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Compiler/TMS320C6713: embedded dsp

Part Number: TMS320C6713

Tool/software: TI C/C++ Compiler

Dear all,

I am sending analog signals to my DSP. I use CCS 5, compiler 7.3.4. The first cycles of my data are transient and I need to calculate a setting after that very first cycles have passed.
I also need to calculate the same setting once a bit is asserted (a logic has detected sth). 

How can I apply these. I am not familiar with timers or interrupts that much.

Please advise.

Thanks in advance,
Hessam