Music analysis is very often taught and practiced without reflecting on the method(s) used. Analysis is not possible without language and concepts. If 'pure' cognition of composition does not exist, then practicing analysis must include some reflection on its purposes. In this respect, analytical methods must be classified. This article reflects on methodological problems in music analysis. Traditional classifications of music analysis are re-visited and changes towards a more consistent system of classification are suggested with regards to the approaches taken. Finally, these methodological observations are applied to the use of computer technology in music analysis. Since methods of computer-assisted music analysis have not been classified yet, such a system is proposed here, based on detailed historical studies in this field. Each of the categories in this system of classification of computer-assisted music analysis are briefly characterized.