This week in the project I have focused on the requirements specification and the design of what the system will look like. I have created a document that describes the overview of the system - what it should look like and do - as well as create a Class diagram so that I know the rough structure and what methods and variables I will need.
In this document I also included a Use Case Diagram that describes what the user requirements are and what they should be able to do with the program.
This week I also did comparative test of alignment algorithms these where the results.
the hacked one : 4sec Av.
NeedlemanWusch : 5 secs Av.
SmithWaterman : 6 secs Av.
With some alteration I maybe able to get the Needleman and Waterman algorithms time down. I think they take longer as they need to accept Character arrays where as I am reading in Stings. If I read into a Character array it would save on the process of converting a string to an array.
In the following week I shall make these changes and select the quickest and most efficient in terms of memory usage as the target device will not be powerful.
In this document I also included a Use Case Diagram that describes what the user requirements are and what they should be able to do with the program.
This week I also did comparative test of alignment algorithms these where the results.
the hacked one : 4sec Av.
NeedlemanWusch : 5 secs Av.
SmithWaterman : 6 secs Av.
With some alteration I maybe able to get the Needleman and Waterman algorithms time down. I think they take longer as they need to accept Character arrays where as I am reading in Stings. If I read into a Character array it would save on the process of converting a string to an array.
In the following week I shall make these changes and select the quickest and most efficient in terms of memory usage as the target device will not be powerful.