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#include<structs.h>
#include<score.h>
#include<leftinfluence.h>
#include<rightinfluence.h>
#include<fstream>
extern vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
float Score::getScore(Fragment *up, Fragment * down) {
long long int absSeq1,absSeq2,absDiagonal,absMin,absMax;
absSeq1= Myabs((up->seq1End) - (down->seq1Start));
absSeq2= Myabs((up->seq2End) - (down->seq2Start));
absMin = Mymin(absSeq1,absSeq2);
absMax=Mymax(absSeq1,absSeq2);
absDiagonal = absMax-absMin;
return absMin*(-minConstant) + absMax* (-maxConstant) + absDiagonal *(-diagConstant) -openConstant +up->totalScore;
}
ScoreInterface::ScoreInterface (float iopenConstant, float iminConstant, float imaxConstant, float idiagConstant) {
openConstant = iopenConstant;
minConstant = iminConstant;
maxConstant = imaxConstant;
diagConstant = idiagConstant;
}
Score::Score (float iopenConstant , float iminConstant ,float imaxConstant,float idiagConstant):ScoreInterface(iopenConstant,iminConstant, imaxConstant, idiagConstant) {
}
void initScoreFunctionPointers(char * scoreFileName) {
ifstream SFP;
char line[255];
SFP.open(scoreFileName);
if (!SFP.good()) {
printf("The score file is invalid");
exit(0);
}
while (1) {
SFP.getline(line,255);
if (line[0]=='\0') { break; }
createScoreFunctionObjects(line);
}
}
void createScoreFunctionObjects(char * line) {
long long int i;
long long int j;
long long int rem[4];
long long int remCases[MAXCASES],remObjects[MAXOBJECTS];
long long int numCases;
long long int numObjects;
long long int cases [MAXCASES];
float objects[MAXOBJECTS][4];
char updir,downdir,relpos;
Score * SFObjects[MAXOBJECTS];
j=0;
for (i=0; (unsigned)i<strlen(line); i++) {
if (line[i]=='{' || line[i]=='}') {
rem[j++]=i;
}
}
//forming cases
numCases=0;
for (i=rem[0]; i<=rem[1]; i++) {
if (line[i]=='{' ||line[i]=='}'||line[i]==';') {
remCases[numCases++]=i;
}
}
numCases--;
for (i=0; i<numCases; i++) {
sscanf(&line[remCases[i]+1],"%c %c %c",&updir,&relpos,&downdir);
if (DEBUG) { fprintf(stderr,"\n%c %c %c",updir,downdir,relpos); }
cases[i]= charToCase(updir)<<UPSTRANDSHIFT | charToCase(downdir)<<DOWNSTRANDSHIFT |charToCase(relpos)<<RELPOSSHIFT;
}
numObjects=0;
for (i=rem[2]; i<=rem[3]; i++) {
if (line[i]=='{' || line[i]=='}' || line[i]==';') {
remObjects[numObjects++]=i;
}
}
numObjects--;
for (i=0; i<numObjects; i++) {
sscanf(&line[remObjects[i]+1],"%f %f %f %f",&objects[i][0],&objects[i][1],&objects[i][2],&objects[i][3]);
if (DEBUG) { fprintf(stderr,"\t%f %f %f %f\n",objects[i][0],objects[i][1],objects[i][2],objects[i][3]); }
SFObjects[i] = new Score(objects[i][0],objects[i][2],objects[i][3],objects[i][1]);
}
for (i=0; i<numCases; i++) {
for (j=0; j<numObjects; j++) {
scoreFunctions[cases[i]].push_back(SFObjects[j]);
}
}
}
long long int charToCase(char in) {
switch(in) {
case '+': return POSITIVE;
case '-': return NEGATIVE;
case 'R': return RIGHT;
case 'L': return LEFT;
case 'U': return UNRELATED;
default:
{
fprintf(stderr,"\n Unrecognisable character in score file");
exit(0);
}
}
}
float scoreAll(Fragment * up, Fragment * down, long long int ret_case) {
unsigned long long int i;
// TODO TODO TODO
float ret_score=NEGINF;
// float ret_score = -99999999999;
float temp_score;
if (up->nameIter != down->nameIter) {
if (ret_case >> RELPOSSHIFT != UNRELATED) {
//MUKCHECK HOPE THIS WORKS
return NEGINF;
}
}
for (i=0; i<scoreFunctions[ret_case].size(); i++) {
temp_score = scoreFunctions[ret_case][i]->getScore(up,down);
if (temp_score > ret_score) {
ret_score = temp_score;
}
}
if (ret_score == NEGINF) {
printf("Score function case not handled::%lld\n",ret_case);
//exit(0);
}
return ret_score;
}
long long int Mymax(long long int a, long long int b) {
return (a>=b ? a : b);
}
long long int Mymin(long long int a,long long int b) {
return (a<=b ? a : b);
}
long long int Myabs(long long int a) {
return (a<0 ? -a : a);
}
float fragmentSetScore(Fragment * current, Fragment *owner, LI *LeftInfluence, RI * RightInfluence, long long int rightInfluenceFlag) {
/*SLAGANCHANGE change call to the score based on the Leftinfluence, this has to be passed i guess*/
float tempScore;
if (rightInfluenceFlag == 3) {
tempScore = scoreAll(owner,current, current->strand << DOWNSTRANDSHIFT | owner->strand <<UPSTRANDSHIFT | UNRELATED<< RELPOSSHIFT);
if (tempScore == NEGINF) { // TODO
if (current->totalScore <= 0) {
current->totalScore = current->score;
current->back = owner;
}
} else
if (tempScore + current->score > current->totalScore) {
current->totalScore = tempScore + current->score;
current->back = owner;
}
} else if (rightInfluenceFlag == TRUE) {
tempScore = scoreAll(owner,current,RightInfluence->scoreIndex);
if (tempScore == NEGINF) { // TODO
if (current->totalScore <= 0) {
current->totalScore = current->score;
current->back = owner;
}
} else
if (tempScore + current->score > current->totalScore) {
current->totalScore = tempScore + current->score;
current->back = owner;
}
} else {
tempScore = scoreAll(owner,current,LeftInfluence->scoreIndex);
if (tempScore == NEGINF) { // TODO
if (current->totalScore <= 0) {
current->totalScore = current->score;
current->back = owner;
}
} else
if (tempScore + current->score > current->totalScore) {
current->totalScore = tempScore + current->score;
current->back = owner;
}
}
return current->totalScore;
}
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