harshvladha / lass Goto Github PK

This is a sub issue of #4
Task:
Traverse the database, and keep calculating the score of k length subsequences till
the score of k length subsequence matches the score of LSS.

Using hashing values from #1 and #2 make a probability function in ScoringMatrix.java using n-gram model.

This is the sub issue of #4
Task:
Calculate score of each seed

Hash the input file such that count of each character is maintained in an array or a HashMap.

Change fixed seed length such that user can give it from command line. If not given by user then it should take seed length = 3.

i.e.,

Seed Length = s = args[4] or 3

Maintain a count of occurrences of all characters with respect to each other.

This is a sub issue of issue #4
Task :
Using the search pattern create the k length seeds. If pattern length is of m length then m-k+1 seeds will be generated.

This is a subissue of #4
Task:
Identify the least scoring seeds (LSS)

Naming conventions used in the algorithm are as follows :-
• w - Query string.
• wi - Seeds.
• k - Size of a seed.
• D - Database.
• T - Threshold.

Related Issues will tag this issue in their description!

This issue is a sub issue of #4.
Task :
Read scoring matrix stored in a text file.