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Play m4a files in Java

I want to create a media player in Java. The mp3 support already works with the JLayer library but which library can play m4a files?
I read about vlcj here on stackoverflow, but this seems to depend on Swing/AWT which I wouldn't use because I want to port the application to Android later on.

Have you looked at JAAD? It's a Javasound SPI that decodes AAC audio, I've used it with success previously.
Note that m4a is a container format, and while it usually contains (in my experience) AAC audio, in theory it could contain other formats instead.
You can find some information about getting it working without Javasound (and a test case) here.

This answer is indirect. I don't really know anything about m4a files. But what I have found is an open source library that can stream them as a flash server named red5. It's written in Java so theoretically you should be able to browse their code to figure out how to do it.
Hopefully someone here can give a more direct answer, this is the best I can do.

If you have Java 7 or later, you have access to the Javafx library. You can also use your media player (like iTunes or Windows Media Player) to convert to the simpler mp3 version and run that. I wouldn't recommend .wav files as they have significantly more data usage than mp3s, (which condense the file size by compressing the .wav data and omitting inaudible and otherwise garbage-y data).
import javafx.scene.media.*;
String name = "song.mp3";
Media song = new Media(name);
MediaPlayer player = new MediaPlayer(song);
player.play();

Writing to text file in GAE

Has anyone figured out a way to write to text file on the server-side using Google App Engine (GAE). I understand the limitation of not being able to use FileWriter, but I was wondering if there was a work around. Thanks!

Not only can you not use FileWriter, you can not write to files at all, since you do not have access to the filesystem from within the GAE. It's impossible by design.
As a "work-around" (which I hesistate designating as such since this is a technically valid solution), you can emulate a filesystem using the GAE datastore using GAEVFS: http://code.google.com/p/gaevfs/

Try the blob store. Now, you can write to the blob store like you write files to the file system.
https://developers.google.com/appengine/docs/java/blobstore/overview#Writing_Files_to_the_Blobstore

Downloading large files with HttpClient

Is it possible to download large files (>=1Gb) from a servlet to an applet using HttpClient? And what servlet-side lib is useful in this case? Is there another way to approach this?

Any server-side lib that allows you access to the raw output stream should be just fine.
Servlets or JAX-RS for example.
Get the output stream, get the input stream of your file, use a nice big buffer (4k maybe) and pump the bytes from input to output.
On the client side, your applet needs access to the file system. I assume you don't want to keep the 1GB in memory. (maybe we want to stream it to the screen, in which case you don't need elevated access).
Avoid client libraries that try to fully materialize the returned content before handing it to.
Example code here:
Streaming large files in a java servlet

MP4 container writer in Java

I would like to find a FREE MP4 (container) writer for Java. I do not need an encoder, only something which can write the correct atoms given their expected values. Bonus for such a library that also can write "valid" F4V.
I would prefer a pure Java solution rather than something using JNI or external executables.

Even though my answer comes very late you could have a look into my MP4 Parser/Unparser at Github. You can parse MP4 files, modify them and write the result. You can even start from scratch creating boxes programatically and write your object representation to some sink.

You can have a look at JCodec ( http://jcodec.org ). It contains an MP4 library and MP4 demuxer and muxer.

May be you are looking for something like StreamBaby.

Can't vouch for it, but red5 is an open source flash server written in Java, which claims support for streaming mp4 and has implementations of mp4 IO objects which may be able to create said format.
Also, IBM created their Toolkit For MPEG-4 a while back and though it's not free, it might help.

FFMPEG's java bindings?
http://fobs.sourceforge.net/f4jmf_first.html
Or simpler a JNA proxy over some C++ MP4 library.

I have implemented a QuickTimeWriter class which can write a QuickTime container in pure Java.
As far as I know, the QuickTime file format is structurally equivalent to MPEG-4 Part 14. There are only a few minor differences in the fields inside atoms/boxes.
So, with an MPEG-4 spec on your lap, and a few hours of work, you should be good.

The Java I've seen which modifies MP4 files would invoke Nero AAC Codec externally (a Windows native .exe which Nero does not supply the source for) to modify AAC files (which are Apple's audio-only MP4 files). It works for audio only, not to video.

audio processing using java

We have a requirement where we need to convert from .wav file to .mp3 and we are currently using "Tritonus" library to do that . The concern with that library is that requires "installation" of some "dll" files to the class path.
I am wondering are there any API's those allow better processing without local installation.
And other question is ,having mp3 format files will make it easier to join the files into a single file than having .wav files ?

As a former contributor to the JLayer MP3 Library, I'm fairly sure that it doesn't do WAV to MP3 - just MP3 playback and conversion to WAV. (I spent some time optimizing the decoder :-)
Regarding appending files (and possibly other operations), it is generally better to perform edit operations using the uncompressed format, and compress at the end.
I think the spec allows mp3 files to be concatenated, since they are a series of frames, but behaviour may vary from player to player.
So, to be safe, and maintain quality, I'd concat using WAVs and then compress the final result to MP3. Concating files is not so straightforward - you have to at least make sure they are at the same percieved volume, or you will get a noticible shift in volume from one file to the next. Such operations are definitely best performed on the uncompressed data.

The JLayer MP3 Library appears to support several operations on MP3 and WAV files including conversion, with no native libraries to install.

You can use MP3SPI to do this. This is a java sound plugin, just include the jar into the classpath, and you can use java sound api to convert between wav and mp3.