What to do with the Exception when you fail to close() a resource?
At least in code that I've seen, it is very common to ignore exceptions when closing a resource. In fact Apache Commons IO has a number of closeQuietly functions just for this purpose.

Also, the work being done with raFile should be wrapped in a try, with the close/closeQuietly being called in the finally. This ensures that close/closeQuietly is called even if an exception occurs while working with the file.

RandomAccessFile raFile = new RandomAccessFile(articleFile, "r");
try {
  if (this.isToInclude(raFile, conditionMap)) {
    return true;
  }
}
finally {
  IOUtils.closeQuietly(raFile);
}


Also, if you are using Java 7, you might want to check out the new try-with-resources statement.