From: tama3 <tama3@acee48c3-7b26-0410-bdac-b3d0e5314bbc>
Date: Tue, 25 Sep 2007 08:51:24 +0000 (+0000)
Subject: update control flow
X-Git-Url: http://git.osdn.net/view?a=commitdiff_plain;h=53cb0b2d48cbea683eb75721be7e82cc73d831bd;p=stigmata%2Fstigmata.git

update control flow

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/stigmata/trunk@210 acee48c3-7b26-0410-bdac-b3d0e5314bbc
---

diff --git a/src/main/java/jp/naist/se/stigmata/BirthmarkEngine.java b/src/main/java/jp/naist/se/stigmata/BirthmarkEngine.java
index b690a57..72b0d84 100755
--- a/src/main/java/jp/naist/se/stigmata/BirthmarkEngine.java
+++ b/src/main/java/jp/naist/se/stigmata/BirthmarkEngine.java
@@ -9,11 +9,9 @@ import java.io.ByteArrayOutputStream;
 import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
-import java.lang.reflect.InvocationTargetException;
 import java.net.MalformedURLException;
 import java.util.ArrayList;
 import java.util.HashMap;
-import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Stack;
@@ -35,11 +33,12 @@ import jp.naist.se.stigmata.reader.WarClassFileArchive;
 import jp.naist.se.stigmata.result.CertainPairComparisonResultSet;
 import jp.naist.se.stigmata.result.ExtractionResultSetFactory;
 import jp.naist.se.stigmata.result.RoundRobinComparisonResultSet;
-import jp.naist.se.stigmata.spi.BirthmarkSpi;
-
-import org.apache.commons.beanutils.BeanUtils;
 
 /**
+ * This class is birthmarking engine. 
+ * This class extracts birthmarks from given Java class files, compares results of extractions, and filters results of comparisons.
+ * 
+ * This class is not thread safe.
  * 
  * @author Haruaki Tamada
  * @version $Revision$ $Date$
@@ -53,11 +52,17 @@ public class BirthmarkEngine{
     private OperationType targetType;
     private BirthmarkExtractorFactory factory;
 
+    /**
+     * constructor.
+     */
     public BirthmarkEngine(BirthmarkEnvironment env){
         this.environment = env;
         factory = new BirthmarkExtractorFactory(env);
     }
 
+    /**
+     * returns an environment of this object.
+     */
     public BirthmarkEnvironment getEnvironment(){
         return environment;
     }
@@ -70,7 +75,14 @@ public class BirthmarkEngine{
         listeners.remove(listener);
     }
 
-    public ComparisonResultSet filter(String[] target, BirthmarkContext context) throws BirthmarkExtractionFailedException, BirthmarkComparisonFailedException{
+    /**
+     * filters comparison of birthmarks from target files.
+     * @see #extract(String[], BirthmarkContext)
+     * @see #compare(String[], BirthmarkContext)
+     * @see #filter(ComparisonResultSet)
+     * @see BirthmarkContext#getFilterTypes()
+     */
+    public synchronized ComparisonResultSet filter(String[] target, BirthmarkContext context) throws BirthmarkExtractionFailedException, BirthmarkComparisonFailedException{
         operationStart(OperationType.FILTER_BIRTHMARKS);
 
         ComparisonResultSet crs = compare(target, context);
@@ -81,7 +93,14 @@ public class BirthmarkEngine{
         return crs;
     }
 
-    public ComparisonResultSet filter(String[] targetX, String[] targetY, BirthmarkContext context) throws BirthmarkExtractionFailedException, BirthmarkComparisonFailedException{
+    /**
+     * filters comparison of birthmarks from given two targets targetx, and targetY
+     * @see #extract(String[], String[], BirthmarkContext)
+     * @see #compare(String[], String[], BirthmarkContext)
+     * @see #filter(ComparisonResultSet)
+     * @see BirthmarkContext#getFilterTypes()
+     */
+    public synchronized ComparisonResultSet filter(String[] targetX, String[] targetY, BirthmarkContext context) throws BirthmarkExtractionFailedException, BirthmarkComparisonFailedException{
         operationStart(OperationType.FILTER_BIRTHMARKS);
 
         ComparisonResultSet crs = compare(targetX, targetY, context);
@@ -92,7 +111,14 @@ public class BirthmarkEngine{
         return crs;
     }
 
-    public ComparisonResultSet filter(ExtractionResultSet er) throws BirthmarkExtractionFailedException, BirthmarkComparisonFailedException{
+    /**
+     * filters comparison of birthmarks from given extraction result set.
+     * @see #compare(ExtractionResultSet)
+     * @see #filter(ComparisonResultSet)
+     * @see ExtractionResultSet#getContext()
+     * @see BirthmarkContext#getFilterTypes()
+     */
+    public synchronized ComparisonResultSet filter(ExtractionResultSet er) throws BirthmarkExtractionFailedException, BirthmarkComparisonFailedException{
         operationStart(OperationType.FILTER_BIRTHMARKS);
 
         ComparisonResultSet crs = compare(er);
@@ -103,7 +129,12 @@ public class BirthmarkEngine{
         return crs;
     }
 
-    public ComparisonResultSet filter(ComparisonResultSet crs) throws BirthmarkExtractionFailedException, BirthmarkComparisonFailedException{
+    /**
+     * filters comparison of birthmarks.
+     * @see ExtractionResultSet#getContext()
+     * @see BirthmarkContext#getFilterTypes()
+     */
+    public synchronized ComparisonResultSet filter(ComparisonResultSet crs) throws BirthmarkExtractionFailedException, BirthmarkComparisonFailedException{
         operationStart(OperationType.FILTER_BIRTHMARKS);
 
         String[] filterTypes = crs.getContext().getFilterTypes();
@@ -129,11 +160,14 @@ public class BirthmarkEngine{
         return crs;
     }
 
-    public ComparisonPair compareDetails(BirthmarkSet bs1, BirthmarkSet bs2, BirthmarkContext context) throws BirthmarkComparisonFailedException{
+    /**
+     * compares two given birthmarks and returns comparison pair.
+     */
+    public synchronized ComparisonPair compareDetails(BirthmarkSet bs1, BirthmarkSet bs2, BirthmarkContext context) throws BirthmarkComparisonFailedException{
         return new ComparisonPair(bs1, bs2, context);
     }
 
-    public ComparisonResultSet compare(String[] target, BirthmarkContext context) throws BirthmarkExtractionFailedException, BirthmarkComparisonFailedException{
+    public synchronized ComparisonResultSet compare(String[] target, BirthmarkContext context) throws BirthmarkExtractionFailedException, BirthmarkComparisonFailedException{
         operationStart(OperationType.COMPARE_BIRTHMARKS);
 
         ExtractionResultSet er = extract(target, context);
@@ -144,7 +178,7 @@ public class BirthmarkEngine{
         return crs;
     }
 
-    public ComparisonResultSet compare(String[] targetX, String[] targetY, BirthmarkContext context) throws BirthmarkExtractionFailedException, BirthmarkComparisonFailedException{
+    public synchronized ComparisonResultSet compare(String[] targetX, String[] targetY, BirthmarkContext context) throws BirthmarkExtractionFailedException, BirthmarkComparisonFailedException{
         operationStart(OperationType.COMPARE_BIRTHMARKS);
 
         ExtractionResultSet er = extract(targetX, targetY, context);
@@ -155,7 +189,7 @@ public class BirthmarkEngine{
         return crs;
     }
 
-    public ComparisonResultSet compare(ExtractionResultSet er) throws BirthmarkExtractionFailedException, BirthmarkComparisonFailedException{
+    public synchronized ComparisonResultSet compare(ExtractionResultSet er) throws BirthmarkExtractionFailedException, BirthmarkComparisonFailedException{
         operationStart(OperationType.COMPARE_BIRTHMARKS);
         BirthmarkContext context = er.getContext();
 
@@ -181,46 +215,14 @@ public class BirthmarkEngine{
         return crs;
     }
 
-    public ExtractionResultSet extract(String[] target, BirthmarkContext context) throws BirthmarkExtractionFailedException{
+    public synchronized ExtractionResultSet extract(String[] target, BirthmarkContext context) throws BirthmarkExtractionFailedException{
         operationStart(OperationType.EXTRACT_BIRTHMARKS);
         ExtractionResultSet er = extract(target, null, context);
         operationDone(OperationType.EXTRACT_BIRTHMARKS);
         return er;
     }
 
-    public ExtractionResultSet extract(String[] targetX, String[] targetY, BirthmarkContext context) throws BirthmarkExtractionFailedException{
-        operationStart(OperationType.EXTRACT_BIRTHMARKS);
-        ExtractionResultSet er = ExtractionResultSetFactory.getInstance().createResultSet(context);
-
-        try{
-            switch(context.getComparisonMethod()){
-            case ROUND_ROBIN_SAME_PAIR:
-            case ROUND_ROBIN_WITHOUT_SAME_PAIR:
-                er.setTableType(false);
-                String[] targetXY = mergeTarget(targetX, targetY);
-                extractImpl2(targetXY, er, ExtractionTarget.TARGET_XY);
-                break;
-            case GUESSED_PAIR:
-            case SPECIFIED_PAIR:
-            case ROUND_ROBIN_XY:
-            default:
-                if(targetX == null || targetY == null){
-                    throw new BirthmarkExtractionFailedException("targetX or targetY is null");
-                }
-                er.setTableType(true);
-                extractImpl2(targetX, er, ExtractionTarget.TARGET_X);
-                extractImpl2(targetY, er, ExtractionTarget.TARGET_Y);
-                break;
-            }
-            return er;
-        } catch(IOException e){
-            throw new BirthmarkExtractionFailedException(e);
-        } finally{
-            operationDone(OperationType.EXTRACT_BIRTHMARKS);
-        }
-    }
-
-    public ExtractionResultSet extract2(String[] targetX, String[] targetY, BirthmarkContext context) throws BirthmarkExtractionFailedException{
+    public synchronized ExtractionResultSet extract(String[] targetX, String[] targetY, BirthmarkContext context) throws BirthmarkExtractionFailedException{
         operationStart(OperationType.EXTRACT_BIRTHMARKS);
         ExtractionResultSet er = ExtractionResultSetFactory.getInstance().createResultSet(context);
 
@@ -230,8 +232,7 @@ public class BirthmarkEngine{
             case ROUND_ROBIN_WITHOUT_SAME_PAIR:
                 er.setTableType(false);
                 String[] targetXY = mergeTarget(targetX, targetY);
-                BirthmarkSet[] s = extractImpl(targetXY, context);
-                er.setBirthmarkSets(ExtractionTarget.TARGET_XY, s);
+                extractImpl(targetXY, er, ExtractionTarget.TARGET_XY);
                 break;
             case GUESSED_PAIR:
             case SPECIFIED_PAIR:
@@ -241,11 +242,8 @@ public class BirthmarkEngine{
                     throw new BirthmarkExtractionFailedException("targetX or targetY is null");
                 }
                 er.setTableType(true);
-                BirthmarkSet[] extractResultX = extractImpl(targetX, context);
-                BirthmarkSet[] extractResultY = extractImpl(targetY, context);
-
-                er.setBirthmarkSets(ExtractionTarget.TARGET_X, extractResultX);
-                er.setBirthmarkSets(ExtractionTarget.TARGET_Y, extractResultY);
+                extractImpl(targetX, er, ExtractionTarget.TARGET_X);
+                extractImpl(targetY, er, ExtractionTarget.TARGET_Y);
                 break;
             }
             return er;
@@ -272,88 +270,25 @@ public class BirthmarkEngine{
         }
     }
 
-    private BirthmarkSet[] extractImpl2(String[] target, ExtractionResultSet er, ExtractionTarget et) throws BirthmarkExtractionFailedException, IOException{
+    private BirthmarkSet[] extractImpl(String[] target, ExtractionResultSet er, ExtractionTarget et) throws BirthmarkExtractionFailedException, IOException{
         ClassFileArchive[] archives = createArchives(target, environment);
         BirthmarkContext context = er.getContext();
         ExtractionUnit unit = context.getExtractionUnit();
 
         BirthmarkSet[] extractResult = null;
         if(unit == ExtractionUnit.CLASS){
-            extractFromClass2(archives, er, et);
+            extractFromClass(archives, er, et);
         }
         else if(unit == ExtractionUnit.PACKAGE){
-            extractFromPackage2(archives, er, et);
+            extractFromPackage(archives, er, et);
         }
         else if(unit == ExtractionUnit.ARCHIVE){
-            extractFromProduct2(archives, er, et);
+            extractFromProduct(archives, er, et);
         }
 
         return extractResult;
     }
 
-    private BirthmarkSet[] extractImpl(String[] target, BirthmarkContext context) throws BirthmarkExtractionFailedException, IOException{
-        ClassFileArchive[] archives = createArchives(target, environment);
-        BirthmarkExtractor[] extractors = createExtractors(context.getExtractionTypes(), environment);
-        ExtractionUnit unit = context.getExtractionUnit();
-
-        BirthmarkSet[] extractResult = null;
-        if(unit == ExtractionUnit.CLASS){
-            extractResult = extractFromClass(archives, extractors, environment);
-        }
-        else if(unit == ExtractionUnit.PACKAGE){
-            extractResult = extractFromPackage(archives, extractors, environment);
-        }
-        else if(unit == ExtractionUnit.ARCHIVE){
-            extractResult = extractFromProduct(archives, extractors, environment);
-        }
-
-        return extractResult;
-    }
-
-    private BirthmarkExtractor[] createExtractors(String[] birthmarkTypes, BirthmarkEnvironment environment){
-        List<BirthmarkExtractor> list = new ArrayList<BirthmarkExtractor>();
-        for(String type: birthmarkTypes){
-            BirthmarkExtractor extractor = createExtractor(type, environment);
-            list.add(extractor);
-        }
-        return list.toArray(new BirthmarkExtractor[list.size()]);
-    }
-
-    @SuppressWarnings("unchecked")
-    private BirthmarkExtractor createExtractor(String birthmarkType, BirthmarkEnvironment environment){
-        BirthmarkSpi spi = environment.getService(birthmarkType);
-        BirthmarkExtractor extractor = null;
-        if(spi != null){
-            extractor = spi.getExtractor();
-            try{
-                if(extractor != null){
-                    Map props = BeanUtils.describe(extractor);
-                    props.remove("class");
-                    props.remove("provider");
-                    for(Object keyObject: props.keySet()){
-                        String key = "extractor." + spi.getType() + "." + String.valueOf(keyObject);
-                        if(environment.getProperty(key) != null){
-                            BeanUtils.setProperty(
-                                extractor, (String)keyObject, environment.getProperty(key)
-                            );
-                        }
-                    }
-                }
-            } catch(InvocationTargetException e){
-                throw new InternalError(e.getMessage());
-            } catch(NoSuchMethodException e){
-                throw new InternalError(e.getMessage());
-            } catch(IllegalAccessException e){
-                throw new InternalError(e.getMessage());
-            }
-        }
-        if(extractor == null){
-            warnings.addMessage(new ExtractorNotFoundException("extractor not found"), birthmarkType);
-        }
-
-        return extractor;
-    }
-
     private byte[] inputStreamToByteArray(InputStream in) throws IOException{
         ByteArrayOutputStream bout = new ByteArrayOutputStream();
         int read;
@@ -367,7 +302,7 @@ public class BirthmarkEngine{
         return data;
     }
 
-    private void extractFromPackage2(ClassFileArchive[] archives, ExtractionResultSet er, ExtractionTarget et) throws IOException, BirthmarkExtractionFailedException{
+    private void extractFromPackage(ClassFileArchive[] archives, ExtractionResultSet er, ExtractionTarget et) throws IOException, BirthmarkExtractionFailedException{
         Map<String, BirthmarkSet> map = new HashMap<String, BirthmarkSet>();
         BirthmarkContext context = er.getContext();
 
@@ -408,40 +343,6 @@ public class BirthmarkEngine{
         }
     }
 
-    private BirthmarkSet[] extractFromPackage(ClassFileArchive[] archives, BirthmarkExtractor[] extractors, BirthmarkEnvironment context) throws IOException, BirthmarkExtractionFailedException{
-        Map<String, BirthmarkSet> list = new HashMap<String, BirthmarkSet>();
-
-        for(ClassFileArchive archive: archives){
-            for(ClassFileEntry entry: archive){
-                try{
-                    String name = entry.getClassName();
-                    String packageName = parsePackageName(name);
-                    BirthmarkSet bs = list.get(packageName);
-                    if(bs == null){
-                        bs = new BirthmarkSet(packageName, archive.getLocation());
-                        list.put(packageName, bs);
-                    }
-
-                    byte[] data = inputStreamToByteArray(entry.getLocation().openStream());
-                    for(BirthmarkExtractor extractor: extractors){
-                        if(extractor.isAcceptable(ExtractionUnit.PACKAGE)){
-                            Birthmark b = bs.getBirthmark(extractor.getProvider().getType());
-                            if(b == null){
-                                b = extractor.createBirthmark();
-                                bs.addBirthmark(b);
-                            }
-                            extractor.extract(b, new ByteArrayInputStream(data), context);
-                        }
-                    }
-                } catch(IOException e){
-                    warnings.addMessage(e, archive.getName());
-                }
-            }
-        }
-
-        return list.values().toArray(new BirthmarkSet[list.size()]);
-    }
-
     private String parsePackageName(String name){
         String n = name.replace('/', '.');
         int index = n.lastIndexOf('.');
@@ -452,7 +353,7 @@ public class BirthmarkEngine{
         return n;
     }
 
-    private void extractFromClass2(ClassFileArchive[] archives, ExtractionResultSet er,
+    private void extractFromClass(ClassFileArchive[] archives, ExtractionResultSet er,
             ExtractionTarget et) throws IOException, BirthmarkExtractionFailedException{
         BirthmarkContext context = er.getContext();
 
@@ -481,31 +382,7 @@ public class BirthmarkEngine{
         }
     }
 
-    private BirthmarkSet[] extractFromClass(ClassFileArchive[] archives,
-            BirthmarkExtractor[] extractors, BirthmarkEnvironment context) throws IOException, BirthmarkExtractionFailedException{
-        List<BirthmarkSet> list = new ArrayList<BirthmarkSet>();
-
-        for(ClassFileArchive archive: archives){
-            for(ClassFileEntry entry: archive){
-                try{
-                    BirthmarkSet birthmarkset = new BirthmarkSet(entry.getClassName(), entry.getLocation());
-                    list.add(birthmarkset);
-                    byte[] data = inputStreamToByteArray(entry.getLocation().openStream());
-                    for(BirthmarkExtractor extractor: extractors){
-                        if(extractor.isAcceptable(ExtractionUnit.CLASS)){
-                            Birthmark b = extractor.extract(new ByteArrayInputStream(data), context);
-                            birthmarkset.addBirthmark(b);
-                        }
-                    }
-                } catch(IOException e){
-                    warnings.addMessage(e, entry.getClassName());
-                }
-            }
-        }
-        return list.toArray(new BirthmarkSet[list.size()]);
-    }
-
-    private void extractFromProduct2(ClassFileArchive[] archives, ExtractionResultSet er, ExtractionTarget et) throws IOException, BirthmarkExtractionFailedException{
+    private void extractFromProduct(ClassFileArchive[] archives, ExtractionResultSet er, ExtractionTarget et) throws IOException, BirthmarkExtractionFailedException{
         BirthmarkContext context = er.getContext();
 
         for(ClassFileArchive archive: archives){
@@ -539,41 +416,6 @@ public class BirthmarkEngine{
         }
     }
 
-    private BirthmarkSet[] extractFromProduct(ClassFileArchive[] archives, BirthmarkExtractor[] extractors, BirthmarkEnvironment context) throws IOException, BirthmarkExtractionFailedException{
-        List<BirthmarkSet> list = new ArrayList<BirthmarkSet>();
-
-        for(ClassFileArchive archive: archives){
-            BirthmarkSet birthmarkset = new BirthmarkSet(archive.getName(), archive.getLocation());
-            list.add(birthmarkset);
-
-            for(ClassFileEntry entry: archive){
-                try{
-                    byte[] data = inputStreamToByteArray(entry.getLocation().openStream());
-                    for(BirthmarkExtractor extractor: extractors){
-                        if(extractor.isAcceptable(ExtractionUnit.ARCHIVE)){
-                            Birthmark b = birthmarkset.getBirthmark(extractor.getProvider().getType());
-                            if(b == null){
-                                b = extractor.createBirthmark();
-                                birthmarkset.addBirthmark(b);
-                            }
-                            extractor.extract(b, new ByteArrayInputStream(data), context);
-                        }
-                    }
-                } catch(IOException e){
-                    warnings.addMessage(e, entry.getClassName());
-                }
-            }
-        }
-        for(Iterator<BirthmarkSet> i = list.iterator(); i.hasNext(); ){
-            BirthmarkSet set = i.next();
-            if(set.getBirthmarksCount() == 0){
-                i.remove();
-            }
-        }
-
-        return list.toArray(new BirthmarkSet[list.size()]);
-    }
-
     private ClassFileArchive[] createArchives(String[] files, BirthmarkEnvironment environment) throws IOException, MalformedURLException{
         ClasspathContext bytecode = environment.getClasspathContext();
         List<ClassFileArchive> archives = new ArrayList<ClassFileArchive>();
diff --git a/src/main/java/jp/naist/se/stigmata/ComparisonResultSet.java b/src/main/java/jp/naist/se/stigmata/ComparisonResultSet.java
index 426d87d..1f824b0 100644
--- a/src/main/java/jp/naist/se/stigmata/ComparisonResultSet.java
+++ b/src/main/java/jp/naist/se/stigmata/ComparisonResultSet.java
@@ -48,5 +48,8 @@ public interface ComparisonResultSet extends Iterable<ComparisonPair>{
      */
     public BirthmarkSet[] getPairSources();
 
+    /**
+     * returns an array of comparison sources.
+     */
     public Iterator<BirthmarkSet> pairSources();
 }
diff --git a/src/main/java/jp/naist/se/stigmata/ExtractionResultSet.java b/src/main/java/jp/naist/se/stigmata/ExtractionResultSet.java
index 5cb5838..e2d86fd 100755
--- a/src/main/java/jp/naist/se/stigmata/ExtractionResultSet.java
+++ b/src/main/java/jp/naist/se/stigmata/ExtractionResultSet.java
@@ -7,56 +7,123 @@ package jp.naist.se.stigmata;
 import java.util.Iterator;
 
 /**
+ * This interface represents a set of extracted birthmarks.
  * 
  * @author Haruaki Tamada
  * @version $Revision$ $Date$
  */
 public interface ExtractionResultSet extends Iterable<BirthmarkSet>{
+    /**
+     * returns an environment of extraction result.
+     */
     public BirthmarkEnvironment getEnvironment();
 
+    /**
+     * returns a context of extraction result.
+     */
     public BirthmarkContext getContext();
 
     /**
-     * 
+     * sets extraction 
      */
     public boolean isTableType();
 
     /**
-     * 
+     * sets table type comparison flag.
+     * @see #isTableType()
      */
     public void setTableType(boolean flag);
 
+    /**
+     * returns types of extracted birthmarks.
+     */
     public String[] getBirthmarkTypes();
 
+    /**
+     * returns the number of target birthmark-set size (# of classes, packages, or jar files).
+     */
     public int getBirthmarkSetSize();
 
+    /**
+     * returns an iterator for all of birthmark-sets.
+     */
     public Iterator<BirthmarkSet> iterator();
 
+    /**
+     * returns a birthmark-set of given index.
+     */
     public BirthmarkSet getBirthmarkSet(int index);
 
+    /**
+     * returns a birthmark-set of given name.
+     */
     public BirthmarkSet getBirthmarkSet(String name);
 
+    /**
+     * returns an array for all of birthmark-sets.
+     */
     public BirthmarkSet[] getBirthmarkSets();
 
-    public int getBirthmarkSetSize(ExtractionTarget target);
-
+    /**
+     * removes given birthmark-set from this object.
+     */
     public void removeBirthmarkSet(BirthmarkSet bs);
 
+    /**
+     * removes all of birthmark-set this object has.
+     */
     public void removeAllBirthmarkSets();
 
+    /**
+     * returns the number of birthmark-set to specified extraction target (TARGET_X, TARGET_Y, TARGET_XY, or TARGET_BOTH).
+     */
+    public int getBirthmarkSetSize(ExtractionTarget target);
+
+    /**
+     * returns an iterator of birthmark-sets from specified extraction target.
+     */
     public Iterator<BirthmarkSet> birthmarkSets(ExtractionTarget target);
 
+    /**
+     * 
+     */
     public BirthmarkSet getBirthmarkSet(ExtractionTarget target, int index);
 
+    /**
+     * 
+     */
     public BirthmarkSet getBirthmarkSet(ExtractionTarget target, String setname);
 
+    /**
+     * 
+     */
     public BirthmarkSet[] getBirthmarkSets(ExtractionTarget target);
 
+    /**
+     * adds birthmark-set to extraction target.
+     * This method must be called when building birthmark-set is completely finished.
+     * All of birthmark must be added to birthmark-set.
+     * Because, if the concrete class of this interface stores given birthmark-set to database,
+     * birthmarks is parsed and store into target database in this method.
+     * @throws IllegalArgumentsException target is ExtractionTarget.TARGET_BOTH 
+     */
     public void addBirthmarkSet(ExtractionTarget target, BirthmarkSet set);
 
+    /**
+     * remove all of birthmark-set this object has, then, adds each birthmark-sets to this object. 
+     * @see #removeAllBirthmarkSets(ExtractionTarget)
+     * @see #addBirthmarkSet(ExtractionTarget, BirthmarkSet)
+     * @throws IllegalArgumentsException target is ExtractionTarget.TARGET_BOTH 
+     */
     public void setBirthmarkSets(ExtractionTarget target, BirthmarkSet[] sets);
 
+    /**
+     * remove specified birthmark-set from specified extraction target.
+     */
     public void removeBirthmarkSet(ExtractionTarget target, BirthmarkSet set);
 
+    /**
+     * remove all birthmark-sets from specified extraction target.
+     */
     public void removeAllBirthmarkSets(ExtractionTarget target);
 }
diff --git a/src/main/java/jp/naist/se/stigmata/ExtractionTarget.java b/src/main/java/jp/naist/se/stigmata/ExtractionTarget.java
index f16d17d..510f251 100755
--- a/src/main/java/jp/naist/se/stigmata/ExtractionTarget.java
+++ b/src/main/java/jp/naist/se/stigmata/ExtractionTarget.java
@@ -5,6 +5,7 @@ package jp.naist.se.stigmata;
  */
 
 /**
+ * This enum represents the mean of extracted birthmarks.
  * 
  * @author Haruaki Tamada
  * @version $Revision$ $Date$
diff --git a/src/main/java/jp/naist/se/stigmata/ExtractionUnit.java b/src/main/java/jp/naist/se/stigmata/ExtractionUnit.java
index 66772e7..94ad087 100755
--- a/src/main/java/jp/naist/se/stigmata/ExtractionUnit.java
+++ b/src/main/java/jp/naist/se/stigmata/ExtractionUnit.java
@@ -5,13 +5,19 @@ package jp.naist.se.stigmata;
  */
 
 /**
- * This enum type represents birthmark extraction unit. The name of
- * {@link jp.naist.se.stigmata.BirthmarkSet <code>BirthmarkSet</code>} is class
- * name, method name, package name, or product name.
+ * This enum type represents birthmark extraction unit.
+ * 
+ * The name of
+ * {@link jp.naist.se.stigmata.BirthmarkSet <code>BirthmarkSet</code>} will be
+ * class name, method name, package name, or product name.
  * 
  * @author Haruaki TAMADA
  * @version $Revision$ $Date$
  */
 public enum ExtractionUnit{
-    CLASS, PACKAGE, ARCHIVE,
+    CLASS,
+    PACKAGE,
+    ARCHIVE,
+    @Deprecated
+    METHOD,
 }
diff --git a/src/main/java/jp/naist/se/stigmata/Stigmata.java b/src/main/java/jp/naist/se/stigmata/Stigmata.java
index 824ee3b..6028a1b 100755
--- a/src/main/java/jp/naist/se/stigmata/Stigmata.java
+++ b/src/main/java/jp/naist/se/stigmata/Stigmata.java
@@ -25,14 +25,23 @@ import jp.naist.se.stigmata.utils.ConfigFileImporter;
  * @version $Revision$ $Date$
  */
 public class Stigmata{
+    /**
+     * instance. singleton pattern.
+     */
     private static Stigmata stigmata;
     private BirthmarkEnvironment defaultEnvironment;
     private List<BirthmarkEngineListener> listeners = new ArrayList<BirthmarkEngineListener>();
 
+    /**
+     * private constructor.
+     */
     private Stigmata(){
         configuration();
     }
 
+    /**
+     * gets only instance of this class.
+     */
     public static synchronized Stigmata getInstance(){
         if(stigmata == null){
             stigmata = new Stigmata();
@@ -40,21 +49,35 @@ public class Stigmata{
         return stigmata;
     }
 
+    /**
+     * creates a new birthmark context.
+     */
     public BirthmarkContext createContext(){
         return new BirthmarkContext(createEnvironment());
     }
 
+    /**
+     * creates a new birthmark environment.
+     */
     public BirthmarkEnvironment createEnvironment(){
         return new BirthmarkEnvironment(defaultEnvironment);
     }
 
+    /**
+     * creates a new birthmark engine.
+     */
     public BirthmarkEngine createEngine(){
-        BirthmarkEngine engine = new BirthmarkEngine(createEnvironment());
-        return engine;
+        return createEngine(createEnvironment());
     }
 
+    /**
+     * creates a new birthmark engine with given environment.
+     */
     public BirthmarkEngine createEngine(BirthmarkEnvironment environment){
         BirthmarkEngine engine = new BirthmarkEngine(environment);
+        for(BirthmarkEngineListener listener: listeners){
+            engine.addBirthmarkEngineListener(listener);
+        }
         return engine;
     }
 
diff --git a/src/main/java/jp/naist/se/stigmata/birthmarks/kgram/KGram.java b/src/main/java/jp/naist/se/stigmata/birthmarks/kgram/KGram.java
index 90a2634..1974c39 100644
--- a/src/main/java/jp/naist/se/stigmata/birthmarks/kgram/KGram.java
+++ b/src/main/java/jp/naist/se/stigmata/birthmarks/kgram/KGram.java
@@ -5,60 +5,106 @@ package jp.naist.se.stigmata.birthmarks.kgram;
  */
 
 import java.io.Serializable;
-import java.util.ArrayList;
+import java.lang.reflect.Array;
+import java.util.Arrays;
 import java.util.LinkedHashSet;
-import java.util.List;
 import java.util.Set;
 
 /**
+ * This class represents k-gram of the some sequence. 
  * 
  * @author Haruaki TAMADA
  * @version $Revision$ $Date$
  */
 public class KGram<T> implements Serializable{
     private static final long serialVersionUID = 273465874532523L;
-    private List<T> list = new ArrayList<T>();
+    // private List<T> list = new ArrayList<T>();
     private int maxLength = 4;
+    private T[] values;
 
+    /**
+     * constructor.
+     * @param kvalue the number of elements of this object.
+     */
     public KGram(int kvalue){
         setKValue(kvalue);
     }
 
+    /**
+     * sets k-value. 
+     * @param kvalue the number of elements of this object.
+     */
     public void setKValue(int kvalue){
         this.maxLength = kvalue;
     }
 
+    /**
+     * returns k-value which is the number of elements.
+     * @return the number of elements.
+     */
     public int getKValue(){
         return maxLength;
     }
 
+    /**
+     * returns string representation of this object.
+     */
     public String toString(){
         StringBuffer buffer = new StringBuffer("{ ");
         for(int i = 0; i < maxLength; i++){
             if(i != 0) buffer.append(", ");
-            buffer.append(list.get(i));
+            buffer.append(get(i));
         }
         buffer.append(" }");
         return new String(buffer);
     }
 
+    /**
+     * sets a element to given index.
+     * @param index element index.
+     * @param value element value.
+     */
+    @SuppressWarnings("unchecked")
     public void set(int index, T value){
         if(index < 0 || index >= maxLength){
-            throw new ArrayIndexOutOfBoundsException("expected 0-" + maxLength + ": " + index);
+            throw new ArrayIndexOutOfBoundsException("expected 0-" + (maxLength - 1) + ": " + index);
         }
-        if(list.size() == index){
-            list.add(value);
+        if(value == null){
+            throw new NullPointerException("null value");
         }
-        else{
-            list.set(index, value);
+        if(values == null){
+            values = (T[])Array.newInstance(value.getClass(), getKValue());
         }
+        values[index] = value;
     }
 
+    /**
+     * returns an object of given index.
+     */
     public T get(int index){
+        T returnValue = null;
         if(index < 0 || index >= maxLength){
-            throw new ArrayIndexOutOfBoundsException("expected 0-" + maxLength + ": " + index);
+            throw new ArrayIndexOutOfBoundsException("expected 0-" + (maxLength - 1) + ": " + index);
+        }
+        if(values != null){
+            returnValue = values[index];
+        }
+
+        return returnValue;
+    }
+
+    /**
+     * returns an array of elements this object has.
+     * @return
+     */
+    @SuppressWarnings("unchecked")
+    public T[] toArray(){
+        if(values == null){
+            throw new IllegalStateException("this object has no elements.");
         }
-        return list.get(index);
+        T[] newarray = (T[])Array.newInstance(values[0].getClass(), getKValue());
+        System.arraycopy(values, 0, newarray, 0, getKValue());
+        return newarray;
     }
 
     @SuppressWarnings("unchecked")
@@ -77,7 +123,7 @@ public class KGram<T> implements Serializable{
     }
 
     public int hashCode(){
-        return list.hashCode();
+        return Arrays.hashCode(values);
     }
 
     @SuppressWarnings("unchecked")
diff --git a/src/main/java/jp/naist/se/stigmata/ui/swing/StigmataFrame.java b/src/main/java/jp/naist/se/stigmata/ui/swing/StigmataFrame.java
index 3c16cf2..69f164f 100644
--- a/src/main/java/jp/naist/se/stigmata/ui/swing/StigmataFrame.java
+++ b/src/main/java/jp/naist/se/stigmata/ui/swing/StigmataFrame.java
@@ -177,7 +177,7 @@ public class StigmataFrame extends JFrame{
     public void compareRoundRobin(String[] targetX, String[] targetY, 
             BirthmarkContext context){
         try{
-            BirthmarkEngine engine = new BirthmarkEngine(context.getEnvironment());
+            BirthmarkEngine engine = getStigmata().createEngine(context.getEnvironment());
             ExtractionResultSet ers = engine.extract(targetX, targetY, context);
 
             RoundRobinComparisonResultPane compare = new RoundRobinComparisonResultPane(this, ers);
@@ -200,7 +200,7 @@ public class StigmataFrame extends JFrame{
     public void compareRoundRobinFilter(String[] targetX, String[] targetY, 
             BirthmarkContext context){
         try{
-            BirthmarkEngine engine = new BirthmarkEngine(context.getEnvironment());
+            BirthmarkEngine engine = getStigmata().createEngine(context.getEnvironment());
 
             ExtractionResultSet ers = engine.extract(targetX, targetY, context);
             ComparisonResultSet resultset = engine.compare(ers);
@@ -225,7 +225,7 @@ public class StigmataFrame extends JFrame{
 
     public void compareGuessedPair(String[] targetX, String[] targetY, BirthmarkContext context){
         try{
-            BirthmarkEngine engine = new BirthmarkEngine(context.getEnvironment());
+            BirthmarkEngine engine = getStigmata().createEngine(context.getEnvironment());
             ExtractionResultSet extraction = engine.extract(targetX, targetY, context);
             int comparePair = getNextCount("compare_pair");
 
@@ -253,7 +253,7 @@ public class StigmataFrame extends JFrame{
             Map<String, String> mapping = constructMapping(file);
 
             try{
-                BirthmarkEngine engine = new BirthmarkEngine(context.getEnvironment());
+                BirthmarkEngine engine = getStigmata().createEngine(context.getEnvironment());
                 context.setNameMappings(mapping);
                 ComparisonResultSet crs = engine.compare(targetX, targetY, context);
                 int comparePair = getNextCount("compare_pair");
@@ -318,7 +318,7 @@ public class StigmataFrame extends JFrame{
 
     public void extract(String[] targets, BirthmarkContext context){
         try{
-            BirthmarkEngine engine = new BirthmarkEngine(context.getEnvironment());
+            BirthmarkEngine engine = getStigmata().createEngine(context.getEnvironment());
             ExtractionResultSet ers = engine.extract(targets, context);
             showExtractionResult(ers);
         }catch(Throwable e){
diff --git a/src/main/java/jp/naist/se/stigmata/utils/WarClassLoader.java b/src/main/java/jp/naist/se/stigmata/utils/WarClassLoader.java
index ca69e94..fd48031 100755
--- a/src/main/java/jp/naist/se/stigmata/utils/WarClassLoader.java
+++ b/src/main/java/jp/naist/se/stigmata/utils/WarClassLoader.java
@@ -56,11 +56,14 @@ public class WarClassLoader extends URLClassLoader{
                         in.close();
                         out.close();
                     
-                        return defineClass(name, classdata, 0, classdata.length);
+                        clazz = defineClass(name, classdata, 0, classdata.length);
+                        break;
                     } catch(IOException exp){
                     }
                 }
             }
+        }
+        if(clazz == null){
             throw new ClassNotFoundException(name);
         }
         return clazz;