Revision: 17616
          http://sourceforge.net/p/gate/code/17616
Author:   markagreenwood
Date:     2014-03-10 16:09:07 +0000 (Mon, 10 Mar 2014)
Log Message:
-----------
fixed or supressed a bunch more generics warnings -- warning count is now 
measured in 3 figures :)

Modified Paths:
--------------
    gate/trunk/src/main/gate/annotation/AnnotationImpl.java
    gate/trunk/src/main/gate/annotation/AnnotationSetImpl.java
    gate/trunk/src/main/gate/annotation/NodeImpl.java
    gate/trunk/src/main/gate/corpora/DocumentImpl.java
    gate/trunk/src/main/gate/corpora/SerialCorpusImpl.java
    gate/trunk/src/main/gate/corpora/TextualDocumentFormat.java
    gate/trunk/src/main/gate/creole/AbstractController.java
    gate/trunk/src/main/gate/creole/annic/Indexer.java
    gate/trunk/src/main/gate/creole/annic/Parser.java
    gate/trunk/src/main/gate/creole/annic/Searchable.java
    gate/trunk/src/main/gate/creole/annic/lucene/LuceneIndexer.java
    gate/trunk/src/main/gate/creole/annic/lucene/LuceneQueryResult.java
    gate/trunk/src/main/gate/creole/annic/lucene/LuceneSearchThread.java
    gate/trunk/src/main/gate/creole/annic/lucene/LuceneSearcher.java
    gate/trunk/src/main/gate/creole/annic/lucene/LuceneTokenizer.java
    gate/trunk/src/main/gate/creole/coref/NominalCoref.java
    gate/trunk/src/main/gate/creole/coref/PronominalCoref.java
    gate/trunk/src/main/gate/gui/CollectionSelectionDialog.java
    gate/trunk/src/main/gate/gui/FeaturesSchemaEditor.java
    gate/trunk/src/main/gate/gui/ListEditorDialog.java
    gate/trunk/src/main/gate/gui/SyntaxTreeViewer.java
    gate/trunk/src/main/gate/jape/SinglePhaseTransducer.java
    gate/trunk/src/main/gate/jape/SourceInfo.java
    gate/trunk/src/main/gate/jape/Transducer.java
    gate/trunk/src/main/gate/persist/LuceneDataStoreImpl.java
    gate/trunk/src/main/gate/persist/PersistenceException.java
    gate/trunk/src/main/gate/persist/SerialDataStore.java
    gate/trunk/src/main/gate/util/Benchmark.java

Modified: gate/trunk/src/main/gate/annotation/AnnotationImpl.java
===================================================================
--- gate/trunk/src/main/gate/annotation/AnnotationImpl.java     2014-03-10 
11:10:08 UTC (rev 17615)
+++ gate/trunk/src/main/gate/annotation/AnnotationImpl.java     2014-03-10 
16:09:07 UTC (rev 17616)
@@ -32,9 +32,6 @@
 public class AnnotationImpl extends AbstractFeatureBearer
                             implements Annotation, FeatureBearer {
 
-  /** Debug flag
-   */
-  private static final boolean DEBUG = false;
   /** Freeze the serialization UID. */
   static final long serialVersionUID = -5658993256574857725L;
 

Modified: gate/trunk/src/main/gate/annotation/AnnotationSetImpl.java
===================================================================
--- gate/trunk/src/main/gate/annotation/AnnotationSetImpl.java  2014-03-10 
11:10:08 UTC (rev 17615)
+++ gate/trunk/src/main/gate/annotation/AnnotationSetImpl.java  2014-03-10 
16:09:07 UTC (rev 17616)
@@ -64,7 +64,6 @@
 import java.util.Vector;
 
 import org.apache.commons.lang.StringUtils;
-import org.apache.log4j.Logger;
 
 /**
  * Implementation of AnnotationSet. Has a number of indices, all bar one of
@@ -86,7 +85,6 @@
  */
 public class AnnotationSetImpl extends AbstractSet<Annotation> implements
                                                               AnnotationSet {
-  private static final Logger log = Logger.getLogger(AnnotationSetImpl.class);
   /** Freeze the serialization UID. */
   static final long serialVersionUID = 1479426765310434166L;
   /** The name of this set */

Modified: gate/trunk/src/main/gate/annotation/NodeImpl.java
===================================================================
--- gate/trunk/src/main/gate/annotation/NodeImpl.java   2014-03-10 11:10:08 UTC 
(rev 17615)
+++ gate/trunk/src/main/gate/annotation/NodeImpl.java   2014-03-10 16:09:07 UTC 
(rev 17616)
@@ -23,10 +23,6 @@
  */
 public class NodeImpl implements Node, Comparable<Node>
 {
-  /** Debug flag
-   */
-  private static final boolean DEBUG = false;
-
   /** Freeze the serialization UID. */
   static final long serialVersionUID = -8240414984367916298L;
 

Modified: gate/trunk/src/main/gate/corpora/DocumentImpl.java
===================================================================
--- gate/trunk/src/main/gate/corpora/DocumentImpl.java  2014-03-10 11:10:08 UTC 
(rev 17615)
+++ gate/trunk/src/main/gate/corpora/DocumentImpl.java  2014-03-10 16:09:07 UTC 
(rev 17616)
@@ -957,6 +957,7 @@
    * @return The XML document obtained from raw text + the information from the
    *         dump annotation set.
    */
+  @SuppressWarnings("unused")
   private String saveAnnotationSetAsXml(AnnotationSet aDumpAnnotSet,
           boolean includeFeatures) {
     String content = null;
@@ -1770,6 +1771,7 @@
    *          The annotation set possibly containing the root annotation.
    * @return The root annotation or null is it fails
    */
+  @SuppressWarnings("unused")
   private Annotation identifyTheRootAnnotation(AnnotationSet anAnnotationSet) {
     if(anAnnotationSet == null) return null;
     // If the starting node of this annotation is not null, then the annotation
@@ -2040,20 +2042,6 @@
   }// toXml
 
   /**
-   * This method saves an AnnotationSet as XML.
-   * May be removed once GLEAM doc-service is updated.
-   * 
-   * @param anAnnotationSet
-   *          The annotation set that has to be saved as XML.
-   * @return a String like this: <AnnotationSet> <Annotation>....
-   *         </AnnotationSet>
-   */
-  private void annotationSetToXml(AnnotationSet anAnnotationSet,
-          StringBuffer buffer) {
-    DocumentXmlUtils.annotationSetToXml(anAnnotationSet, buffer);
-  }// annotationSetToXml
-
-  /**
    * Returns a map (possibly empty) with the named annotation sets. It returns 
<code>null</code>
    * if no named annotaton set exists.
    */

Modified: gate/trunk/src/main/gate/corpora/SerialCorpusImpl.java
===================================================================
--- gate/trunk/src/main/gate/corpora/SerialCorpusImpl.java      2014-03-10 
11:10:08 UTC (rev 17615)
+++ gate/trunk/src/main/gate/corpora/SerialCorpusImpl.java      2014-03-10 
16:09:07 UTC (rev 17616)
@@ -147,8 +147,8 @@
    * @return a {@link List} of Objects representing the persistent IDs
    *         of the documents in this corpus.
    */
-  public List getDocumentPersistentIDs() {
-    List docsIDs = new ArrayList();
+  public List<Object> getDocumentPersistentIDs() {
+    List<Object> docsIDs = new ArrayList<Object>();
     if(docDataList == null) return docsIDs;
     Iterator<DocumentData> iter = docDataList.iterator();
     while(iter.hasNext()) {

Modified: gate/trunk/src/main/gate/corpora/TextualDocumentFormat.java
===================================================================
--- gate/trunk/src/main/gate/corpora/TextualDocumentFormat.java 2014-03-10 
11:10:08 UTC (rev 17615)
+++ gate/trunk/src/main/gate/corpora/TextualDocumentFormat.java 2014-03-10 
16:09:07 UTC (rev 17616)
@@ -156,6 +156,7 @@
   } // setNewLineProperty()
 
   /** Delete '\r' in combination CRLF or LFCR in document content */
+  @SuppressWarnings("unused")
   private void removeExtraNewLine(Document doc) {
     String content = doc.getContent().toString();
     StringBuffer buff = new StringBuffer(content);

Modified: gate/trunk/src/main/gate/creole/AbstractController.java
===================================================================
--- gate/trunk/src/main/gate/creole/AbstractController.java     2014-03-10 
11:10:08 UTC (rev 17615)
+++ gate/trunk/src/main/gate/creole/AbstractController.java     2014-03-10 
16:09:07 UTC (rev 17616)
@@ -51,7 +51,7 @@
   /**
    * Shared featureMap
    */
-  protected Map<String,String> benchmarkFeatures = new 
HashMap<String,String>();
+  protected Map<Object,Object> benchmarkFeatures = new 
HashMap<Object,Object>();
 
   // executable code
   /**

Modified: gate/trunk/src/main/gate/creole/annic/Indexer.java
===================================================================
--- gate/trunk/src/main/gate/creole/annic/Indexer.java  2014-03-10 11:10:08 UTC 
(rev 17615)
+++ gate/trunk/src/main/gate/creole/annic/Indexer.java  2014-03-10 16:09:07 UTC 
(rev 17616)
@@ -27,7 +27,7 @@
    *          depend on the implementing IndexManager
    * @throws IndexException
    */
-  public void createIndex(Map parameters) throws IndexException;
+  public void createIndex(Map<String,Object> parameters) throws IndexException;
 
   /** Optimize the existing index */
   public void optimizeIndex() throws IndexException;
@@ -51,7 +51,7 @@
    * @param removedDocumentPersistenceIds
    * @throws Exception
    */
-  public void remove(List removedDocumentPersistenceIds) throws IndexException;
+  public void remove(List<Object> removedDocumentPersistenceIds) throws 
IndexException;
 
   /**
    * Set the corpus to be indexed
@@ -68,5 +68,5 @@
   /**
    * Returns the parameters
    */
-  public Map getParameters();
+  public Map<String,Object> getParameters();
 }

Modified: gate/trunk/src/main/gate/creole/annic/Parser.java
===================================================================
--- gate/trunk/src/main/gate/creole/annic/Parser.java   2014-03-10 11:10:08 UTC 
(rev 17615)
+++ gate/trunk/src/main/gate/creole/annic/Parser.java   2014-03-10 16:09:07 UTC 
(rev 17616)
@@ -238,7 +238,7 @@
 
     // rootElement is HITS
     // this will internally contains instances of HIT
-    List hitsChildren = rootElement.getChildren(HIT);
+    List<?> hitsChildren = rootElement.getChildren(HIT);
     Hit[] hits = new Hit[hitsChildren.size()];
 
     for(int i = 0; i < hitsChildren.size(); i++) {
@@ -255,7 +255,7 @@
         continue;
       }
 
-      List patAnnots = patternAnnotations.getChildren(PATTERN_ANNOTATION);
+      List<?> patAnnots = patternAnnotations.getChildren(PATTERN_ANNOTATION);
       List<PatternAnnotation> patAnnotsList = new 
ArrayList<PatternAnnotation>();
       for(int j = 0; j < patAnnots.size(); j++) {
         Element patAnnot = (Element)patAnnots.get(j);
@@ -269,7 +269,7 @@
         // we need to find out its features
         Element featuresElem = patAnnot.getChild(FEATURES);
         // more than one features possible
-        List featuresElemsList = featuresElem.getChildren(FEATURE);
+        List<?> featuresElemsList = featuresElem.getChildren(FEATURE);
         for(int k = 0; k < featuresElemsList.size(); k++) {
           Element featureElem = (Element)featuresElemsList.get(k);
           String key = featureElem.getChildText(KEY);

Modified: gate/trunk/src/main/gate/creole/annic/Searchable.java
===================================================================
--- gate/trunk/src/main/gate/creole/annic/Searchable.java       2014-03-10 
11:10:08 UTC (rev 17615)
+++ gate/trunk/src/main/gate/creole/annic/Searchable.java       2014-03-10 
16:09:07 UTC (rev 17616)
@@ -27,7 +27,7 @@
    *          implementation of provided indexer
    * @throws IndexException
    */
-  public void setIndexer(Indexer indexer, Map parameters) throws 
IndexException;
+  public void setIndexer(Indexer indexer, Map<String,Object> parameters) 
throws IndexException;
 
   /**
    * Returns the Indexer
@@ -55,7 +55,7 @@
    * @return true if the search was successful
    * @throws SearchException
    */
-  public boolean search(String query, Map searchParameters)
+  public boolean search(String query, Map<String,Object> searchParameters)
           throws SearchException;
 
   /**

Modified: gate/trunk/src/main/gate/creole/annic/lucene/LuceneIndexer.java
===================================================================
--- gate/trunk/src/main/gate/creole/annic/lucene/LuceneIndexer.java     
2014-03-10 11:10:08 UTC (rev 17615)
+++ gate/trunk/src/main/gate/creole/annic/lucene/LuceneIndexer.java     
2014-03-10 16:09:07 UTC (rev 17616)
@@ -50,7 +50,7 @@
   /**
    * Various parameters such as location of the Index etc.
    */
-  protected Map parameters;
+  protected Map<String,Object> parameters;
 
   /**
    * Constructor
@@ -67,7 +67,7 @@
   /**
    * Checks the Index Parameters to see if they are all compatible
    */
-  protected void checkIndexParameters(Map parameters) throws IndexException {
+  protected void checkIndexParameters(Map<String,Object> parameters) throws 
IndexException {
     this.parameters = parameters;
 
     if(parameters == null) {
@@ -123,7 +123,7 @@
   /**
    * Returns the indexing parameters
    */
-  protected Map getIndexParameters() {
+  protected Map<String,Object> getIndexParameters() {
     return this.parameters;
   }
 
@@ -148,7 +148,7 @@
    * 
    */
   @Override
-  public void createIndex(Map indexParameters) throws IndexException {
+  public void createIndex(Map<String,Object> indexParameters) throws 
IndexException {
     checkIndexParameters(indexParameters);
     URL indexLocation = (URL)parameters.get(Constants.INDEX_LOCATION_URL);
 
@@ -324,7 +324,7 @@
    * @throws Exception
    */
   @Override
-  public void remove(List removedIDs) throws IndexException {
+  public void remove(List<Object> removedIDs) throws IndexException {
 
     String location = null;
     try {
@@ -404,15 +404,19 @@
     String indexUnitAnnotationType = (String)parameters
             .get(Constants.INDEX_UNIT_ANNOTATION_TYPE);
 
+    @SuppressWarnings("unchecked")
     List<String> featuresToExclude = new 
ArrayList<String>((List<String>)parameters
             .get(Constants.FEATURES_TO_EXCLUDE));
 
+    @SuppressWarnings("unchecked")
     List<String> featuresToInclude = new 
ArrayList<String>((List<String>)parameters
             .get(Constants.FEATURES_TO_INCLUDE));
 
+    @SuppressWarnings("unchecked")
     List<String> annotationSetsToExclude = new 
ArrayList<String>((List<String>)parameters
             .get(Constants.ANNOTATION_SETS_NAMES_TO_EXCLUDE));
 
+    @SuppressWarnings("unchecked")
     List<String> annotationSetsToInclude = new 
ArrayList<String>((List<String>)parameters
             .get(Constants.ANNOTATION_SETS_NAMES_TO_INCLUDE));
 
@@ -461,6 +465,7 @@
    * @param indexLocationUrl
    * @throws IOException
    */
+  @SuppressWarnings("unchecked")
   private void readParametersFromDisk(URL indexLocationUrl) throws IOException 
{
     // we create a hashmap to store index definition in the index
     // directory
@@ -482,7 +487,7 @@
               new com.thoughtworks.xstream.io.xml.StaxDriver());
   
       // Saving is accomplished just using XML serialization of the map.
-      this.parameters = (Map)xstream.fromXML(fileReader);
+      this.parameters = (Map<String,Object>)xstream.fromXML(fileReader);
       // setting the index location URL
       this.parameters.put(Constants.INDEX_LOCATION_URL, indexLocationUrl);
     }
@@ -509,10 +514,10 @@
     }
 
     java.io.FileWriter fileWriter = new java.io.FileWriter(file);
-    Map indexInformation = new HashMap();
-    Iterator iter = parameters.keySet().iterator();
+    Map<String,Object> indexInformation = new HashMap<String,Object>();
+    Iterator<String> iter = parameters.keySet().iterator();
     while(iter.hasNext()) {
-      Object key = iter.next();
+      String key = iter.next();
       if(key.equals(Constants.INDEX_LOCATION_URL)) continue;
       indexInformation.put(key, parameters.get(key));
     }
@@ -540,7 +545,7 @@
    * Returns the set parameters
    */
   @Override
-  public Map getParameters() {
+  public Map<String,Object> getParameters() {
     return this.parameters;
   }
 

Modified: gate/trunk/src/main/gate/creole/annic/lucene/LuceneQueryResult.java
===================================================================
--- gate/trunk/src/main/gate/creole/annic/lucene/LuceneQueryResult.java 
2014-03-10 11:10:08 UTC (rev 17615)
+++ gate/trunk/src/main/gate/creole/annic/lucene/LuceneQueryResult.java 
2014-03-10 16:09:07 UTC (rev 17616)
@@ -23,7 +23,7 @@
   
   private String annotationSetName;
 
-  private List firstTermPositions;
+  private List<?> firstTermPositions;
 
   private List<Integer> patternLength;
 
@@ -43,7 +43,7 @@
    * @param gateAnnotations
    * @param query
    */
-  public LuceneQueryResult(Object docID, String annotationSetName, List 
firstTermPositions,
+  public LuceneQueryResult(Object docID, String annotationSetName, List<?> 
firstTermPositions,
           List<Integer> patternLength, int queryType, 
List<List<PatternAnnotation>> gateAnnotations,
           String query) {
     this.docID = docID;
@@ -81,7 +81,7 @@
    *         Integer values indicating positions of first annotations of
    *         found patterns in the token stream.
    */
-  public List getFirstTermPositions() {
+  public List<?> getFirstTermPositions() {
     return firstTermPositions;
   }
 

Modified: gate/trunk/src/main/gate/creole/annic/lucene/LuceneSearchThread.java
===================================================================
--- gate/trunk/src/main/gate/creole/annic/lucene/LuceneSearchThread.java        
2014-03-10 11:10:08 UTC (rev 17615)
+++ gate/trunk/src/main/gate/creole/annic/lucene/LuceneSearchThread.java        
2014-03-10 16:09:07 UTC (rev 17616)
@@ -146,6 +146,7 @@
    *          instance of SearchThread is invoked
    * @return true iff search was successful false otherwise
    */
+  @SuppressWarnings("unchecked")
   public boolean search(String query, int patternWindow, String indexLocation,
           String corpusToSearchIn, String annotationSetToSearchIn,
           LuceneSearcher luceneSearcher) throws SearchException {
@@ -213,14 +214,14 @@
       java.io.FileReader fileReader = new java.io.FileReader(indexLocation
               + "LuceneIndexDefinition.xml");
 
-      HashMap indexInformation = null;
+      Map<String,Object> indexInformation = null;
       try {
         // other wise read this file
         com.thoughtworks.xstream.XStream xstream = new 
com.thoughtworks.xstream.XStream(
                 new com.thoughtworks.xstream.io.xml.StaxDriver());
   
         // Saving was accomplished by using XML serialization of the map.
-        indexInformation = (HashMap)xstream.fromXML(fileReader);
+        indexInformation = (Map<String,Object>)xstream.fromXML(fileReader);
       }
       finally {
         fileReader.close();
@@ -283,7 +284,7 @@
            * returned results. first term position is the position of the
            * first term in the found pattern
            */
-          ArrayList[] firstTermPositions = searcher.getFirstTermPositions();
+          List<?>[] firstTermPositions = searcher.getFirstTermPositions();
           // if no result available, set null to our scores
           if(firstTermPositions[0].size() == 0) {
             // do nothing
@@ -300,7 +301,7 @@
   
             // we fetch all the first term positions for the query
             // issued
-            ArrayList ftp = (ArrayList)firstTermPositions[1].get(index);
+            List<?> ftp = (List<?>)firstTermPositions[1].get(index);
 
             /*
              * pattern length (in terms of total number of annotations
@@ -367,7 +368,7 @@
   /**
    * First term positions.
    */
-  private List ftp;
+  private List<?> ftp;
 
   /**
    * This method returns a list containing instances of Pattern
@@ -496,7 +497,7 @@
   private List<Pattern> createAnnicPatterns(LuceneQueryResult aResult) {
     // get the result from search engine
     List<Pattern> annicPatterns = new ArrayList<Pattern>();
-    List firstTermPositions = aResult.getFirstTermPositions();
+    List<?> firstTermPositions = aResult.getFirstTermPositions();
     if(firstTermPositions != null && firstTermPositions.size() > 0) {
       List<Integer> patternLength = aResult.patternLength();
       // locate Pattern
@@ -523,12 +524,12 @@
    */
   private List<Pattern> locatePatterns(String docID, String annotationSetName,
           List<List<PatternAnnotation>> gateAnnotations,
-          List firstTermPositions, List<Integer> patternLength,
+          List<?> firstTermPositions, List<Integer> patternLength,
           String queryString) {
 
     // patterns
     List<Pattern> pats = new ArrayList<Pattern>();
-    outer: for(int i = 0; i < gateAnnotations.size(); i++) {
+    for(int i = 0; i < gateAnnotations.size(); i++) {
 
       // each element in the tokens stream is a pattern
       List<PatternAnnotation> annotations = gateAnnotations.get(i);
@@ -671,6 +672,7 @@
     ObjectInput input = new ObjectInputStream(buffer);
 
     // deserialize the List
+    @SuppressWarnings("unchecked")
     List<gate.creole.annic.apache.lucene.analysis.Token> recoveredTokenStream 
= 
       (List<gate.creole.annic.apache.lucene.analysis.Token>)input.readObject();
     if(input != null) {
@@ -765,6 +767,7 @@
    * @param query String
    * @return PatternResult
    */
+  @SuppressWarnings({"rawtypes", "unchecked"})
   private PatternResult getPatternResult(
           List<gate.creole.annic.apache.lucene.analysis.Token> subTokens,
           String annotationSetName, int patLen, int patWindow, String query,
@@ -1061,6 +1064,7 @@
     
     String annotationSetName;
 
+    @SuppressWarnings("rawtypes")
     List firstTermPositions;
 
     List<Integer> patternLegths;
@@ -1073,18 +1077,22 @@
    * 
    */
   private class QueryItem {
+    @SuppressWarnings("unused")
     float score;
 
+    @SuppressWarnings("unused")
     int id;
 
     String documentID;
     
+    @SuppressWarnings("rawtypes")
     List ftp;
 
     int patLen;
 
     int qType;
 
+    @SuppressWarnings("unused")
     Query query;
 
     String queryString;
@@ -1124,6 +1132,7 @@
   /**
    * Checks if two first term positions are identical. 
    */
+  @SuppressWarnings({"unused", "rawtypes"})
   private boolean areTheyEqual(List ftp, List ftp1, int qType) {
     if(qType == 1) {
       if(ftp.size() == ftp1.size()) {

Modified: gate/trunk/src/main/gate/creole/annic/lucene/LuceneSearcher.java
===================================================================
--- gate/trunk/src/main/gate/creole/annic/lucene/LuceneSearcher.java    
2014-03-10 11:10:08 UTC (rev 17615)
+++ gate/trunk/src/main/gate/creole/annic/lucene/LuceneSearcher.java    
2014-03-10 16:09:07 UTC (rev 17616)
@@ -191,6 +191,7 @@
   /**
    * Method retunrs true/false indicating whether results were found or not.
    */
+  @SuppressWarnings("unchecked")
   @Override
   public boolean search(String query, Map<String, Object> parameters)
       throws SearchException {

Modified: gate/trunk/src/main/gate/creole/annic/lucene/LuceneTokenizer.java
===================================================================
--- gate/trunk/src/main/gate/creole/annic/lucene/LuceneTokenizer.java   
2014-03-10 11:10:08 UTC (rev 17615)
+++ gate/trunk/src/main/gate/creole/annic/lucene/LuceneTokenizer.java   
2014-03-10 16:09:07 UTC (rev 17616)
@@ -20,7 +20,7 @@
 public class LuceneTokenizer extends TokenStream {
        Document document;
        List<Token> tokens;
-       List featuresToExclude;
+       //List featuresToExclude;
        int pointer = 0;
 
   /**

Modified: gate/trunk/src/main/gate/creole/coref/NominalCoref.java
===================================================================
--- gate/trunk/src/main/gate/creole/coref/NominalCoref.java     2014-03-10 
11:10:08 UTC (rev 17615)
+++ gate/trunk/src/main/gate/creole/coref/NominalCoref.java     2014-03-10 
16:09:07 UTC (rev 17616)
@@ -502,6 +502,7 @@
   }
        
   /** Get the text of an annotation */
+  @SuppressWarnings("unused")
   private String stringValue(Annotation ann) {
     Object[] tokens = getSortedTokens(ann);
        

Modified: gate/trunk/src/main/gate/creole/coref/PronominalCoref.java
===================================================================
--- gate/trunk/src/main/gate/creole/coref/PronominalCoref.java  2014-03-10 
11:10:08 UTC (rev 17615)
+++ gate/trunk/src/main/gate/creole/coref/PronominalCoref.java  2014-03-10 
16:09:07 UTC (rev 17616)
@@ -1246,8 +1246,10 @@
   private class Sentence {
 
     /** --- */
+    @SuppressWarnings("unused")
     private int sentNumber;
     /** --- */
+    @SuppressWarnings("unused")
     private int paraNumber;
     /** --- */
     private Long startOffset;

Modified: gate/trunk/src/main/gate/gui/CollectionSelectionDialog.java
===================================================================
--- gate/trunk/src/main/gate/gui/CollectionSelectionDialog.java 2014-03-10 
11:10:08 UTC (rev 17615)
+++ gate/trunk/src/main/gate/gui/CollectionSelectionDialog.java 2014-03-10 
16:09:07 UTC (rev 17616)
@@ -16,12 +16,28 @@
 
 package gate.gui;
 
-import java.awt.*;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Frame;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Iterator;
+import java.util.List;
 
-import javax.swing.*;
+import javax.swing.Box;
+import javax.swing.BoxLayout;
+import javax.swing.DefaultListModel;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JFileChooser;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JOptionPane;
+import javax.swing.JScrollPane;
+import javax.swing.ListSelectionModel;
 
 
 /** This class visually selects some items from a collection and returns
@@ -80,11 +96,12 @@
   /** Init local data from a source collection
     * @param aSourceData is the collection from what the user will choose
     */
+  @SuppressWarnings({"rawtypes", "unchecked"})
   protected void initLocalData(Collection aSourceData){
     targetListModel = new DefaultListModel();
     sourceListModel = new DefaultListModel();
     if (aSourceData == null) return;
-    ArrayList source = new ArrayList(aSourceData);
+    List source = new ArrayList(aSourceData);
     Collections.sort(source);
     Iterator iter = source.iterator();
     while(iter.hasNext()){
@@ -234,8 +251,9 @@
     }// end for
   }// doAdd();
   /** Returns the target collection*/
+  @SuppressWarnings({"rawtypes", "unchecked"})
   public Collection getSelectedCollection(){
-    ArrayList resultsList = new ArrayList();
+    List resultsList = new ArrayList();
     for (int i=0; i<targetListModel.getSize(); i++){
       resultsList.add(targetListModel.getElementAt(i));
     }// End for
@@ -243,6 +261,7 @@
   }// getSelectedCollection()
 
   /** This method displays the CollectionSelectionDialog*/
+  @SuppressWarnings("rawtypes")
   public int show(String aTitle,Collection aSourceData){
     if (aTitle == null){
       JOptionPane.showMessageDialog(mainFrame,

Modified: gate/trunk/src/main/gate/gui/FeaturesSchemaEditor.java
===================================================================
--- gate/trunk/src/main/gate/gui/FeaturesSchemaEditor.java      2014-03-10 
11:10:08 UTC (rev 17615)
+++ gate/trunk/src/main/gate/gui/FeaturesSchemaEditor.java      2014-03-10 
16:09:07 UTC (rev 17616)
@@ -198,6 +198,7 @@
    * Fire a table data changed event for the feature table whith featureList
    * used as data model.
    */
+  @SuppressWarnings({"rawtypes", "unchecked"})
   protected void populate(){
     featureList.clear();
     //get all the existing features

Modified: gate/trunk/src/main/gate/gui/ListEditorDialog.java
===================================================================
--- gate/trunk/src/main/gate/gui/ListEditorDialog.java  2014-03-10 11:10:08 UTC 
(rev 17615)
+++ gate/trunk/src/main/gate/gui/ListEditorDialog.java  2014-03-10 16:09:07 UTC 
(rev 17616)
@@ -30,7 +30,7 @@
 /**
  * A simple editor for Collection values.
  */
-@SuppressWarnings("serial")
+@SuppressWarnings({"serial","rawtypes","unchecked"})
 public class ListEditorDialog extends JDialog {
 
   /**
@@ -108,7 +108,7 @@
       
       if(SortedSet.class.isAssignableFrom(collectionType)
               && data != null) {
-        comparator = ((SortedSet)data).comparator();
+        comparator = ((SortedSet<?>)data).comparator();
       }
       if(comparator == null) {
         comparator = new NaturalComparator();

Modified: gate/trunk/src/main/gate/gui/SyntaxTreeViewer.java
===================================================================
--- gate/trunk/src/main/gate/gui/SyntaxTreeViewer.java  2014-03-10 11:10:08 UTC 
(rev 17615)
+++ gate/trunk/src/main/gate/gui/SyntaxTreeViewer.java  2014-03-10 16:09:07 UTC 
(rev 17616)
@@ -253,6 +253,7 @@
   }
 
   //CONSTRUCTORS
+  @SuppressWarnings("unused")
   private SyntaxTreeViewer(String annotType) {
 
     treeNodeAnnotationType = annotType;
@@ -1466,14 +1467,17 @@
       super(text);
     }
   
+    @SuppressWarnings("unused")
     public FocusButton() {
       super();
     }
   
+    @SuppressWarnings("unused")
     public FocusButton(Icon icon) {
       super(icon);
     }
   
+    @SuppressWarnings("unused")
     public FocusButton(String text, Icon icon) {
       super(text, icon);
     }// public FocusButton

Modified: gate/trunk/src/main/gate/jape/SinglePhaseTransducer.java
===================================================================
--- gate/trunk/src/main/gate/jape/SinglePhaseTransducer.java    2014-03-10 
11:10:08 UTC (rev 17615)
+++ gate/trunk/src/main/gate/jape/SinglePhaseTransducer.java    2014-03-10 
16:09:07 UTC (rev 17616)
@@ -285,6 +285,7 @@
     List<FSMInstance> acceptingFSMInstances = new LinkedList<FSMInstance>();
 
     // find the first node of the document
+    @SuppressWarnings("unchecked")
     Node startNode = ((List<Annotation>)annotationsByOffset.get(offsets
             .first())).get(0).getStartNode();
 
@@ -656,6 +657,7 @@
    * @return true if processing should keep going, false otherwise.
    */
 
+  @SuppressWarnings("unchecked")
   protected boolean fireRule(List<FSMInstance> acceptingFSMInstances,
           SearchState state, long lastNodeOff, SimpleSortedSet offsets,
           AnnotationSet inputAS, AnnotationSet outputAS, Document doc,

Modified: gate/trunk/src/main/gate/jape/SourceInfo.java
===================================================================
--- gate/trunk/src/main/gate/jape/SourceInfo.java       2014-03-10 11:10:08 UTC 
(rev 17615)
+++ gate/trunk/src/main/gate/jape/SourceInfo.java       2014-03-10 16:09:07 UTC 
(rev 17616)
@@ -149,6 +149,7 @@
       return (startLine <= lineNumber && lineNumber <= endLine);
     }
 
+    @SuppressWarnings("unused")
     public String getNumberedSource(String source) {
       return Strings.addLineNumbers(getSource(source), japeLine);
     }

Modified: gate/trunk/src/main/gate/jape/Transducer.java
===================================================================
--- gate/trunk/src/main/gate/jape/Transducer.java       2014-03-10 11:10:08 UTC 
(rev 17615)
+++ gate/trunk/src/main/gate/jape/Transducer.java       2014-03-10 16:09:07 UTC 
(rev 17616)
@@ -49,7 +49,7 @@
   /**
    * Shared featureMap
    */
-  protected Map benchmarkFeatures = new HashMap();
+  protected Map<Object,Object> benchmarkFeatures = new 
HashMap<Object,Object>();
 
   /**
    * Benchmark ID of this transducer.

Modified: gate/trunk/src/main/gate/persist/LuceneDataStoreImpl.java
===================================================================
--- gate/trunk/src/main/gate/persist/LuceneDataStoreImpl.java   2014-03-10 
11:10:08 UTC (rev 17615)
+++ gate/trunk/src/main/gate/persist/LuceneDataStoreImpl.java   2014-03-10 
16:09:07 UTC (rev 17616)
@@ -51,6 +51,8 @@
 import java.util.concurrent.TimeUnit;
 import java.util.concurrent.atomic.AtomicBoolean;
 
+import org.apache.commons.io.IOUtils;
+
 public class LuceneDataStoreImpl extends SerialDataStore implements
                                                         SearchableDataStore,
                                                         CorpusListener,
@@ -109,7 +111,7 @@
   /**
    * Index Parameters
    */
-  protected Map indexParameters;
+  protected Map<String,Object> indexParameters;
 
   /**
    * URL of the index
@@ -124,7 +126,7 @@
   /**
    * This is where we store the search parameters
    */
-  protected Map searchParameters;
+  protected Map<String,Object> searchParameters;
 
   /** Close the data store. */
   @Override
@@ -173,9 +175,9 @@
      * want to support old style: String versionInVersionFile = "1.0";
      * (but this means it will open *any* directory)
      */
+    BufferedReader isr = null;
     try {
-      FileReader fis = new FileReader(getVersionFile());
-      BufferedReader isr = new BufferedReader(fis);
+      isr = new BufferedReader(new FileReader(getVersionFile()));
       currentProtocolVersion = isr.readLine();
       String indexDirRelativePath = isr.readLine();
 
@@ -196,10 +198,12 @@
         this.searcher = new LuceneSearcher();
         ((LuceneSearcher)this.searcher).setLuceneDatastore(this);
       }
-      isr.close();
     } catch(IOException e) {
       throw new PersistenceException("Invalid storage directory: " + e);
+    } finally {
+      IOUtils.closeQuietly(isr);
     }
+    
     if(!isValidProtocolVersion(currentProtocolVersion))
       throw new PersistenceException("Invalid protocol version number: "
               + currentProtocolVersion);
@@ -439,7 +443,7 @@
    * Sets the Indexer to be used for indexing Datastore
    */
   @Override
-  public void setIndexer(Indexer indexer, Map indexParameters)
+  public void setIndexer(Indexer indexer, Map<String,Object> indexParameters)
           throws IndexException {
 
     this.indexer = indexer;
@@ -504,7 +508,7 @@
    * Search the datastore
    */
   @Override
-  public boolean search(String query, Map searchParameters)
+  public boolean search(String query, Map<String,Object> searchParameters)
           throws SearchException {
     return this.searcher.search(query, searchParameters);
   }
@@ -701,7 +705,7 @@
              * belongs to one easy way is to check all instances of
              * serial corpus loaded in memory
              */
-            List scs =
+            List<LanguageResource> scs =
                     Gate.getCreoleRegister().getLrInstances(
                             SerialCorpusImpl.class.getName());
             if(scs != null) {
@@ -709,7 +713,7 @@
                * we need to check which corpus the deleted class
                * belonged to
                */
-              Iterator iter = scs.iterator();
+              Iterator<LanguageResource> iter = scs.iterator();
               while(iter.hasNext()) {
                 SerialCorpusImpl sci = (SerialCorpusImpl)iter.next();
                 if(sci != null) {
@@ -728,7 +732,7 @@
              * relevant corpus won't exist in memory
              */
             if(corpusPID == null) {
-              List corpusPIDs = getLrIds(SerialCorpusImpl.class.getName());
+              List<String> corpusPIDs = 
getLrIds(SerialCorpusImpl.class.getName());
               if(corpusPIDs != null) {
                 for(int i = 0; i < corpusPIDs.size(); i++) {
                   Object corpusID = corpusPIDs.get(i);

Modified: gate/trunk/src/main/gate/persist/PersistenceException.java
===================================================================
--- gate/trunk/src/main/gate/persist/PersistenceException.java  2014-03-10 
11:10:08 UTC (rev 17615)
+++ gate/trunk/src/main/gate/persist/PersistenceException.java  2014-03-10 
16:09:07 UTC (rev 17616)
@@ -21,9 +21,9 @@
 /** This exception indicates failure during persistence operations.
   */
 public class PersistenceException extends GateException {
-  /** Debug flag */
-  private static final boolean DEBUG = false;
 
+  private static final long serialVersionUID = 3021649267577030175L;
+
   /** Default construction */
   public PersistenceException() { super(); }
 

Modified: gate/trunk/src/main/gate/persist/SerialDataStore.java
===================================================================
--- gate/trunk/src/main/gate/persist/SerialDataStore.java       2014-03-10 
11:10:08 UTC (rev 17615)
+++ gate/trunk/src/main/gate/persist/SerialDataStore.java       2014-03-10 
16:09:07 UTC (rev 17616)
@@ -67,6 +67,8 @@
 public class SerialDataStore
 extends AbstractFeatureBearer implements DataStore {
 
+  private static final long serialVersionUID = -2109852254191554517L;
+
   /** Debug flag */
   private static final boolean DEBUG = false;
 
@@ -807,6 +809,7 @@
   }
 
   /** Get a list of LRs that satisfy some set or restrictions */
+  @SuppressWarnings("rawtypes")
   @Override
   public List findLrIds(List constraints) throws PersistenceException {
     throw new UnsupportedOperationException(
@@ -817,6 +820,7 @@
    *  Get a list of LRs that satisfy some set or restrictions and are
    *  of a particular type
    */
+  @SuppressWarnings("rawtypes")
   @Override
   public List findLrIds(List constraints, String lrType) throws 
PersistenceException {
     throw new UnsupportedOperationException(

Modified: gate/trunk/src/main/gate/util/Benchmark.java
===================================================================
--- gate/trunk/src/main/gate/util/Benchmark.java        2014-03-10 11:10:08 UTC 
(rev 17615)
+++ gate/trunk/src/main/gate/util/Benchmark.java        2014-03-10 16:09:07 UTC 
(rev 17616)
@@ -155,7 +155,7 @@
    *          invoked on the objects.
    */
   public static void checkPoint(long startTime, String benchmarkID,
-          Object objectInvokingThisCheckPoint, Map benchmarkingFeatures) {
+          Object objectInvokingThisCheckPoint, Map<Object,Object> 
benchmarkingFeatures) {
 
     // check if logging is disabled
     if(!benchmarkingEnabled) return;
@@ -181,7 +181,7 @@
    *          invoked on the objects.
    */
   public static void checkPointWithDuration(long totalTime, String benchmarkID,
-          Object objectInvokingThisCheckPoint, Map benchmarkingFeatures) {
+          Object objectInvokingThisCheckPoint, Map<Object,Object> 
benchmarkingFeatures) {
 
     // check if logging is disabled
     if(!benchmarkingEnabled) return;
@@ -197,7 +197,7 @@
    * @see #checkPoint(long, String, Object, Map)
    */
   public static void checkPoint(String benchmarkID,
-          Object objectInvokingThisCheckPoint, Map benchmarkingFeatures) {
+          Object objectInvokingThisCheckPoint, Map<Object,Object> 
benchmarkingFeatures) {
     if(!benchmarkingEnabled) return;
     logCheckPoint("END", benchmarkID, objectInvokingThisCheckPoint,
             benchmarkingFeatures);
@@ -211,7 +211,7 @@
    */
   private static void logCheckPoint(String processingTimeOrFlag,
           String benchmarkID, Object objectInvokingThisCheckPoint,
-          Map benchmarkingFeatures) {
+          Map<Object,Object> benchmarkingFeatures) {
     // finally build the string to be logged
     StringBuilder messageToLog = new StringBuilder();
     messageToLog.append("" + System.currentTimeMillis() + " ");
@@ -286,7 +286,7 @@
    */
   public static void executeWithBenchmarking(Executable executable,
           String benchmarkID, Object objectInvokingThisCheckPoint,
-          Map benchmarkingFeatures) throws ExecutionException {
+          Map<Object,Object> benchmarkingFeatures) throws ExecutionException {
     if(!benchmarkingEnabled) {
       executable.execute();
     }
@@ -302,7 +302,7 @@
         executable.execute();
       }
       catch(Exception e) {
-        Map tempFeatures = new HashMap();
+        Map<Object,Object> tempFeatures = new HashMap<Object,Object>();
         if(benchmarkingFeatures != null) {
           tempFeatures.putAll(benchmarkingFeatures);
         }

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