Hi Peter It's me again Paiu Alexandru from Romania .
I've started to study for 2 days about amino acids , but i didn't find anything in romanian about the properties I have to implement for this project . I found only about amino acids in general . I went to the university library to find books about amino acids but i wasn't so lucky . I'm really stucked in getting some information about that properties . I found on wikipedia formulas and some informations about every method , but I really can't understand exactly what is every formula trying to do . I'd need some concrete examples for every method I have to implement . There are to many abbreviations that I don't understand . I tried to get some help from some friends that are studying pharmacy , but they couldn't help me . I studied that tool http://expasy.org/tools/<http://expasy.org/tools/protparam-doc.html>, but i haven't figured out yet exactly how those methods work (which are the inputs for each method and how they obtain those outputs ) I've started to work the goals on Selection criteria . I've finished the first 2 , now i'm working on using threads . I'll use threads for taking multiple lines from the input file . Each Thread will take a line at a time , will take the 2 strings separated by '\t' and will be applied StringOverlapFinder over the 2 Strings . In StringOverlapFinder i look for the last 5 characters of String 1 in String 2 . If it isn't found i print String 1 . If is found an overlap , then there are more cases to take care of . Some examples : Ex 1 : x = "abcdefghijklm" and y = "hijklmnopqrst" (your example) then the output is =abcdefg Ex 2 : x="asdcsadvsasevenfiveseven" and y="sevenfivesevenasdasdas" then the output is = asdcsadvsa Ex 3: x="ascdaeseven" and y="bseven" and the output is x So after this 3 examples i've found the "right" implementation . And for this I'll take Ex Nr 2 , because I think it's the most complex . I find that the the last 5 chars (seven) is found on index 0 . I take the substring from y starting with index 0 and ending with the index of the first overlap that is 0 too . So having a null substring the program should stop here and the output would be asdcsadvsasevenfive . But the real output shoud be asdcsadvsa . So , after finding that this is a posible output , i should look for a second overlap in y . It is found at index 9 ( the second seven) . I take the substring again from y that starts with index 0 and end with index 8 ( 9-1 ) and that is sevenfive . The lenght of this substring is 9 . Now i take another substring but this time from x . It starts from index (x.length()-5-9) and ends with index ( x.length()-5) . In this case this substrings are equall and the program will write the correct output that is asdcsadvsa . But before that , it should search for another possible overlap , but in this case there isn't one . In Ex Nr 3 it is found the "seven" string in y . It's taken the substring from y , that is "b" , and is compared with the substring from x that is "e" . They aren't equal so there is not an overlap . The program will look for another string "seven" in y , but there isn't one so the output will be x , because there wasn't found any overlap . I hope you understand my Ideeas . I'll send to you the jar when it's finished Is there a deadline for this selection criteria ? That's it for today Best Regards , Alex _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
