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Is serializing in Java the best/easiest way to store and later access (a small amount of) data?

I am relatively new to Java and have much more experience with Matlab. I was wondering what the best way is to store a relatively small amount of data, which has been calculated in one program, that should be used in another program.
Example: program A computes 100 values to be stored in an array. Now I would like to access this array in program B, as it needs these values. Of course, I could just write one program all together, which also implements the part of A. However, now every time I want to execute the total program, all the values have to be calculated again (in part A), which is a waste of resources. In Matlab, I was able to easily save the array in a .mat file and load it in a different script.
Looking around to find my answer I found the option of serializing (What is object serialization? ), which I think would be a suitable for doing what I want. My question: is serializing the easiest and quickest solution to store a small amount of data in Java, or is there a quicker, more user-friendly option (like .mat files in Matlab)?

I think you have several options to do this job. Java object serialization is one possible way. From my point of view there are other options to serialize the data:
Write and read a simple text file to store the computed values.
Using Java Architecture for XML Binding (JAXB) to write annotated Java classes to XML file. Same for JSON is also available.
Using a lightweight database like SQLite or HSQLDB (native Java database).
Using Apache Thrift or Protocol Buffer to de/serializing Java objects to files.

Deserializing Objects in Java

Say I have a large file with many objects already serialized (this is the easy part). I need to be able to have random access to the objects in the file when I go to deserialize. The only way I can think to do this would be to somehow store the file pointer to each object.
Basically I will end up with a large file of serialized objects and don't want to deserialize the entire file when I go to retrieve just one object.
Can anyone point me in the right direction on this one?

You can't. Serialization is called serialization for a reason. It is serial. Random access into a stream of objects will not work, for several reasons including the stream header, object handles, ...

Straight serialization will never be the solution you want.
The serial portion of the name means that the objects are written linearly to the ObjectOutputStream.
The serialization format is well known,
here is a link to the java 6 serialization format.
You have several options:
Unserialize the entire file and go from there.
Write code to read the serialized file and generate an index.
Maybe even store the index in a file for future use.
Abandon serialization to a file and store the objects in a database.

Text file to string matrix java

I am making an auto chat client like Cleverbot for school. I have everything working, but I need a way to make a knowledge base of responses. I was going to make a matrix with all the responses that I need the bot to say, but I think it would be hard to edit the code every time I want to add a responses to the bot. This is the code that I have for the knowledge base matrix:
`String[][] Database={
{"hi","hello","howdy","hey"},//possible user input
{"hi","hello","hey"},//response
{"how are you", "how r u", "how r you", "how are u"},
{"good","doing well"}`
How would I make a matrix like this from a text file? Is there a better way than reading from a text file to deal with this?

You could...
Use a properties file
The properties file is something that can easily be read into (and stored from, but you're not interested in that) Java. The class java.util.Properties can make that easier, but it's fairly simple to load it and then you access it like a Map.
hello.input=hi,hello,howdy,hey
hello.output=hi,hello,hey
Note the matching formats there. This has its own set of problems and challenges to work with, but it lets you easily pull things in to and out of properties files.
Store it in JSON
Lots of things use JSON for a serialization format. And thus, there are lots of libraries that you can use to read and store from it. It would again make some things easier and have its own set of challenges.
{
"greeting":{
"input":["hi","hello","howdy","hey"],
"output":["hi","hello","hey"]
}
}
Something like that. And then again, you read this and store it into your data structures. You could store JSON in a number of places such as document databases (like couch) which would make for easy updates, changes, and access... given you're running that database.
Which brings us to...
Embedded databases
There are lots of databases that you can stick right in your application and access it like a database. Nice queries, proper relationships between objects. There are lots of advantages to using a database when you actually want a database rather than hobbling strings together and doing all the work yourself.
Custom serialization
You could create a class (instead of a 2d array) and then store the data in a class (in which it might be a 2d array, but that's an implementation detail). At this point, you could implement Serializable and write the writeObject and readObject methods and store the data somehow in a file which you could then read back into the object directly. If you have the administration ability of adding new things as part of this application (or another that uses the same class) you could forgo the human readable aspect of it and use the admin tool (that you write) to update the object.
Lots of others
This is just the tip of the iceberg. There are lots of ways to go about this.
P.S.
Please change the name of the variable from Database to something in lower case that better describes it such as input2output or the like. Upper case names are typically reserved for class names (unless its all upper case, in which case it's a final static field)

A common solution would be to dump the data in to a properties file, and then load it with the standard Properties.load(...) method.
Once you have your data like that, you can then access the data by a map-like interface.
You could find different ways of storing the data in the file like:
userinput=hi,hello,howdy,hey
response=hi,hello,hey
...
Then, when you read the file, you can split the values on the comma:
String[] expectHello = properties.getProperty("userinput").split(",");

Using list of serialized objects

I'm learning Android/Java programming, but I'm confused about persistant data.
After a lot of research it seems that the best way to store objects is to serialize them in a file, but I couldn't find a simple way to retrieve these objects.
If I create two objects and save their serialized versions, how can I retieve and list both of them? Do I need to create a file for each object with a specific ID in the filename so I can list them with a getFilesDir?

Depends on how complex those objects are (your personal preferences I guess), I have used SharedPreferences to store simple objects before, just for the sake of simplicity, while a co-worker makes generous use of SQLite, but that suits his needs.
Since you do not state what is being stored, the best advice I can give you right now is have read here, it covers how persistent data should be dealt with on Android.

"best" way? Please define your criteria.
There are databases (relational and non-relational) or file systems. You can serialize lots of ways: Java serialization, XML, Google's protobuf, and others.
Yes, you'll need a way to specify a unique representation with its object. In a relational database, you'd use a primary key. You need something like that in any system you use.
If you serialize via some mechanism to a file system, you'll have to write the object into the desired format and stream it to a file. To go the other way, specify the key for the object, read the serialized data, and parse it back into the object.

best practices question: How to save a collection of images and a java object in a single file? File is read to be rendered

I am making a java program that has a collection of flash-card like objects. I store the objects in a jtree composed of defaultmutabletreenodes. Each node has a user object attached to it with has a few string/native data type parameters. However, i also want each of these objects to have an image (typical formats, jpg, png etc).
I would like to be able to store all of this information, including the images and the tree data to the disk in a single file so the file can be transferred between users and the entire tree, including the images and parameters for each object, can be reconstructed.
I had not approached a problem like this before so I was not sure what the best practices were. I found XLMEncoder (http://java.sun.com/j2se/1.4.2/docs/api/java/beans/XMLEncoder.html) to be a very effective way of storing my tree and the native data type information. However I couldn't figure out how to save the image data itself inside of the XML file, and I'm not sure it is possible since the data is binary (so restricted characters would be invalid). My next thought was to associate a hash string instead of an image within each user object, and then gzip together all of the images, with the hash strings as the names and the XMLencoded tree in the same compmressed file. That seemed really contrived though.
Does anyone know a good approach for this type of issue?
THanks!
Thanks!

Assuming this isn't just a serializable graph, consider bundling the files together in Jar format. If you already have your data structures working with XMLEncoder, you can reuse this code by saving the data as a jar entry.
If memory serves, the jar library has better support for Unicode name entries than the zip package, which is why I would favour it.

You might consider using an MS JET database (.mdb file) and storing all the stuff in there. That'll also make it easy to examine and edit the data in (for example) MS Access.

You can employ some virtual file system, which stores it's data in a single container. We develop and offer one of such files sytems, SolFS, however right now there's no Java binding for it. We will release Java JNI interface for SolFS within a month.