converting translateTransExonFragmentStruct to return a char array UPDATE: done. Read More

should translateNucleotideSequence return a const array of chars rather than a mutable array? UPDATE: No, as some processing of the sequence may be necessary this wouldn’t work. Read More

Fuzzy String Matching May considering using these two often used in Bioinformatics: Needleman-Wunsch algorithm Smith-Waterman algorithm A Java applet demonstrating these algorithms: here Okay, maybe the Levenshtein distance is all we need. Read More

matchTagsFiltered is where the unnecessary charToIntRepresentation is used. Though charToIntRepresentation may not be entirely unnecessary as tags are as an NSArray, which still need to be converted…. Need to look at this later. Too distracted by converting NSStrings to chars… Read More

Converting the acid sequence from NSString to a char array is going to take a few days…. I have everything crossable crossed that once the refactoring has taken place and proper compilation happens that there aren’t any logic bugs and that the returned results match previously verified results. Read More

This is like tapping one domino which then falls and topples an ever widening fan of other dominoes. Each method I change contains other methods which also need to be changed. I’m concerned about the use of the toupper method regarding our acid sequence. It seems like if we are careful we could avoid it [...] Read More

Strings are essentially arrays of UTF characters which take up 4 bytes. As we are comparing proteome data, we don’t need that size of a data container to represent the amino acids. If rather than Srings we used arrays of characters (one byte each) then comparisons and assignment operators could be sped up as much [...] Read More

using: // calculate the sizes of C-Primitives int i = 1; NSLog(@”Primitive sizes:”); NSLog(@”%d The size of a char is: %d.”, i++, sizeof(char)); NSLog(@”%d The size of short is: %d.”, i++, sizeof(short)); NSLog(@”%d The size of int is: %d.”, i++, sizeof(int)); NSLog(@”%d The size of long is: %d.”, i++, sizeof(long)); NSLog(@”%d The size of long [...] Read More

Working from home (waiting for plumber). Had to quickly drop by lab to pick up source files and parameters list. Future Idea: need to make “getting started with GFS” intro guide. Success! Found that if we create a temp variable to store acidArrayAsInts[i] for comparisons then we save 2% to 3% of time on findLongestCommonSubstring Read More

The past couple of weeks has been kind of piecemeal optimization… now I’m looking through the code, line-by-line, to see how everything fits together. Read More

I need to find how longestCommonSubstring relates to the overall score. I’m concerned that it may not be the proper algorithm for first-pass selection of potential loci. For example, compare the following two strings: xxxxxxxAyyyyyyy xxxxxxxByyyyyyy the longest common substring between the two is only 7 characters long, when there are really 14 in common. [...] Read More

It would be interesting to check results to see if longestCommonSubstring were skipped where the query sequence were significantly longer than the comparison sequence.  perhaps an if clause which has a cut-off based on the length of the existing longest string relative to the length of the sequence string. Read More

As I believe characters are stored as a type of integer, converting to an integer array may be redundant and counter to its goal of expediting comparisons.  Test time performance when removing this step. Read More

Site created.  Getting back to reviewing grant.  Yesterday all admin related duties completed (TIM account now working). Read More