Quantum computers can solve certain problems more efficiently compared to conventional classical methods. In the endeavor to build a quantum computer, several competing platforms have emerged that can implement certain quantum algorithms using a few qubits. However, the demonstrations so far have been done usually by tailoring the hardware to meet the requirements of a particular algorithm implemented for a limited number of instances. Although such proof of principal implementations are important to verify the working of algorithms on a physical system, they further need to have the potential to serve as a general purpose quantum computer allowing the flexibility required for running multiple algorithms and be scaled up to host more qubits. Here we demonstrate a small programmable quantum computer based on five trapped atomic ions each of which serves as a qubit. By optically resolving each ion we can individually address them in order to perform a complete set of single-qubit and fully connected two-qubit quantum gates and alsoperform efficient individual qubit measurements. We implement a computation architecture that accepts an algorithm from a user interface in the form of a standard logic gate sequence and decomposes it into fundamental quantum operations that are native to the hardware using a set of compilation instructions that are defined within the software. These operations are then effected through a pattern of laser pulses that perform coherent rotations on targeted qubits in the chain. The architecture implemented in the experiment therefore gives us unprecedented flexibility in the programming of any quantum algorithm while staying blind to the underlying hardware. As a demonstration we implement the Deutsch-Jozsa and Bernstein-Vazirani algorithms on the five-qubit processor and achieve average success rates of 95 and 90 percent, respectively. We also implement a five-qubit coherent quantum Fourier transform and examine its performance in the period finding and phase estimation protocol. We find fidelities of 84 and 62 percent, respectively. While maintaining the same computation architecture the system can be scaled to more ions using resources that scale favorably (O(N^2)) with the number of qubits N.