Commit aeddf091 authored by Mathieu Giraud's avatar Mathieu Giraud

core/dynprog.{h,cpp}: clean old comments, remove never used Costs

parent 365bf20e
......@@ -93,18 +93,6 @@ int Cost::substitution(char a, char b)
return (a == b) ? match : mismatch ;
}
/*
int Cost::ins(char current, char next)
{
return (next == current) ? homopolymer : insertion ;
}
int Cost::del(char current, char next)
{
return (next == current) ? homopolymer : deletion ;
}
*/
int Cost::homo2(char xa, char xb, char y)
{
return ((xa == xb) && (xb == y)) ? homopolymer : MINUS_INF ;
......
......@@ -44,8 +44,6 @@ class Cost
int deletion_end;
int homopolymer;
int substitution(char a, char b);
//int ins(char current, char next);
//int del(char current, char next);
int homo2(char xa, char xb, char y);
int open_insertion;
......@@ -59,25 +57,18 @@ class Cost
ostream& operator<<(ostream& out, const Cost& cost);
// Usual costs
const Cost Hamming = Cost(0, -1, MINUS_INF);
const Cost Levenshtein = Cost(0, -1, -1);
const Cost DNA = Cost(+5, -4, -10);
/* const Cost DNA = Cost(+5, -4, -10); */
/* const Cost VDJ = Cost(+5, -8, -8, -1); */
const Cost DNA = Cost(+5, -4, -10, 0, 0);
// Vidjil costs
const Cost VDJ = Cost(+4, -6, -10, -1, -2);
const Cost VDJaffine = Cost(+4, -6, -15, -1, -1, -2);
const Cost Identity = Cost(+1, -1, -1, 0, 0);
const Cost Homopolymers = Cost(+1, MINUS_INF, -1); // TODO: true homopolymer
const Cost IdentityToto= Cost(+1, -1, -1); // avec seuil de length-2: un homopoly xou une substituion
/* const Cost Identity = Cost(+1, 0, 0); */
const Cost IdentityDirty = Cost(+1000, -1, -1); // pour avoir une estimation de longueur de l'alignement, utilise dans compare-all
const Cost Hamming = Cost(0, -1, MINUS_INF);
const Cost Levenshtein = Cost(0, -1, -1);
const Cost Cluster = Cost(+1, -4, -4, 0, 0);
//const Cost Hamming = Cost();
const char* const mode_description[] = {
"XXX",
......
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