diff --git a/src/file_analysis/Analyzer.h b/src/file_analysis/Analyzer.h
index 6ba76317a7..d32532b264 100644
--- a/src/file_analysis/Analyzer.h
+++ b/src/file_analysis/Analyzer.h
@@ -17,6 +17,11 @@ class File;
  */
 class Analyzer {
 public:
+
+	/**
+	 * Destructor.  Nothing special about it. Virtual since we definitely expect
+	 * to delete instances of derived classes via pointers to this class.
+	 */
 	virtual ~Analyzer()
 		{
 		DBG_LOG(DBG_FILE_ANALYSIS, "Destroy file analyzer %d", tag);
@@ -24,7 +29,10 @@ public:
 		}
 
 	/**
-	 * Subclasses may override this to receive file data non-sequentially.
+	 * Subclasses may override this metod to receive file data non-sequentially.
+	 * @param data points to start of a chunk of file data.
+	 * @param len length in bytes of the chunk of data pointed to by \a data.
+	 * @param offset the byte offset within full file that data chunk starts.
 	 * @return true if the analyzer is still in a valid state to continue
 	 *         receiving data/events or false if it's essentially "done".
 	 */
@@ -32,7 +40,9 @@ public:
 		{ return true; }
 
 	/**
-	 * Subclasses may override this to receive file sequentially.
+	 * Subclasses may override this method to receive file sequentially.
+	 * @param data points to start of the next chunk of file data.
+	 * @param len length in bytes of the chunk of data pointed to by \a data.
 	 * @return true if the analyzer is still in a valid state to continue
 	 *         receiving data/events or false if it's essentially "done".
 	 */
@@ -40,7 +50,7 @@ public:
 		{ return true; }
 
 	/**
-	 * Subclasses may override this to specifically handle an EOF signal,
+	 * Subclasses may override this method to specifically handle an EOF signal,
 	 * which means no more data is going to be incoming and the analyzer
 	 * may be deleted/cleaned up soon.
 	 * @return true if the analyzer is still in a valid state to continue
@@ -50,7 +60,10 @@ public:
 		{ return true; }
 
 	/**
-	 * Subclasses may override this to handle missing data in a file stream.
+	 * Subclasses may override this method to handle missing data in a file.
+	 * @param offset the byte offset within full file at which the missing
+	 *        data chunk occurs.
+	 * @param len the number of missing bytes.
 	 * @return true if the analyzer is still in a valid state to continue
 	 *         receiving data/events or false if it's essentially "done".
 	 */
@@ -73,8 +86,10 @@ public:
 	File* GetFile() const { return file; }
 
 	/**
+	 * Retrieves an analyzer tag field from full analyzer argument record.
+	 * @param args an \c AnalyzerArgs (script-layer type) value.
 	 * @return the analyzer tag equivalent of the 'tag' field from the
-	 *         AnalyzerArgs value \a args.
+	 *         \c AnalyzerArgs value \a args.
 	 */
 	static FA_Tag ArgsTag(const RecordVal* args)
 		{
@@ -84,6 +99,13 @@ public:
 		}
 
 protected:
+
+	/**
+	 * Constructor.  Only derived classes are meant to be instantiated.
+	 * @param arg_args an \c AnalyzerArgs (script-layer type) value specifiying
+	 *        tunable options, if any, related to a particular analyzer type.
+	 * @param arg_file the file to which the the analyzer is being attached.
+	 */
 	Analyzer(RecordVal* arg_args, File* arg_file)
 	    : tag(file_analysis::Analyzer::ArgsTag(arg_args)),
 	      args(arg_args->Ref()->AsRecordVal()),
@@ -91,9 +113,10 @@ protected:
 		{}
 
 private:
-	FA_Tag tag;
-	RecordVal* args;
-	File* file;
+
+	FA_Tag tag; /**< The particular analyzer type of the analyzer instance. */
+	RecordVal* args; /**< \c AnalyzerArgs val gives tunable analyzer params. */
+	File* file; /**< The file to which the analyzer is attached. */
 };
 
 typedef file_analysis::Analyzer* (*AnalyzerInstantiator)(RecordVal* args,
diff --git a/src/file_analysis/AnalyzerSet.h b/src/file_analysis/AnalyzerSet.h
index e982cc9f8f..7481e9020e 100644
--- a/src/file_analysis/AnalyzerSet.h
+++ b/src/file_analysis/AnalyzerSet.h
@@ -16,67 +16,144 @@ class File;
 declare(PDict,Analyzer);
 
 /**
- * A set of file analysis analyzers indexed by AnalyzerArgs.  Allows queueing
- * of addition/removals so that those modifications can happen at well-defined
- * times (e.g. to make sure a loop iterator isn't invalidated).
+ * A set of file analysis analyzers indexed by an \c AnalyzerArgs (script-layer
+ * type) value.  Allows queueing of addition/removals so that those
+ * modifications can happen at well-defined times (e.g. to make sure a loop
+ * iterator isn't invalidated).
  */
 class AnalyzerSet {
 public:
+
+	/**
+	 * Constructor.  Nothing special.
+	 * @param arg_file the file to which all analyzers in the set are attached.
+	 */
 	AnalyzerSet(File* arg_file);
 
+	/**
+	 * Destructor.  Any queued analyzer additions/removals are aborted and
+	 * will not occur.
+	 */
 	~AnalyzerSet();
 
 	/**
+	 * Attach an analyzer to #file immediately.
+	 * @param args an \c AnalyzerArgs value which specifies an analyzer.
 	 * @return true if analyzer was instantiated/attached, else false.
 	 */
 	bool Add(RecordVal* args);
 
 	/**
+	 * Queue the attachment of an analyzer to #file.
+	 * @param args an \c AnalyzerArgs value which specifies an analyzer.
 	 * @return true if analyzer was able to be instantiated, else false.
 	 */
 	bool QueueAdd(RecordVal* args);
 
 	/**
+	 * Remove an analyzer from #file immediately.
+	 * @param args an \c AnalyzerArgs value which specifies an analyzer.
 	 * @return false if analyzer didn't exist and so wasn't removed, else true.
 	 */
 	bool Remove(const RecordVal* args);
 
 	/**
+	 * Queue the removal of an analyzer from #file.
+	 * @param args an \c AnalyzerArgs value which specifies an analyzer.
 	 * @return true if analyzer exists at time of call, else false;
 	 */
 	bool QueueRemove(const RecordVal* args);
 
 	/**
-	 * Perform all queued modifications to the currently active analyzers.
+	 * Perform all queued modifications to the current analyzer set.
 	 */
 	void DrainModifications();
 
+	/**
+	 * Prepare the analyzer set to be iterated over.
+	 * @see Dictionary#InitForIteration
+	 * @return an iterator that may be used to loop over analyzers in the set.
+	 */
 	IterCookie* InitForIteration() const
 		{ return analyzer_map.InitForIteration(); }
 
+	/**
+	 * Get next entry in the analyzer set.
+	 * @see Dictionary#NextEntry
+	 * @param c a set iterator.
+	 * @return the next analyzer in the set or a null pointer if there is no
+	 *         more left (in that case the cookie is also deleted).
+	 */
 	file_analysis::Analyzer* NextEntry(IterCookie* c)
 		{ return analyzer_map.NextEntry(c); }
 
 protected:
+
+	/**
+	 * Get a hash key which represents an analyzer instance.
+	 * @param args an \c AnalyzerArgs value which specifies an analyzer.
+	 * @return the hash key calculated from \a args
+	 */
 	HashKey* GetKey(const RecordVal* args) const;
+
+	/**
+	 * Create an instance of a file analyzer.
+	 * @param args an \c AnalyzerArgs value which specifies an analyzer.
+	 * @return a new file analyzer instance.
+	 */
 	file_analysis::Analyzer* InstantiateAnalyzer(RecordVal* args) const;
+
+	/**
+	 * Insert an analyzer instance in to the set.
+	 * @param a an analyzer instance.
+	 * @param key the hash key which represents the analyzer's \c AnalyzerArgs.
+	 */
 	void Insert(file_analysis::Analyzer* a, HashKey* key);
+
+	/**
+	 * Remove an analyzer instance from the set.
+	 * @param tag enumarator which specifies type of the analyzer to remove,
+	 *        just used for debugging messages.
+	 * @param key the hash key which represents the analyzer's \c AnalyzerArgs.
+	 */
 	bool Remove(FA_Tag tag, HashKey* key);
 
 private:
-	File* file;
+
+	File* file;                                  /**< File which owns the set */
 	CompositeHash* analyzer_hash;                /**< AnalyzerArgs hashes. */
 	PDict(file_analysis::Analyzer) analyzer_map; /**< Indexed by AnalyzerArgs. */
 
+	/**
+	 * Abstract base class for analyzer set modifications.
+	 */
 	class Modification {
 	public:
 		virtual ~Modification() {}
+
+		/**
+		 * Perform the modification on an analyzer set.
+		 * @param set the analyzer set on which the modification will happen.
+		 * @return true if the modification altered \a set.
+		 */
 		virtual bool Perform(AnalyzerSet* set) = 0;
+
+		/**
+		 * Don't perform the modification on the analyzer set and clean up.
+		 */
 		virtual void Abort() = 0;
 	};
 
+	/**
+	 * Represents a request to add an analyzer to an analyzer set.
+	 */
 	class AddMod : public Modification {
 	public:
+		/**
+		 * Construct request which can add an analyzer to an analyzer set.
+		 * @param arg_a an analyzer instance to add to an analyzer set.
+		 * @param arg_key hash key representing the analyzer's \c AnalyzerArgs.
+		 */
 		AddMod(file_analysis::Analyzer* arg_a, HashKey* arg_key)
 			: Modification(), a(arg_a), key(arg_key) {}
 		virtual ~AddMod() {}
@@ -88,8 +165,16 @@ private:
 		HashKey* key;
 	};
 
+	/**
+	 * Represents a request to remove an analyzer from an analyzer set.
+	 */
 	class RemoveMod : public Modification {
 	public:
+		/**
+		 * Construct request which can remove an analyzer from an analyzer set.
+		 * @param arg_a an analyzer instance to add to an analyzer set.
+		 * @param arg_key hash key representing the analyzer's \c AnalyzerArgs.
+		 */
 		RemoveMod(FA_Tag arg_tag, HashKey* arg_key)
 			: Modification(), tag(arg_tag), key(arg_key) {}
 		virtual ~RemoveMod() {}
@@ -102,7 +187,7 @@ private:
 	};
 
 	typedef queue<Modification*> ModQueue;
-	ModQueue mod_queue;
+	ModQueue mod_queue; /**< A queue of analyzer additions/removals requests. */
 };
 
 } // namespace file_analysiss
diff --git a/src/file_analysis/DataEvent.h b/src/file_analysis/DataEvent.h
index 40a7f5971f..60b0487a6f 100644
--- a/src/file_analysis/DataEvent.h
+++ b/src/file_analysis/DataEvent.h
@@ -12,17 +12,50 @@
 namespace file_analysis {
 
 /**
- * An analyzer to send file data to script-layer events.
+ * An analyzer to send file data to script-layer via events.
  */
 class DataEvent : public file_analysis::Analyzer {
 public:
+
+	/**
+	 * Generates the event, if any, specified by the "chunk_event" field of this
+	 * analyzer's \c AnalyzerArgs.  This is for non-sequential file data input.
+	 * @param data pointer to start of file data chunk.
+	 * @param len number of bytes in the data chunk.
+	 * @param offset number of bytes from start of file at which chunk occurs.
+	 * @return always true
+	 */
 	virtual bool DeliverChunk(const u_char* data, uint64 len, uint64 offset);
 
+	/**
+	 * Generates the event, if any, specified by the "stream_event" field of
+	 * this analyzer's \c AnalyzerArgs.  This is for sequential file data input.
+	 * @param data pointer to start of file data chunk.
+	 * @param len number of bytes in the data chunk.
+	 * @return always true
+	 */
 	virtual bool DeliverStream(const u_char* data, uint64 len);
 
+	/**
+	 * Create a new instance of a DataEvent analyzer.
+	 * @param args the \c AnalyzerArgs value which represents the analyzer.
+	 * @param file the file to which the analyzer will be attached.
+	 * @return the new DataEvent analyzer instance or a null pointer if
+	 *         no "chunk_event" or "stream_event" field was specfied in \a args.
+	 */
 	static file_analysis::Analyzer* Instantiate(RecordVal* args, File* file);
 
 protected:
+
+	/**
+	 * Constructor.
+	 * @param args the \c AnalyzerArgs value which represents the analyzer.
+	 * @param file the file to which the analyzer will be attached.
+	 * @param ce pointer to event handler which will be called to receive
+	 *        non-sequential file data.
+	 * @param se pointer to event handler which will be called to receive
+	 *        sequential file data.
+	 */
 	DataEvent(RecordVal* args, File* file,
 	          EventHandlerPtr ce, EventHandlerPtr se);
 
diff --git a/src/file_analysis/Extract.h b/src/file_analysis/Extract.h
index 1f5ee3a185..85d2a9e7a8 100644
--- a/src/file_analysis/Extract.h
+++ b/src/file_analysis/Extract.h
@@ -12,17 +12,44 @@
 namespace file_analysis {
 
 /**
- * An analyzer to extract files to disk.
+ * An analyzer to extract content of files to local disk.
  */
 class Extract : public file_analysis::Analyzer {
 public:
+
+	/**
+	 * Destructor.  Will close the file that was used for data extraction.
+	 */
 	virtual ~Extract();
 
+	/**
+	 * Write a chunk of file data to the local extraction file.
+	 * @param data pointer to a chunk of file data.
+	 * @param len number of bytes in the data chunk.
+	 * @param offset number of bytes from start of file at which chunk starts.
+	 * @return false if there was no extraction file open and the data couldn't
+	 *         be written, else true.
+	 */
 	virtual bool DeliverChunk(const u_char* data, uint64 len, uint64 offset);
 
+	/**
+	 * Create a new instance of an Extract analyzer.
+	 * @param args the \c AnalyzerArgs value which represents the analyzer.
+	 * @param file the file to which the analyzer will be attached.
+	 * @return the new Extract analyzer instance or a null pointer if the
+	 *         the "extraction_file" field of \a args wasn't set.
+	 */
 	static file_analysis::Analyzer* Instantiate(RecordVal* args, File* file);
 
 protected:
+
+	/**
+	 * Constructor.
+	 * @param args the \c AnalyzerArgs value which represents the analyzer.
+	 * @param file the file to which the analyzer will be attached.
+	 * @param arg_filename a file system path which specifies the local file
+	 *        to which the contents of the file will be extracted/written.
+	 */
 	Extract(RecordVal* args, File* file, const string& arg_filename);
 
 private:
diff --git a/src/file_analysis/File.h b/src/file_analysis/File.h
index 0a7b9be30d..e889af3ea4 100644
--- a/src/file_analysis/File.h
+++ b/src/file_analysis/File.h
@@ -19,10 +19,15 @@ namespace file_analysis {
  */
 class File {
 public:
+
+	/**
+	 * Destructor.  Nothing fancy, releases a reference to the wrapped
+	 * \c fa_file value.
+	 */
 	~File();
 
 	/**
-	 * @return the #val record.
+	 * @return the wrapped \c fa_file record value, #val.
 	 */
 	RecordVal* GetVal() const { return val; }
 
@@ -34,6 +39,7 @@ public:
 
 	/**
 	 * Set the "source" field from #val record to \a source.
+	 * @param source the new value of the "source" field.
 	 */
 	void SetSource(const string& source);
 
@@ -44,6 +50,7 @@ public:
 
 	/**
 	 * Set the "timeout_interval" field from #val record to \a interval seconds.
+	 * @param interval the new value of the "timeout_interval" field.
 	 */
 	void SetTimeoutInterval(double interval);
 
@@ -64,13 +71,15 @@ public:
 
 	/**
 	 * Set "total_bytes" field of #val record to \a size.
+	 * @param size the new value of the "total_bytes" field.
 	 */
 	void SetTotalBytes(uint64 size);
 
 	/**
-	 * Compares "seen_bytes" field to "total_bytes" field of #val record
-	 * and returns true if the comparison indicates the full file was seen.
-	 * If "total_bytes" hasn't been set yet, it returns false.
+	 * Compares "seen_bytes" field to "total_bytes" field of #val record to
+	 * determine if the full file has been seen.
+	 * @return false if "total_bytes" hasn't been set yet or "seen_bytes" is
+	 *         less than it, else true.
 	 */
 	bool IsComplete() const;
 
@@ -84,23 +93,30 @@ public:
 	/**
 	 * Queues attaching an analyzer.  Only one analyzer per type can be attached
 	 * at a time unless the arguments differ.
+	 * @param args an \c AnalyzerArgs value representing a file analyzer.
 	 * @return false if analyzer can't be instantiated, else true.
 	 */
 	bool AddAnalyzer(RecordVal* args);
 
 	/**
 	 * Queues removal of an analyzer.
+	 * @param args an \c AnalyzerArgs value representing a file analyzer.
 	 * @return true if analyzer was active at time of call, else false.
 	 */
 	bool RemoveAnalyzer(const RecordVal* args);
 
 	/**
 	 * Pass in non-sequential data and deliver to attached analyzers.
+	 * @param data pointer to start of a chunk of file data.
+	 * @param len number of bytes in the data chunk.
+	 * @param offset number of bytes from start of file at which chunk occurs.
 	 */
 	void DataIn(const u_char* data, uint64 len, uint64 offset);
 
 	/**
 	 * Pass in sequential data and deliver to attached analyzers.
+	 * @param data pointer to start of a chunk of file data.
+	 * @param len number of bytes in the data chunk.
 	 */
 	void DataIn(const u_char* data, uint64 len);
 
@@ -111,10 +127,13 @@ public:
 
 	/**
 	 * Inform attached analyzers about a gap in file stream.
+	 * @param offset number of bytes in to file at which missing chunk starts.
+	 * @param len length in bytes of the missing chunk of file data.
 	 */
 	void Gap(uint64 offset, uint64 len);
 
 	/**
+	 * @param h pointer to an event handler.
 	 * @return true if event has a handler and the file isn't ignored.
 	 */
 	bool FileEventAvailable(EventHandlerPtr h);
@@ -122,11 +141,14 @@ public:
 	/**
 	 * Raises an event related to the file's life-cycle, the only parameter
 	 * to that event is the \c fa_file record..
+	 * @param h pointer to an event handler.
 	 */
 	void FileEvent(EventHandlerPtr h);
 
 	/**
 	 * Raises an event related to the file's life-cycle.
+	 * @param h pointer to an event handler.
+	 * @param vl list of argument values to pass to event call.
 	 */
 	void FileEvent(EventHandlerPtr h, val_list* vl);
 
@@ -135,6 +157,13 @@ protected:
 
 	/**
 	 * Constructor; only file_analysis::Manager should be creating these.
+	 * @param file_id an identifier string for the file in pretty hash form
+	 *        (similar to connection uids).
+	 * @param conn a network connection over which the file is transferred.
+	 * @param tag the network protocol over which the file is transferred.
+	 * @param is_orig true if the file is being transferred from the originator
+	 *        of the connection to the responder.  False indicates the other
+	 *        direction.
 	 */
 	File(const string& file_id, Connection* conn = 0,
 	     AnalyzerTag::Tag tag = AnalyzerTag::Error, bool is_orig = false);
@@ -142,28 +171,37 @@ protected:
 	/**
 	 * Updates the "conn_ids" and "conn_uids" fields in #val record with the
 	 * \c conn_id and UID taken from \a conn.
+	 * @param conn the connection over which a part of the file has been seen.
 	 */
 	void UpdateConnectionFields(Connection* conn);
 
 	/**
 	 * Increment a byte count field of #val record by \a size.
+	 * @param size number of bytes by which to increment.
+	 * @param field_idx the index of the field in \c fa_file to increment.
 	 */
 	void IncrementByteCount(uint64 size, int field_idx);
 
 	/**
 	 * Wrapper to RecordVal::LookupWithDefault for the field in #val at index
 	 * \a idx which automatically unrefs the Val and returns a converted value.
+	 * @param idx the index of a field of type "count" in \c fa_file.
+	 * @return the value of the field, which may be it &default.
 	 */
 	uint64 LookupFieldDefaultCount(int idx) const;
 
 	/**
 	 * Wrapper to RecordVal::LookupWithDefault for the field in #val at index
 	 * \a idx which automatically unrefs the Val and returns a converted value.
+	 * @param idx the index of a field of type "interval" in \c fa_file.
+	 * @return the value of the field, which may be it &default.
 	 */
 	double LookupFieldDefaultInterval(int idx) const;
 
 	/**
 	 * Buffers incoming data at the beginning of a file.
+	 * @param data pointer to a data chunk to buffer.
+	 * @param len number of bytes in the data chunk.
 	 * @return true if buffering is still required, else false
 	 */
 	bool BufferBOF(const u_char* data, uint64 len);
@@ -176,11 +214,15 @@ protected:
 	/**
 	 * Does mime type detection and assigns type (if available) to \c mime_type
 	 * field in #val.
+	 * @param data pointer to a chunk of file data.
+	 * @param len number of bytes in the data chunk.
 	 * @return whether mime type was available.
 	 */
 	bool DetectMIME(const u_char* data, uint64 len);
 
 	/**
+	 * Lookup a record field index/offset by name.
+	 * @param field_name the name of the \c fa_file record field.
 	 * @return the field offset in #val record corresponding to \a field_name.
 	 */
 	static int Idx(const string& field_name);
@@ -198,7 +240,7 @@ private:
 	bool missed_bof;           /**< Flags that we missed start of file. */
 	bool need_reassembly;      /**< Whether file stream reassembly is needed. */
 	bool done;                 /**< If this object is about to be deleted. */
-	AnalyzerSet analyzers;
+	AnalyzerSet analyzers;     /**< A set of attached file analyzer. */
 
 	struct BOF_Buffer {
 		BOF_Buffer() : full(false), replayed(false), size(0) {}
diff --git a/src/file_analysis/FileTimer.h b/src/file_analysis/FileTimer.h
index 32d4e63254..bdfd1fe165 100644
--- a/src/file_analysis/FileTimer.h
+++ b/src/file_analysis/FileTimer.h
@@ -13,11 +13,20 @@ namespace file_analysis {
  */
 class FileTimer : public Timer {
 public:
+
+	/**
+	 * Constructor, nothing interesting about it.
+	 * @param t unix time at which the timer should start ticking.
+	 * @param id the file identifier which will be checked for inactivity.
+	 * @param interval amount of time after \a t to check for inactivity.
+	 */
 	FileTimer(double t, const string& id, double interval);
 
 	/**
 	 * Check inactivity of file_analysis::File corresponding to #file_id,
 	 * reschedule if active, else call file_analysis::Manager::Timeout.
+	 * @param t current unix time
+	 * @param is_expire true if all pending timers are being expired.
 	 */
 	void Dispatch(double t, int is_expire);
 
diff --git a/src/file_analysis/Hash.h b/src/file_analysis/Hash.h
index e4bc8f1747..e44af337aa 100644
--- a/src/file_analysis/Hash.h
+++ b/src/file_analysis/Hash.h
@@ -17,17 +17,50 @@ namespace file_analysis {
  */
 class Hash : public file_analysis::Analyzer {
 public:
+
+	/**
+	 * Destructor.
+	 */
 	virtual ~Hash();
 
+	/**
+	 * Incrementally hash next chunk of file contents.
+	 * @param data pointer to start of a chunk of a file data.
+	 * @param len number of bytes in the data chunk.
+	 * @return false if the digest is in an invalid state, else true.
+	 */
 	virtual bool DeliverStream(const u_char* data, uint64 len);
 
+	/**
+	 * Finalizes the hash and raises a "file_hash" event.
+	 * @return always false so analyze will be deteched from file.
+	 */
 	virtual bool EndOfFile();
 
+	/**
+	 * Missing data can't be handled, so just indicate the this analyzer should
+	 * be removed from receiving further data.  The hash will not be finalized.
+	 * @param offset byte offset in file at which missing chunk starts.
+	 * @param len number of missing bytes.
+	 * @return always false so analyzer will detach from file.
+	 */
 	virtual bool Undelivered(uint64 offset, uint64 len);
 
 protected:
+
+	/**
+	 * Constructor.
+	 * @param args the \c AnalyzerArgs value which represents the analyzer.
+	 * @param file the file to which the analyzer will be attached.
+	 * @param hv specific hash calculator object.
+	 * @param kind human readable name of the hash algorithm to use.
+	 */
 	Hash(RecordVal* args, File* file, HashVal* hv, const char* kind);
 
+	/**
+	 * If some file contents have been seen, finalizes the hash of them and
+	 * raises the "file_hash" event with the results.
+	 */
 	void Finalize();
 
 private:
@@ -36,34 +69,85 @@ private:
 	const char* kind;
 };
 
+/**
+ * An analyzer to produce an MD5 hash of file contents.
+ */
 class MD5 : public Hash {
 public:
+
+	/**
+	 * Create a new instance of the MD5 hashing file analyzer.
+	 * @param args the \c AnalyzerArgs value which represents the analyzer.
+	 * @param file the file to which the analyzer will be attached.
+	 * @return the new MD5 analyzer instance or a null pointer if there's no
+	 *         handler for the "file_hash" event.
+	 */
 	static file_analysis::Analyzer* Instantiate(RecordVal* args, File* file)
 		{ return file_hash ? new MD5(args, file) : 0; }
 
 protected:
+
+	/**
+	 * Constructor.
+	 * @param args the \c AnalyzerArgs value which represents the analyzer.
+	 * @param file the file to which the analyzer will be attached.
+	 */
 	MD5(RecordVal* args, File* file)
 		: Hash(args, file, new MD5Val(), "md5")
 		{}
 };
 
+/**
+ * An analyzer to produce a SHA1 hash of file contents.
+ */
 class SHA1 : public Hash {
 public:
+
+	/**
+	 * Create a new instance of the SHA1 hashing file analyzer.
+	 * @param args the \c AnalyzerArgs value which represents the analyzer.
+	 * @param file the file to which the analyzer will be attached.
+	 * @return the new MD5 analyzer instance or a null pointer if there's no
+	 *         handler for the "file_hash" event.
+	 */
 	static file_analysis::Analyzer* Instantiate(RecordVal* args, File* file)
 		{ return file_hash ? new SHA1(args, file) : 0; }
 
 protected:
+
+	/**
+	 * Constructor.
+	 * @param args the \c AnalyzerArgs value which represents the analyzer.
+	 * @param file the file to which the analyzer will be attached.
+	 */
 	SHA1(RecordVal* args, File* file)
 		: Hash(args, file, new SHA1Val(), "sha1")
 		{}
 };
 
+/**
+ * An analyzer to produce a SHA256 hash of file contents.
+ */
 class SHA256 : public Hash {
 public:
+
+	/**
+	 * Create a new instance of the SHA256 hashing file analyzer.
+	 * @param args the \c AnalyzerArgs value which represents the analyzer.
+	 * @param file the file to which the analyzer will be attached.
+	 * @return the new MD5 analyzer instance or a null pointer if there's no
+	 *         handler for the "file_hash" event.
+	 */
 	static file_analysis::Analyzer* Instantiate(RecordVal* args, File* file)
 		{ return file_hash ? new SHA256(args, file) : 0; }
 
 protected:
+
+	/**
+	 * Constructor.
+	 * @param args the \c AnalyzerArgs value which represents the analyzer.
+	 * @param file the file to which the analyzer will be attached.
+	 */
 	SHA256(RecordVal* args, File* file)
 		: Hash(args, file, new SHA256Val(), "sha256")
 		{}
diff --git a/src/file_analysis/Manager.h b/src/file_analysis/Manager.h
index 8e985d6ce3..7a5edd0783 100644
--- a/src/file_analysis/Manager.h
+++ b/src/file_analysis/Manager.h
@@ -26,7 +26,15 @@ namespace file_analysis {
  */
 class Manager {
 public:
+
+	/**
+	 * Constructor.
+	 */
 	Manager();
+
+	/**
+	 * Destructor.  Times out any currently active file analyses.
+	 */
 	~Manager();
 
 	/**
@@ -35,48 +43,97 @@ public:
 	void Terminate();
 
 	/**
+	 * Creates a file identifier from a unique file handle string.
+	 * @param handle a unique string which identifies a single file.
 	 * @return a prettified MD5 hash of \a handle, truncated to 64-bits.
 	 */
 	string HashHandle(const string& handle) const;
 
 	/**
-	 * Take in a unique file handle string to identify incoming file data.
+	 * Take in a unique file handle string to identify next piece of
+	 * incoming file data/information.
+	 * @param handle a unique string which identifies a single file.
 	 */
 	void SetHandle(const string& handle);
 
 	/**
 	 * Pass in non-sequential file data.
+	 * @param data pointer to start of a chunk of file data.
+	 * @param len number of bytes in the data chunk.
+	 * @param offset number of bytes from start of file that data chunk occurs.
+	 * @param tag network protocol over which the file data is transferred.
+	 * @param conn network connection over which the file data is transferred.
+	 * @param is_orig true if the file is being sent from connection originator
+	 *        or false if is being sent in the opposite direction.
 	 */
 	void DataIn(const u_char* data, uint64 len, uint64 offset,
 		    AnalyzerTag::Tag tag, Connection* conn, bool is_orig);
 
 	/**
 	 * Pass in sequential file data.
+	 * @param data pointer to start of a chunk of file data.
+	 * @param len number of bytes in the data chunk.
+	 * @param tag network protocol over which the file data is transferred.
+	 * @param conn network connection over which the file data is transferred.
+	 * @param is_orig true if the file is being sent from connection originator
+	 *        or false if is being sent in the opposite direction.
 	 */
 	void DataIn(const u_char* data, uint64 len, AnalyzerTag::Tag tag,
 	            Connection* conn, bool is_orig);
 
 	/**
 	 * Pass in sequential file data from external source (e.g. input framework).
+	 * @param data pointer to start of a chunk of file data.
+	 * @param len number of bytes in the data chunk.
+	 * @param file_id an identifier for the file (usually a hash of \a source).
+	 * @param source uniquely identifies the file and should also describe
+	 *        in human-readable form where the file input is coming from (e.g.
+	 *        a local file path).
 	 */
 	void DataIn(const u_char* data, uint64 len, const string& file_id,
 	            const string& source);
 
 	/**
-	 * Signal the end of file data.
+	 * Signal the end of file data regardless of which direction it is being
+	 * sent over the connection.
+	 * @param tag network protocol over which the file data is transferred.
+	 * @param conn network connection over which the file data is transferred.
 	 */
 	void EndOfFile(AnalyzerTag::Tag tag, Connection* conn);
+
+	/**
+	 * Signal the end of file data being transferred over a connection in
+	 * a particular direction.
+	 * @param tag network protocol over which the file data is transferred.
+	 * @param conn network connection over which the file data is transferred.
+	 */
 	void EndOfFile(AnalyzerTag::Tag tag, Connection* conn, bool is_orig);
+
+	/**
+	 * Signal the end of file data being transferred using the file identifier.
+	 * @param file_id the file identifier/hash.
+	 */
 	void EndOfFile(const string& file_id);
 
 	/**
 	 * Signal a gap in the file data stream.
+	 * @param offset number of bytes in to file at which missing chunk starts.
+	 * @param len length in bytes of the missing chunk of file data.
+	 * @param tag network protocol over which the file data is transferred.
+	 * @param conn network connection over which the file data is transferred.
+	 * @param is_orig true if the file is being sent from connection originator
+	 *        or false if is being sent in the opposite direction.
 	 */
 	void Gap(uint64 offset, uint64 len, AnalyzerTag::Tag tag, Connection* conn,
 	         bool is_orig);
 
 	/**
 	 * Provide the expected number of bytes that comprise a file.
+	 * @param size the number of bytes in the full file.
+	 * @param tag network protocol over which the file data is transferred.
+	 * @param conn network connection over which the file data is transferred.
+	 * @param is_orig true if the file is being sent from connection originator
+	 *        or false if is being sent in the opposite direction.
 	 */
 	void SetSize(uint64 size, AnalyzerTag::Tag tag, Connection* conn,
 	             bool is_orig);
@@ -84,12 +141,18 @@ public:
 	/**
 	 * Starts ignoring a file, which will finally be removed from internal
 	 * mappings on EOF or TIMEOUT.
+	 * @param file_id the file identifier/hash.
 	 * @return false if file identifier did not map to anything, else true.
 	 */
 	bool IgnoreFile(const string& file_id);
 
 	/**
 	 * Set's an inactivity threshold for the file.
+	 * @param file_id the file identifier/hash.
+	 * @param interval the amount of time in which no activity is seen for
+	 *        the file identified by \a file_id that will cause the file
+	 *        to be considered stale, timed out, and then resource reclaimed.
+	 * @return false if file identifier did not map to anything, else true.
 	 */
 	bool SetTimeoutInterval(const string& file_id, double interval) const;
 
@@ -97,17 +160,23 @@ public:
 	 * Queue attachment of an analzer to the file identifier.  Multiple
 	 * analyzers of a given type can be attached per file identifier at a time
 	 * as long as the arguments differ.
+	 * @param file_id the file identifier/hash.
+	 * @param args a \c AnalyzerArgs value which describes a file analyzer.
 	 * @return false if the analyzer failed to be instantiated, else true.
 	 */
 	bool AddAnalyzer(const string& file_id, RecordVal* args) const;
 
 	/**
 	 * Queue removal of an analyzer for a given file identifier.
+	 * @param file_id the file identifier/hash.
+	 * @param args a \c AnalyzerArgs value which describes a file analyzer.
 	 * @return true if the analyzer is active at the time of call, else false.
 	 */
 	bool RemoveAnalyzer(const string& file_id, const RecordVal* args) const;
 
 	/**
+	 * Tells whether analysis for a file is active or ignored.
+	 * @param file_id the file identifier/hash.
 	 * @return whether the file mapped to \a file_id is being ignored.
 	 */
 	bool IsIgnored(const string& file_id);
@@ -119,6 +188,16 @@ protected:
 	typedef map<string, File*> IDMap;
 
 	/**
+	 * Create a new file to be analyzed or retrieve an existing one.
+	 * @param file_id the file identifier/hash.
+	 * @param conn network connection, if any, over which the file is
+	 *        transferred.
+	 * @param tag network protocol, if any, over which the file is transferred.
+	 * @param is_orig true if the file is being sent from connection originator
+	 *        or false if is being sent in the opposite direction (or if it
+	 *        this file isn't related to a connection).
+	 * @param update_conn whether we need to update connection-related field
+	 *        in the \c fa_file record value associated with the file.
 	 * @return the File object mapped to \a file_id or a null pointer if
 	 *         analysis is being ignored for the associated file.  An File
 	 *         object may be created if a mapping doesn't exist, and if it did
@@ -130,6 +209,8 @@ protected:
 	              bool is_orig = false, bool update_conn = true);
 
 	/**
+	 * Try to retrieve a file that's being analyzed, using its identifier/hash.
+	 * @param file_id the file identifier/hash.
 	 * @return the File object mapped to \a file_id, or a null pointer if no
 	 *         mapping exists.
 	 */
@@ -138,11 +219,15 @@ protected:
 	/**
 	 * Evaluate timeout policy for a file and remove the File object mapped to
 	 * \a file_id if needed.
+	 * @param file_id the file identifier/hash.
+	 * @param is_termination whether the Manager (and probably Bro) is in a
+	 *        terminating state.  If true, then the timeout cannot be postponed.
 	 */
 	void Timeout(const string& file_id, bool is_terminating = ::terminating);
 
 	/**
 	 * Immediately remove file_analysis::File object associated with \a file_id.
+	 * @param file_id the file identifier/hash.
 	 * @return false if file id string did not map to anything, else true.
 	 */
 	bool RemoveFile(const string& file_id);
@@ -151,11 +236,20 @@ protected:
 	 * Sets #current_file_id to a hash of a unique file handle string based on
 	 * what the \c get_file_handle event derives from the connection params.
 	 * Event queue is flushed so that we can get the handle value immediately.
+	 * @param tag network protocol over which the file is transferred.
+	 * @param conn network connection over which the file is transferred.
+	 * @param is_orig true if the file is being sent from connection originator
+	 *        or false if is being sent in the opposite direction.
 	 */
 	void GetFileHandle(AnalyzerTag::Tag tag, Connection* c, bool is_orig);
 
 	/**
-	 * @return whether file analysis is disabled for the given analyzer.
+	 * Check if analysis is available for files transferred over a given
+	 * network protocol.
+	 * @param tag the network protocol over which files can be transferred and
+	 *        analyzed by the file analysis framework.
+	 * @return whether file analysis is disabled for the analyzer given by
+	 *         \a tag.
 	 */
 	static bool IsDisabled(AnalyzerTag::Tag tag);