Hi Harshad,
The difference between INDI and SAMP is that INDI (like ASCOM) is used for interoperability between hardware and astronomical software (e. g., control mount, camera, focuser, filter wheel), and SAMP is used for interoperability between different astronomical software (e.g., send coordinates, catalogs, selected objects, images).
Also, in case for SkEye, the app could act as a client and read coordinates from an INDI telescope driver (connecting to a remote INDI server), but would have to provide an INDI server and a local telescope driver to share its coordinates with another application (INDI for Java seems to be inactive for a long time).
Now, with SAMP, you can use a remote SAMP hub on a desktop, like TOPCAT or JSAMP, and could share information with another astronomical software (e.g., Cartes du Ciel/Skychart, Aladin):
1- Act like digital encoders: Send the current coordinates of the reticule displayed on SkEye to center the chart of the desktop software;
2- Act like a guide scope: Send the coordinates of a highlighted/searched object on the desktop software to SkEye to guide de user during guiding (just like the search on SkEye does);
3- Allow the user to customize the catalog of objects: Receive a VOtable with a list of objects from the desktop software.
Best,
Andre