diff --git a/src/main/java/org/javacomp/completion/CompletionResult.java b/src/main/java/org/javacomp/completion/CompletionResult.java
index a2597d0..ecdf51c 100644
--- a/src/main/java/org/javacomp/completion/CompletionResult.java
+++ b/src/main/java/org/javacomp/completion/CompletionResult.java
@@ -31,6 +31,9 @@ public static Builder builder() {
    * the cached completion.
    */
   boolean isIncrementalCompletion(Path filePath, int line, int column, String prefix) {
+    if(prefix.length()==0){
+      return false;
+    }
     if (!getFilePath().equals(filePath)) {
       return false;
     }
diff --git a/src/main/java/org/javacomp/completion/Completor.java b/src/main/java/org/javacomp/completion/Completor.java
index 9afc5d4..f5dbef7 100644
--- a/src/main/java/org/javacomp/completion/Completor.java
+++ b/src/main/java/org/javacomp/completion/Completor.java
@@ -66,6 +66,8 @@ public CompletionResult getCompletionResult(
     Optional<PositionContext> positionContext =
         PositionContext.createForPosition(moduleManager, filePath, line, contextColumn);
 
+    logger.fine("filePath: %s, line: %s, contextColumn: %s", filePath, line, contextColumn );
+
     if (!positionContext.isPresent()) {
       return CompletionResult.builder()
           .setCompletionCandidates(ImmutableList.of())
@@ -79,8 +81,10 @@ public CompletionResult getCompletionResult(
     ContentWithLineMap contentWithLineMap =
         ContentWithLineMap.create(positionContext.get().getFileScope(), fileManager, filePath);
     String prefix = contentWithLineMap.extractCompletionPrefix(line, column);
+    logger.fine("prefix:%s", prefix);
     // TODO: limit the number of the candidates.
     if (cachedCompletion.isIncrementalCompletion(filePath, line, column, prefix)) {
+      logger.fine("using cache");
       return getCompletionCandidatesFromCache(line, column, prefix);
     } else {
       cachedCompletion =
diff --git a/src/main/java/org/javacomp/completion/ContentWithLineMap.java b/src/main/java/org/javacomp/completion/ContentWithLineMap.java
index f3fa0da..9e9056a 100644
--- a/src/main/java/org/javacomp/completion/ContentWithLineMap.java
+++ b/src/main/java/org/javacomp/completion/ContentWithLineMap.java
@@ -28,6 +28,7 @@ abstract class ContentWithLineMap {
   /** Gets the content before cursor position (line, column) as prefix for completion. */
   String extractCompletionPrefix(int line, int column) {
     int position = LineMapUtil.getPositionFromZeroBasedLineAndColumn(getLineMap(), line, column);
+    logger.fine("column:%s, position:%s", column, position);
     if (position < 0) {
       logger.warning(
           "Position of (%s, %s): %s is negative when getting completion prefix for file %s",
@@ -44,6 +45,7 @@ String extractCompletionPrefix(int line, int column) {
     while (start >= 0 && Character.isJavaIdentifierPart(getContent().charAt(start))) {
       start--;
     }
+    logger.fine("start:%s", start);
     return getContent().subSequence(start + 1, position).toString();
   }
 
diff --git a/src/main/java/org/javacomp/file/FileWatcher.java b/src/main/java/org/javacomp/file/FileWatcher.java
index 96410d4..9c09b30 100644
--- a/src/main/java/org/javacomp/file/FileWatcher.java
+++ b/src/main/java/org/javacomp/file/FileWatcher.java
@@ -131,6 +131,7 @@ synchronized void shutdown() {
   }
 
   synchronized void notifyFileChange(Path path, WatchEvent.Kind<?> eventKind) {
+    logger.fine("path: %s", path);
     if (PathUtils.shouldIgnorePath(path, projectRoot, ignorePathMatchers)) {
       return;
     }
@@ -179,15 +180,18 @@ private void handleWatchEvent(Path dir, WatchEvent<Path> event) {
       Path fullPath = dir.resolve(event.context());
 
       if (PathUtils.shouldIgnorePath(fullPath, projectRoot, ignorePathMatchers)) {
+        logger.fine("%s ignored", fullPath);
         return;
       }
 
       if (fileSnapshotPaths.contains(fullPath)) {
+        logger.fine("%s is on fileSnapshotPaths", fullPath);
         // The file is managed by file snapshots. Ignore file system events.
         return;
       }
 
       if (Files.isDirectory(fullPath)) {
+        logger.fine("%s is a directory", fullPath);
         handleDirectoryEvent(fullPath, eventKind);
         return;
       }
@@ -196,6 +200,7 @@ private void handleWatchEvent(Path dir, WatchEvent<Path> event) {
     }
 
     private void handleDirectoryEvent(Path path, WatchEvent.Kind<?> eventKind) {
+      logger.fine("path:%s", path);
       if (eventKind == StandardWatchEventKinds.ENTRY_CREATE) {
         // New directory created, watch it.
         watchNewDirectory(path);
diff --git a/src/main/java/org/javacomp/logging/JLogger.java b/src/main/java/org/javacomp/logging/JLogger.java
index d928c10..001cc82 100644
--- a/src/main/java/org/javacomp/logging/JLogger.java
+++ b/src/main/java/org/javacomp/logging/JLogger.java
@@ -18,6 +18,14 @@ public class JLogger {
   private static volatile boolean hasFileHandler = false;
   private final Logger javaLogger;
 
+  static {
+    // remove default logging handlers, we only support a FileHandler set through setLogFile
+    Logger rootLogger = Logger.getLogger("");
+    for(Handler handler : rootLogger.getHandlers()) {
+      rootLogger.removeHandler(handler);
+    }
+  }
+
   public static synchronized void setLogFile(String filePath) {
     Logger rootLogger = Logger.getLogger("");
 
@@ -38,9 +46,6 @@ public static synchronized void setLogFile(String filePath) {
   public static synchronized void setLogLevel(Level level) {
     Logger rootLogger = Logger.getLogger("");
     rootLogger.setLevel(level);
-    for (Handler handler : rootLogger.getHandlers()) {
-      handler.setLevel(level);
-    }
   }
 
   private JLogger(String enclosingClassName) {
@@ -50,14 +55,14 @@ private JLogger(String enclosingClassName) {
   /** Creates a {@link JLogger} and sets its tag to the name of the class that calls it. */
   public static JLogger createForEnclosingClass() {
     StackTraceElement[] stackTrace = new Throwable().getStackTrace();
-    // The top of the stack trace is this method. The one belows it is the caller class.
+    // The top of the stack trace is this method. The one below it is the caller class.
     String enclosingClassName = stackTrace[1].getClassName();
     return new JLogger(enclosingClassName);
   }
 
   /** Logs a message at severe level. */
   public void severe(String msg) {
-    log(Level.SEVERE, msg, null /* thrown */);
+    log(Level.SEVERE, msg);
   }
 
   /**
@@ -67,7 +72,7 @@ public void severe(String msg) {
    * @param args arguments to be filled into {@code msgfmt}
    */
   public void severe(String msgfmt, Object... args) {
-    log(Level.SEVERE, String.format(msgfmt, args), null /* thrown */);
+    log(Level.SEVERE, msgfmt, args);
   }
 
   /**
@@ -78,12 +83,12 @@ public void severe(String msgfmt, Object... args) {
    * @param args arguments to be filled into {@code msgfmt}
    */
   public void severe(Throwable thrown, String msgfmt, Object... args) {
-    log(Level.SEVERE, String.format(msgfmt, args), thrown);
+    log(Level.SEVERE, thrown, msgfmt, args);
   }
 
   /** Logs a message at warning level. */
   public void warning(String msg) {
-    log(Level.WARNING, msg, null /* thrown */);
+    log(Level.WARNING, msg);
   }
 
   /**
@@ -93,7 +98,7 @@ public void warning(String msg) {
    * @param args arguments to be filled into {@code msgfmt}
    */
   public void warning(String msgfmt, Object... args) {
-    log(Level.WARNING, String.format(msgfmt, args), null /* thrown */);
+    log(Level.WARNING, msgfmt, args);
   }
 
   /**
@@ -105,12 +110,12 @@ public void warning(String msgfmt, Object... args) {
    * @param args arguments to be filled into {@code msgfmt}
    */
   public void warning(Throwable thrown, String msgfmt, Object... args) {
-    log(Level.WARNING, String.format(msgfmt, args), thrown);
+    log(Level.WARNING, thrown, msgfmt, args);
   }
 
   /** Logs a message at info level. */
   public void info(String msg) {
-    log(Level.INFO, msg, null /* thrown */);
+    log(Level.INFO, msg);
   }
 
   /**
@@ -120,12 +125,12 @@ public void info(String msg) {
    * @param args arguments to be filled into {@code msgfmt}
    */
   public void info(String msgfmt, Object... args) {
-    log(Level.INFO, String.format(msgfmt, args), null /* thrown */);
+    log(Level.INFO, msgfmt, args);
   }
 
   /** Logs a message at fine level. */
   public void fine(String msg) {
-    log(Level.FINE, msg, null /* thrown */);
+    log(Level.FINE, msg);
   }
 
   /**
@@ -135,10 +140,26 @@ public void fine(String msg) {
    * @param args arguments to be filled into {@code msgfmt}
    */
   public void fine(String msgfmt, Object... args) {
-    log(Level.FINE, String.format(msgfmt, args), null /* thrown */);
+    log(Level.FINE, msgfmt, args);
+  }
+
+  public void log(Level level, String msgFormat, Object... msgArgs) {
+    log(level, null, msgFormat, msgArgs);
   }
 
-  private void log(Level level, String msg, @Nullable Throwable thrown) {
+  public void log(Level level, String msg) {
+    log(level, null, msg);
+  }
+
+  public void log(Level level, @Nullable Throwable thrown, String msgFormat, Object... msgArgs) {
+    if(!javaLogger.isLoggable(level))
+      return;
+    log(level, thrown, String.format(msgFormat, msgArgs));
+  }
+
+  public void log(Level level, @Nullable Throwable thrown, String msg) {
+    if(!javaLogger.isLoggable(level))
+      return;
     LogRecord logRecord = new LogRecord(level, msg);
     if (thrown != null) {
       logRecord.setThrown(thrown);
diff --git a/src/main/java/org/javacomp/model/PackageScope.java b/src/main/java/org/javacomp/model/PackageScope.java
index 050f9a7..b5c1c05 100644
--- a/src/main/java/org/javacomp/model/PackageScope.java
+++ b/src/main/java/org/javacomp/model/PackageScope.java
@@ -11,10 +11,13 @@
 import java.util.List;
 import java.util.Optional;
 import java.util.Set;
+import org.javacomp.logging.JLogger;
 
 /** Scope of sub packages and files in a package. */
 public class PackageScope implements EntityScope {
-  // Map of simple names -> subPackages.
+  static JLogger logger= JLogger.createForEnclosingClass();
+
+// Map of simple names -> subPackages.
   private final Multimap<String, PackageEntity> subPackages;
   private final Set<FileScope> files;
 
@@ -53,11 +56,13 @@ public void removePackage(PackageEntity entity) {
   }
 
   public void addFile(FileScope fileScope) {
-    files.add(fileScope);
+    if(!files.add(fileScope))
+      logger.warning("couldn't add fileScope:%s", fileScope);
   }
 
   public void removeFile(FileScope fileScope) {
-    files.remove(fileScope);
+    if(!files.remove(fileScope))
+      logger.warning("couln't remove fileScope:%s", fileScope);
   }
 
   /** @return whether the package has sub packages or files. */
diff --git a/src/main/java/org/javacomp/parser/AstScanner.java b/src/main/java/org/javacomp/parser/AstScanner.java
index d2db3cc..7ee87d5 100644
--- a/src/main/java/org/javacomp/parser/AstScanner.java
+++ b/src/main/java/org/javacomp/parser/AstScanner.java
@@ -255,6 +255,7 @@ public Void visitMethod(MethodTree node, EntityScope currentScope) {
     methodEntity.setParameters(parameterListBuilder.build());
 
     // TODO: distinguish between static and non-static methods.
+    logger.fine("fileScope:%s, methodEntity:%s", fileScope, methodEntity);
     currentScope.addEntity(methodEntity);
     List<String> previousQualifiers = this.currentQualifiers;
     // No entity defined inside method scope is qualified.
diff --git a/src/main/java/org/javacomp/parser/LineMapUtil.java b/src/main/java/org/javacomp/parser/LineMapUtil.java
index ce13949..a601106 100644
--- a/src/main/java/org/javacomp/parser/LineMapUtil.java
+++ b/src/main/java/org/javacomp/parser/LineMapUtil.java
@@ -7,7 +7,7 @@ public final class LineMapUtil {
   private LineMapUtil() {}
 
   public static int getPositionFromZeroBasedLineAndColumn(LineMap lineMap, int line, int column) {
-    // LineMap accepts 1-based line and column numbers.
-    return (int) lineMap.getPosition(line + 1, column + 1);
+    // LineMap accepts 1-based line.
+    return (int)lineMap.getStartPosition(line+1)+column;
   }
 }
diff --git a/src/main/java/org/javacomp/project/FileSystemModuleManager.java b/src/main/java/org/javacomp/project/FileSystemModuleManager.java
index 89b91f4..4b5bd0d 100644
--- a/src/main/java/org/javacomp/project/FileSystemModuleManager.java
+++ b/src/main/java/org/javacomp/project/FileSystemModuleManager.java
@@ -77,8 +77,10 @@ public synchronized void addOrUpdateFile(Path path, boolean fixContentForParsing
   }
 
   private void addOrUpdateFile(Module module, Path path, boolean fixContentForParsing) {
+    logger.fine("path:%s", path);
     try {
       Optional<FileScope> fileScope = parser.parseSourceFile(path, fixContentForParsing);
+      logger.fine("fileScope:%s", fileScope);
       if (fileScope.isPresent()) {
         module.addOrReplaceFileScope(fileScope.get());
       }
diff --git a/src/main/java/org/javacomp/project/Project.java b/src/main/java/org/javacomp/project/Project.java
index 5c13ffa..22f203e 100644
--- a/src/main/java/org/javacomp/project/Project.java
+++ b/src/main/java/org/javacomp/project/Project.java
@@ -102,6 +102,7 @@ public synchronized void loadTypeIndexFile(String typeIndexFile) {
   private synchronized void addOrUpdateFile(Path filePath) {
     // Only fix content for files that are under completion.
     boolean fixContentForParsing = lastCompletedFile != null && lastCompletedFile.equals(filePath);
+    logger.fine("fixContentForParsing:%s", fixContentForParsing);
     moduleManager.addOrUpdateFile(filePath, fixContentForParsing);
   }
 
diff --git a/src/main/java/org/javacomp/reference/DefinitionSolver.java b/src/main/java/org/javacomp/reference/DefinitionSolver.java
index 3380694..5983f41 100644
--- a/src/main/java/org/javacomp/reference/DefinitionSolver.java
+++ b/src/main/java/org/javacomp/reference/DefinitionSolver.java
@@ -71,6 +71,7 @@ public List<? extends Entity> getDefinitionEntities(
         PositionContext.createForPosition(moduleManager, filePath, line, column);
 
     if (!positionContext.isPresent()) {
+      logger.fine("positionContext not present");
       return ImmutableList.of();
     }
 
@@ -86,8 +87,10 @@ List<? extends Entity> getDefinitionEntities(Module module, PositionContext posi
     if (leafTree instanceof LiteralTree) {
       // LiteralTree is also an ExpressionTree. We don't want to show type definitions for literal
       // constants.
+      logger.fine("leafTree is a LiteralTree");
       return ImmutableList.of();
     } else if (leafTree instanceof ExpressionTree) {
+      logger.fine("leafTree is a ExpressionTree");
       Set<Entity.Kind> allowedKinds = ALLOWED_ENTITY_KINDS;
       if (treeIsMethodName(leafTree, parentTree)) {
         // parentTree is the method we need to solve.
diff --git a/src/main/java/org/javacomp/server/JavaComp.java b/src/main/java/org/javacomp/server/JavaComp.java
index f81e469..44b2b54 100644
--- a/src/main/java/org/javacomp/server/JavaComp.java
+++ b/src/main/java/org/javacomp/server/JavaComp.java
@@ -122,17 +122,18 @@ public synchronized void initialize(
     if (initializeOptions != null) {
       mergeOptions(options, initializeOptions);
     }
-
-    logger.info("Initializing project: %s", projectRootUri);
-    logger.info(
-        "Options:\n  logPath: %s\n  logLevel: %s\n" + "  ignorePaths: %s\n  typeIndexFiles: %s",
-        options.logPath, options.logLevel, options.ignorePaths, options.typeIndexFiles);
+    
     if (options.logPath != null) {
       JLogger.setLogFile(options.logPath);
     }
     if (options.logLevel != null) {
       JLogger.setLogLevel(options.getLogLevel());
     }
+    logger.info("Initializing project: %s", projectRootUri);
+    logger.info(
+        "Options:\n  logPath: %s\n  logLevel: %s\n" + "  ignorePaths: %s\n  typeIndexFiles: %s",
+        options.logPath, options.logLevel, options.ignorePaths, options.typeIndexFiles);
+
     if (options.ignorePaths != null) {
       ignorePaths = options.getIgnorePaths();
     } else {
diff --git a/src/main/java/org/javacomp/server/handler/textdocument/DefinitionHandler.java b/src/main/java/org/javacomp/server/handler/textdocument/DefinitionHandler.java
index 11f1c13..211111e 100644
--- a/src/main/java/org/javacomp/server/handler/textdocument/DefinitionHandler.java
+++ b/src/main/java/org/javacomp/server/handler/textdocument/DefinitionHandler.java
@@ -4,6 +4,7 @@
 import java.nio.file.Paths;
 import java.util.List;
 import java.util.Objects;
+import org.javacomp.logging.JLogger;
 import org.javacomp.model.Entity;
 import org.javacomp.model.EntityScope;
 import org.javacomp.model.FileScope;
@@ -22,6 +23,7 @@
  * https://github.com/Microsoft/language-server-protocol/blob/master/protocol.md#textDocument_definition
  */
 public class DefinitionHandler extends RequestHandler<TextDocumentPositionParams> {
+  private static final JLogger logger=JLogger.createForEnclosingClass();
   private final Server server;
 
   public DefinitionHandler(Server server) {
@@ -43,6 +45,7 @@ public List<Location> handleRequest(Request<TextDocumentPositionParams> request)
     return definitions.stream()
         .map(
             entity -> {
+              logger.fine("getting location for %s", entity);
               com.google.common.collect.Range<Integer> range = entity.getSymbolRange();
               EntityScope scope = entity.getScope();
               while (!(scope instanceof FileScope) && scope.getParentScope().isPresent()) {
@@ -58,6 +61,7 @@ public List<Location> handleRequest(Request<TextDocumentPositionParams> request)
                 // If the file scope is not created from a source code (e.g. it's created from
                 // a type index JSON file or class file), there is no souce code that defines the
                 // symbol.
+                logger.fine("%s is on a non SOURCE_COCE fileScope");
                 return null;
               }
               if (!fileScope.getLineMap().isPresent()) {