter = currentDState.iterator();
 
       while(insideStatesIter.hasNext()) {
-        State innerState = (State)insideStatesIter.next();
-        Iterator transIter = innerState.getTransitions().iterator();
+        State innerState = insideStatesIter.next();
+        Iterator<Transition> transIter = 
innerState.getTransitions().iterator();
 
         while(transIter.hasNext()) {
-          Transition currentTrans = (Transition)transIter.next();
+          Transition currentTrans = transIter.next();
 
           if(currentTrans.getConstraints() !=null) {
             State target = currentTrans.getTarget();
-            AbstractSet<State> newDState = new HashSet<State>();
+            Set<State> newDState = new HashSet<State>();
             newDState.add(target);
             newDState = lambdaClosure(newDState);
 
@@ -481,7 +484,7 @@
               //find out if the new state is a final one
               innerStatesIter = newDState.iterator();
               while(innerStatesIter.hasNext()) {
-                State currentInnerState = (State)innerStatesIter.next();
+                State currentInnerState = innerStatesIter.next();
 
                 if(currentInnerState.isFinal()) {
                   newState.setAction(
@@ -535,14 +538,14 @@
     * @return a set containing all the states accessible from this state via
     * transitions that bear no restrictions.
     */
-  private AbstractSet<State> lambdaClosure(AbstractSet<State> s) {
+  private Set<State> lambdaClosure(Set<State> s) {
     // the stack/queue used by the algorithm
     LinkedList<State> list = new LinkedList<State>(s);
 
     // the set to be returned
-    AbstractSet<State> lambdaClosure = new HashSet<State>(s);
+    Set<State> lambdaClosure = new HashSet<State>(s);
     State top;
-    Iterator transIter;
+    Iterator<Transition> transIter;
     Transition currentTransition;
     State currentState;
     while(!list.isEmpty()){
@@ -550,7 +553,7 @@
       transIter = top.getTransitions().iterator();
 
       while(transIter.hasNext()){
-        currentTransition = (Transition)transIter.next();
+        currentTransition = transIter.next();
 
         if(currentTransition.getConstraints() == null){
           currentState = currentTransition.getTarget();
@@ -717,9 +720,9 @@
     StringBuffer nodes = new StringBuffer(gate.Gate.STRINGBUFFER_SIZE),
                  edges = new StringBuffer(gate.Gate.STRINGBUFFER_SIZE);
 
-    Iterator stateIter = allStates.iterator();
+    Iterator<State> stateIter = allStates.iterator();
     while (stateIter.hasNext()){
-      State currentState = (State)stateIter.next();
+      State currentState = stateIter.next();
       int stateIndex = currentState.getIndex();
         nodes.append("node[ id ");
         nodes.append(stateIndex);
@@ -742,7 +745,7 @@
   @Override
   public String toString(){
     String res = "Starting from:" + initialState.getIndex() + "\n";
-    Iterator stateIter = allStates.iterator();
+    Iterator<State> stateIter = allStates.iterator();
     while (stateIter.hasNext()){
       res += "\n\n" + stateIter.next();
     }
@@ -762,11 +765,11 @@
   /**
     * The set of states for this FSM
     */
-  private transient Collection allStates =  new HashSet();
+  private transient Collection<State> allStates =  new HashSet<State>();
 
   //kalina: added this member here to minimise HashMap allocation
-  private transient Map<AbstractSet,State> newStates = new 
HashMap<AbstractSet,State>();
-  private transient Set<AbstractSet> dStates = new HashSet<AbstractSet>();
+  private transient Map<Set<State>,State> newStates = new 
HashMap<Set<State>,State>();
+  private transient Set<Set<State>> dStates = new HashSet<Set<State>>();
 
 
   //added by Karter start

Modified: gate/trunk/src/main/gate/fsm/FSMInstance.java
===================================================================
--- gate/trunk/src/main/gate/fsm/FSMInstance.java       2014-03-08 12:07:09 UTC 
(rev 17594)
+++ gate/trunk/src/main/gate/fsm/FSMInstance.java       2014-03-08 13:05:32 UTC 
(rev 17595)
@@ -34,10 +34,9 @@
   *  note that a set of bindings is an object of type Map that maps names
   * (java.lang.String) to bags of annotations (gate.AnnotationSet)
   */
-public class FSMInstance implements Comparable, Cloneable, Serializable {
+public class FSMInstance implements Comparable<FSMInstance>, Cloneable, 
Serializable {
 
-  /** Debug flag */
-  private static final boolean DEBUG = false;
+  private static final long serialVersionUID = -2081096002552818621L;
 
   /** Creates a new FSMInstance object.
     * @param supportGraph the transition graph of the FSM
@@ -125,7 +124,7 @@
     * process this FSM instance performed.
     * @return a HashMap object
     */
-  public HashMap<String, AnnotationSet> getBindings() { return bindings; }
+  public Map<String, AnnotationSet> getBindings() { return bindings; }
 
   /** Returns the length of the parsed region in the document under scrutiny.
     * More precisely this is the distnace between the Node in the annotation
@@ -171,7 +170,7 @@
     //do a classic clone except for bindings which need to be cloned themselves
     try {
       FSMInstance clone = (FSMInstance)super.clone();
-      clone.bindings = (HashMap)bindings.clone();
+      clone.bindings = new HashMap<String,AnnotationSet>(bindings);
       return clone;
     } catch (CloneNotSupportedException cnse) {
       cnse.printStackTrace(Err.getPrintWriter());
@@ -201,20 +200,15 @@
     * multiple match.
     */
   @Override
-  public int compareTo(Object obj) {
-    if (obj instanceof FSMInstance) {
-      if(obj == this) return 0;
-      FSMInstance other = (FSMInstance)obj;
-      if(length < other.getLength()) return -1;
+  public int compareTo(FSMInstance other) {
+      if(other == this) return 0;
+            if(length < other.getLength()) return -1;
       else if(length > other.getLength()) return 1;
       //equal length
       else if(priority < other.priority) return -1;
       else if(priority > other.priority) return 1;
       //equal priority
       else return other.fileIndex - fileIndex;
-    } else throw new ClassCastException(
-                    "Attempt to compare a FSMInstance object to an object " +
-                    "of type " + obj.getClass()+"!");
   }
 
   /** Returns a textual representation of this FSM instance.
@@ -278,7 +272,7 @@
     * bindings that took place during matching.
     * needs to be HashMap instead of simply Map in order to cloneable
     */
-  private HashMap<String, AnnotationSet> bindings;
+  private Map<String, AnnotationSet> bindings;
 
   /** The size of the matched region in the Annotation Set*/
   private long length = 0;
@@ -311,7 +305,7 @@
                                                     startNode, AGPosition,
                                                     bindings, doc);
     else {
-      res = (FSMInstance)myInstances.removeFirst();
+      res = myInstances.removeFirst();
       res.supportGraph = supportGraph;
       res.FSMPosition = FSMPosition;
       res.startNode = startNode;
@@ -329,15 +323,15 @@
 
   /** Release all the FSMInstances that are not currently in use */
   public static void clearInstances() {
-    myInstances = new LinkedList();
+    myInstances = new LinkedList<FSMInstance>();
   }
 
   /** The list of existing instances of type FSMInstance */
-  private static LinkedList myInstances;
+  private static LinkedList<FSMInstance> myInstances;
 
   /** The offset in the input List where the last matched annotation was*/
   static{
-    myInstances = new LinkedList();
+    myInstances = new LinkedList<FSMInstance>();
   }
 
 } // FSMInstance

Modified: gate/trunk/src/main/gate/fsm/State.java
===================================================================
--- gate/trunk/src/main/gate/fsm/State.java     2014-03-08 12:07:09 UTC (rev 
17594)
+++ gate/trunk/src/main/gate/fsm/State.java     2014-03-08 13:05:32 UTC (rev 
17595)
@@ -16,24 +16,23 @@
 
 package gate.fsm;
 
-import java.util.ArrayList;
-import java.util.HashMap;
+import gate.jape.BasicPatternElement;
+import gate.jape.JapeConstants;
+import gate.jape.RightHandSide;
+import gate.util.SimpleArraySet;
+
 import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
 
-import gate.jape.*;
-import gate.util.SimpleArraySet;
-
 /**
  * This class implements a Finite State Machine state.
  *
  */
 public class State implements JapeConstants {
 
-  /** Debug flag
-   */
+  private static final long serialVersionUID = 1733852753275942428L;
 
-  private static final boolean DEBUG = false;
-  
   public static final int UNKNOWN_INDEX = 1;
   public static final int VISITED_INDEX = -2;
   public static final int UNVISITED_INDEX = 2;
@@ -66,7 +65,7 @@
    * Determines the appropriate rule by recursively searching this state's 
outbound transitions until
    * we reach a final state.  Record this state in the ruleTimes and 
ruleNameToIndexMap structures
    */
-  public int getRuleForState(HashMap<String,Integer> 
ruleNameToIndexMap,ArrayList<RuleTime>ruleTimes) {
+  public int getRuleForState(Map<String,Integer> ruleNameToIndexMap, 
List<RuleTime>ruleTimes) {
     if (this.getIndexInRuleList() != UNVISITED_INDEX) {
       return this.getIndexInRuleList();  
     }
@@ -235,11 +234,11 @@
 ///    String res = "";
     StringBuffer res = new StringBuffer(gate.Gate.STRINGBUFFER_SIZE);
 
-    Iterator transIter = transitions.iterator();
+    Iterator<Transition> transIter = transitions.iterator();
     BasicPatternElement bpe;
 
     while(transIter.hasNext()) {
-      Transition currentTrans = (Transition)transIter.next();
+      Transition currentTrans = transIter.next();
 /*      res += "edge [ source " + myIndex +
              " target " + currentTrans.getTarget().getIndex() +
              " label \"" + currentTrans.shortDesc() + ":";
@@ -281,7 +280,7 @@
     ///res += "\nTransitions:\n";
     res.append("\nTransitions:\n");
 
-    Iterator transIter = transitions.iterator();
+    Iterator<Transition> transIter = transitions.iterator();
     while(transIter.hasNext()){
       ///res += transIter.next().toString();
       res.append(transIter.next().toString());

Modified: gate/trunk/src/main/gate/fsm/Transition.java
===================================================================
--- gate/trunk/src/main/gate/fsm/Transition.java        2014-03-08 12:07:09 UTC 
(rev 17594)
+++ gate/trunk/src/main/gate/fsm/Transition.java        2014-03-08 13:05:32 UTC 
(rev 17595)
@@ -16,13 +16,14 @@
 
 package gate.fsm;
 
-import java.io.Serializable;
-import java.util.LinkedList;
-
 import gate.Annotation;
 import gate.jape.BasicPatternElement;
 import gate.jape.Constraint;
 
+import java.io.Serializable;
+import java.util.LinkedList;
+import java.util.List;
+
 /**
   * This class implements a Finite State Machine transition.
   * A transition is owned by a gate.fsm.State object and contains set of
@@ -36,12 +37,12 @@
 public class Transition implements Serializable {
 */
 // >>> DAM, TransArray optimzation, now implements the Comparable interface
-public class Transition implements Serializable, Comparable {
+public class Transition implements Serializable, Comparable<Transition> {
+
+  private static final long serialVersionUID = 5970884178025357306L;
+
 // >>> DAM, end
 
-  /** Debug flag */
-  private static final boolean DEBUG = false;
-
   /**
     * Default constructor. Creates a new transition with a new unique index.
     * This constructor should be called by all other constructors.
@@ -57,7 +58,7 @@
     * @param state the target state of this transition
     */
   public Transition(BasicPatternElement constraints, State state) {
-    this(constraints, state, new LinkedList());
+    this(constraints, state, new LinkedList<String>());
   }
 
   /**
@@ -66,7 +67,7 @@
     * (aka annotations).
     */
   public Transition(BasicPatternElement constraints, State state,
-                    LinkedList bindings) {
+                    List<String> bindings) {
     this();
     this.constraints = constraints;
     target = state;
@@ -174,7 +175,7 @@
   /**
     *  Returns the list of bindings associated to this transition
     */
-  public LinkedList getBindings(){ return bindings; }
+  public List<String> getBindings(){ return bindings; }
 
   /**
     * The constraints on this transition.
@@ -189,10 +190,8 @@
   /**
     * A list with all the labels associated to the annotations recognized by
     * this transition.
-    * We need to use the actual object and not the interface (java.util.List)
-    * because we need this object to be cloneable
     */
-  private LinkedList bindings;
+  private List<String> bindings;
 
   /** The unique index of this transition. This value is not used by any of
     * the algorithms. It is only provided as a convenient method of identifying
@@ -207,11 +206,10 @@
 
 // >>> DAM, TransArray optimzation, now implements the Comparable interface
   @Override
-  public int compareTo(Object o)
+  public int compareTo(Transition t)
   throws ClassCastException
   {
-    if (!(o instanceof Transition)) throw new 
ClassCastException("gate.frm.Transition(compareTo)");
-    return myIndex - ((Transition)o).myIndex;
+    return myIndex - t.myIndex;
   }
 // >>> DAM, end
 } // Transition

Modified: gate/trunk/src/main/gate/jape/PrioritisedRuleList.java
===================================================================
--- gate/trunk/src/main/gate/jape/PrioritisedRuleList.java      2014-03-08 
12:07:09 UTC (rev 17594)
+++ gate/trunk/src/main/gate/jape/PrioritisedRuleList.java      2014-03-08 
13:05:32 UTC (rev 17595)
@@ -33,15 +33,14 @@
   * insertion of elements at any point. The highest priority rule is the
   * first in the list, which may be accessed by <CODE>front()</CODE>.
   */
-public class PrioritisedRuleList extends ArrayList implements 
java.io.Serializable
+public class PrioritisedRuleList extends ArrayList<Rule> implements 
java.io.Serializable
 {
-  /** Debug flag */
-  private static final boolean DEBUG = false;
+  private static final long serialVersionUID = 1603854971047597460L;
 
   /** Adds a rule in order. Used for non-matched rules. Implements the
     * ordering based on priority/position.
     */
-  public synchronized void add(Rule newRule) {
+  public synchronized boolean add(Rule newRule) {
     /* for each rule,
      *   if it is higher priority, continue;
      *   else if it is same priority
@@ -50,10 +49,10 @@
      *   else (it is lower priority) break
      * insert newRule before current position (which may be finish)
      */
-    Iterator iterator = this.iterator();
+    Iterator<Rule> iterator = this.iterator();
     int i = 0;
     for(  ; iterator.hasNext(); i++) {
-      Rule rule        =       (Rule) iterator.next();
+      Rule rule        =       iterator.next();
       int rulePriority =       rule.getPriority();
       int newRulePriority =    newRule.getPriority();
       int rulePosition =       rule.getPosition();
@@ -74,6 +73,8 @@
 
 
     this.add(i, newRule);
+    
+    return true;
   } // add(Rule)
 
 

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