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How can I validate certificate chain when CA certs held in Java Key Store

Can someone please help me with the following, I googled before hand but did not find a blog outlining what I wanted to do, thanks in advance.
I have and internal test PKI (based on AD CS). I have imported the Root CA certificate and the Issuing CA Certificate (minus their private keys) into the CACerts java key store (keying the GUI tool "KeyStore Explorer 5.5.1"
I have a leaf (end-entity certificate) 'outside of the Java keystore' as I want to simulate a situation where the client would obtain (be given) the leaf certificate via a WEB browser (for example when opening a TLS connection to a WEB server).
The leaf certificate is stored in a .pem flat file on the same computer where it was create (using Windows default method so private key for the cert is in the Windows keyStore). The computer also contains the Java KeyStore CACerts (where I imported the CA certs as above) and the Java JDK (so Keytool.exe for example)
So what I need to do (ideally using Keytool or a pre-made script suitable for Windows) is point to the leaf .pem certificate and say go check the certificate chain of this leaf certificate but using the CA certs held in CACerts keystore
Can someone kindly tell me how to do this as the only examples I have seen this far are about checking the chain for certs already in the CACerts keystore. Whereas I want to check the chain of a .pem flat file against the CA certs held in the CACerts java keystore

How to add CA certificate to cacerts store so that it works as expected?

UPDATE: After I have found a solution, I edited the question to be more clear for future reference.
I've got a corporate (ie not well known) CA certificate from a company which provides us a web services to be called from Java. I added this CA certificate to default cacerts trust store (keytool -import -file cert.cer -alias myca -keystore jre/lib/security/cacerts), but connection to the service still fails with the dreaded "PKIX path building failed" message. I have checked that issuer field of the end server certificate is the same as in the CA certificate and also validity dates is ok.
I don't know how to explain this. I can think of the following reasons but I don't know which one is true:
I have noticed that when I add also the end server certificate to trust store, the connection is OK. Maybe cacerts by design don't work as I expect (ie all the certificates signed by an authority added there are considered valid), but instead I have to add all the end server certificates to a trust store including CA certificate of their issuer.
I have to add CA certificate in some other way - by different command, to different file etc.
Maybe the CA certificate is not correct and keytool refuses to consider it a certificate authority.
Maybe PKIX path building fails for other reason.
How can I debug this problem more to find an answer?
Details:
The end server certificate is wildcard certificate
There is no intermediate certificate, just root and the end certificate

I was facing the same problem with "PKIX path building failed" with Let's Encrypt signed certificates at a time Java didn't incorporate the Let's encrypt CA certificate in its default trust store.
My story is written in detail here: http://blog.novoj.net/2016/02/29/how-to-make-apache-httpclient-trust-lets-encrypt-certificate-authority/
At the end I was able to make Java trust "the end of the chain" server certificate by creating internal trust store embedded in my application that contains only root CA certificate (and the backup one).
I much more prefer creating internal application truststore than importing certificate in main Java trust store for two reasons:
you don't need another extra step in install procedure for initializing the global trust store
you limit "the trust" to you application and don't affect another applications running on the same JVM (or better you can even limit the trust to the certain instances of client objects in your application if required)
Maybe I had a different scenario than you're facing, so downvote me if I didn't get the point.

The trust store needs to contain the root certificate (the CA's cert).
I'm not sure if that's what you mean by "the last one I'm the chain", but the CA certificate should be the last one in the certificate chain presented by the server.
If your certificate is signed by a well-known CA, then the CA cert should be in the trust store, and if the server's certificate chain is set up properly, everything should just work.
If yours is a self-signed certificate, then the root certificate will not be in the trust store, and you will have to add it.

Thanks to #pedrofb comment I found out that the reason PKIX path fails is simply that the CA certificate I got is not the CA that signed the end certificate. What made it so complicated is the monstrous incompetence of company that gave me the CA certificate which obviously has two CAs with almost the same description (cn, o, st, c) which differs only in SN and which both issued the same wildcard certificate. Only after I became super paranoid and compared the SNs, I understood the problem.

Java Webstart: howto share certificate with users

I developed an application that uses Java Webstart. It needs write access to the disk so it has to be signed, but it would only be used by a limited group of users so I don't want to pay for a trusted certificate.
What is the easiest option to let the users trust my application/self signed certificate? I don't want them to use keytool because it is not really user friendly. I though about creating a certificate that can be imported via the Java Control Panel and first tried creating an importable certificate using the following commands:
keytool -genkeypair -keystore patrickgotthard.jks -alias patrickgotthard
keytool -exportcert -keystore patrickgotthard.jks -alias patrickgotthard -file patrickgotthard.cer
But it is not possible to import the generated .cer file. Then I found Cannot import certificate into java control panel and used the following command:
keytool -genkey -alias patrickgotthard -keystore patrickgotthard.p12 -storetype pkcs12
But as far as I understand, the .p12 file also contains my private key - I don't think that the private key should be shared?! Can you tell me how to create a self signed certificate that can be imported via Java Control Panel but does not contain my private key? Or do you know a better solution for my problem?

In this scenario, it may be sufficient to check the SHA1 fingerprint associated with the self-signed certificate used to sign the JAR:
Sign the JAR with your self-signed certificate.
Use keytool -v -list to determine your certificate's fingerprint.
Communicate the certificate's fingerprint in a mutually agreed way.
Instruct user's to add your secure site to the Exception Site List in the Security tab of the Java Control Panel; this allows the user to retain the minimum recommended security level setting, High.
At the security prompt, click on More Information to compare the communicated fingerprint with the one received.
This approach does not confer trust, but it reduces the risk of the user accepting an altered JAR.
Addendum: The article Self-signed certificates for a known community discusses how to export a self-signed certificate. Members of the community can then import the certificate as warranted.

I was developing Java Web Start app years ago with NetBeans. It did everything for me automatically.
You just have to put permissions tags in JNLP file.
Also 6 month after I had problems to create a new self-signed certificate.
But self signed app still works. (many years after, no modification, certs to install)
Clients do not have to install any certificates.
It just warns everytime when it starts that is signed with self signed cert.

Another option is to have this "limited group of users" lower the security level for Java. In Windows, you go to the Control Panel->Java and then one of the tabs is for Security (sorry on my mac right now and it is not quite the same). I believe that if you push that security level lower to Medium, you can get away with the self-signed certificate.

how to get and SSL CA into Java server

So this may be a stupid question but I have been scouring the internet all day trying to figure out how to get a trusted SSL certificate into my java server.
Details:
I created a java server that creates an SSLServerSocket accepts connections. I used keytool to create a keystore called domain.key as well as a certificate request (csr). I then contacted a certificate authority (starfield) and gave them my csr, they did their thing and returned to me the certificates (crt). I have 3 of them. one is called domain.com.crt, one is called sf_bundle.crt, and one is called sf_intermediate.crt
After much searching I found that I need to import the certificates into a keystore and that the keystore can be the same one that has my public/private keys or it can be in a seperate file. I chose to put it into a seperate file called domain.trust.
I then modified my server to import the trust store as well as the keystore using:
System.setProperty("javax.net.ssl.keyStore", "domain.key");
System.setProperty("javax.net.ssl.trustStore", "domain.trust");
along the corresponding lines for the keystore password and the truststore password.
The problem is that when i try and connect using any client it always says that the certificate is sell signed.
I have been using http://certlogik.com/ssl-checker/ to test it.
I obviously have missed a step but I cant find out where.
Any help would be greatly appreciated

The problem is that when i try and connect using any client it always
says that the certificate is sell signed.
This indicates that the root CA certificate is being send to the client.
You don't mention how you created this separate keystore you use.
You should be doing something like the following:
keystore.setKeyEntry("alias", privateKey, password, chain);
And chain would have:
chain[0] --> Your server's certificate
chain[1] --> The signer's certificate
....
chain[N] --> Signer up to the root

You first need to understand what happens during an SSL Handshake. Maybe then you can narrow down the problem. You can refer to various docs on internet., http://www.pierobon.org/ssl/ch/detail.htm
Your running server must have either have the CA StarField installed in it. Or it should have a trust relationship with the CA StarField.
You rclient certificate must be CSR signed by CA StarField, which I guess you have already done.
Now when you present your certificate to the Server, it checks with the CA's it has.
So, if the Sever has the CA StarField and your certificate is signed by StarField then there is no way you would get the Self Signed error.
You get that only when your certificate is not signed by the CA. Just open your certificate and check it's Issuer details to confirm.

Firstly, you seem to be confused about the difference between keystore and truststore. This answer may be of interest.
Essentially, unless you want to use client-certificate authentication, you have no need to change the trust store, from a server point of view.
After much searching I found that I need to import the certificates
into a keystore and that the keystore can be the same one that has my
public/private keys or it can be in a seperate file.
To be able to use the certificate you got from the CSR you initially had, you MUST import that certificate back in the keystore with which you generated the CSR, and you MUST import it, along with the whole certificate chain, into the correct alias, where the private key is stored.
This is essentially the same problem as the one in this question, but from the server side here.
Find the alias name that has your private key using keytool -list -keystore store.jks:
Your keystore contains 1 entry
myalias, Feb 15, 2012, PrivateKeyEntry,
Certificate fingerprint (MD5): xxxxxxxx
The prepare a bundle with your certificate and the chain of CA certificates in the right order (your own certificate first, and then each issuer one by one):
-----BEGIN CERTIFICATE-----
MIICajCCAdOgAwIBAgIBAjANBgkqhkiG9w0BAQUFADA7MQswCQYDVQQGEwJVSzEa
....
-----END CERTIFICATE-----
-----BEGIN CERTIFICATE-----
MIICkjCCAfugAwIBAgIJAKm5bDEMxZd7MA0GCSqGSIb3DQEBBQUAMDsxCzAJBgNV
....
-----END CERTIFICATE-----
(You can verify the content of each certificate using openssl x509 -text -noout and pasting each ---BEGIN/END--- block, including delimiters into its standard input.)
Then, import that file in a single step:
keytool -importcert -keystore store.jks -alias myalias -file bundle.pem

Sending POST request to a server that uses a self signed certificate

I need to send a POST request to a server that uses some levels of security. Unfortunately I don't know much about self signed certificates, I never used or studied it.
In the developer guide of the service it sais that the server uses a "public 1024-bit self signed certificate".
What does it mean? I've to create a certificate or I've to ask for it?
If i've to create a certificate, then how I should use it?
I'm implementing the client in Java

You need to download the certificate e.g. with your internet browser. Click through the security information and export the certificate.
Then you need to import it into your local java keystore so that the JVM can find it. For import use the keytool which you find in your jre/bin directory. Documentation for the keytool: http://docs.oracle.com/javase/1.4.2/docs/tooldocs/windows/keytool.html
The default keystore is jre/lib/security/cacerts.
Then you can import the downloaded certificate:
jre/bin/keytool -import -keystore jre/lib/security/cacerts -alias mycertificate -file downloads/mycertificate.cer
Hope this helps.
P.S. If it is self signed or verified its not important at this point. Just you (your client) must trust it.