static IDnum expectedNumberOfConnections(IDnum IDA, Connection * connect,
IDnum ** counts, Category cat)
{
Node *A = getNodeInGraph(graph, IDA);
Node *B = connect->destination;
IDnum IDB = getNodeID(B);
double left, middle, right;
Coordinate longLength, shortLength, D;
double M, N, O, P;
Coordinate mu = getInsertLength(graph, cat);
double sigma = sqrt(getInsertLength_var(graph, cat));
double result;
double densityA, densityB, minDensity;
if (mu <= 0)
return 0;
if (getNodeLength(A) == 0 || getNodeLength(B) == 0)
return 0;
if (getNodeLength(A) < getNodeLength(B)) {
longLength = getNodeLength(B);
shortLength = getNodeLength(A);
} else {
longLength = getNodeLength(A);
shortLength = getNodeLength(B);
}
densityA = counts[cat][IDA + nodeCount(graph)] / (double) getNodeLength(A);
densityB = counts[cat][IDB + nodeCount(graph)] / (double) getNodeLength(B);
minDensity = densityA > densityB ? densityB : densityA;
D = getConnectionDistance(connect) - (longLength +
shortLength) / 2;
M = (D - mu) / sigma;
N = (D + shortLength - mu) / sigma;
O = (D + longLength - mu) / sigma;
P = (D + shortLength + longLength - mu) / sigma;
left = ((norm(M) - norm(N)) - M * normInt(M, N)) * sigma;
middle = shortLength * normInt(N, O);
right = ((norm(O) - norm(P)) - P * normInt(O, P)) * (-sigma);
result = (minDensity * (left + middle + right));
if (result > 0)
return (IDnum) result;
else
return 0;
}
static IDnum expectedNumberOfConnections(IDnum IDA, Connection * connect,
IDnum ** counts, Category cat)
{
Node *A = getNodeInGraph(graph, IDA);
Node *B = connect->destination;
double left, middle, right;
Coordinate longLength, shortLength, D;
IDnum longCount;
double M, N, O, P;
Coordinate mu = getInsertLength(graph, cat);
double sigma = sqrt(getInsertLength_var(graph, cat));
double result;
if (mu <= 0)
return 0;
if (getNodeLength(A) < getNodeLength(B)) {
longLength = getNodeLength(B);
shortLength = getNodeLength(A);
longCount = counts[cat][getNodeID(B) + nodeCount(graph)];
} else {
longLength = getNodeLength(A);
shortLength = getNodeLength(B);
longCount = counts[cat][IDA + nodeCount(graph)];
}
D = connect->distance - (longLength + shortLength) / 2;
M = (D - mu) / sigma;
N = (D + shortLength - mu) / sigma;
O = (D + longLength - mu) / sigma;
P = (D + shortLength + longLength - mu) / sigma;
left = ((norm(M) - norm(N)) - M * normInt(M, N)) * sigma;
middle = shortLength * normInt(N, O);
right = ((norm(O) - norm(P)) - P * normInt(O, P)) * (-sigma);
result = (longCount * (left + middle + right)) / longLength;
if (result > 0)
return (IDnum) result;
else
return 0;
}
void data::preprocessPeaks()
{
// trie les pics par masse (ce qu'ils sont sense deja etre, mais juste au cas ou)
qsort(peakList, peakNb, sizeof(PEAKS), compar_PEAK_MASSES);
// je commence par marquer la masse parente et ses isotopes
markParentMass();
// trie les pics par intensite pour la normalisation et l'enlevement
// des pics de basse intensite
qsort(peakList, peakNb, sizeof(PEAKS), compar_PEAKS);
normInt();
// vire les pics qui ont une intensite en dessous du seuil de PEAK_INT_SEUIL
for (int i = 0; i < peakNb; i++) {
if (peakList[i].intensity < runManParam->PEAK_INT_SEUIL) {
peakNb = i;
break;
}
}
// attribution des charges a considerer pour chaque pic
for (int i = 0; i < peakNb; i++) {
if ((peakList[i].mass - 4 > (parentMassM+2)/2) && (peakList[i].mass - 4 < parentMassM)) {
// le +4, c'est pour que tous les isotopes d'un pic parent soient classes comme
// le pic parent, meme s'ils sont a +1, +2 ou +3...
peakList[i].CHARGE1 = true;
}
if ((peakList[i].mass - 4 > (parentMassM+3)/3) && (peakList[i].mass - 4 < (parentMassM+2)/2)) {
peakList[i].CHARGE1 = true;
peakList[i].CHARGE2 = true;
}
if (peakList[i].mass - 4 < (parentMassM+3)/3) {
peakList[i].CHARGE1 = true;
peakList[i].CHARGE2 = true;
peakList[i].CHARGE3 = true;
}
}
// trie les pics par masse pour le controle des isotopes
qsort(peakList, peakNb, sizeof(PEAKS), compar_PEAK_MASSES);
// vire tous les pics isopopiques qui ne sont pas le premier isotope
for (int i = 0; i < peakNb; i++) {
for (int j = i+1; j < peakNb; j++) {
// recherche d'isotopes a +0.333, +0.5, +1 selon les charges a considerer pour le pic courant
// qui dependent de la region du spectre ou se trouve le pic
// +0.333
if (peakList[i].CHARGE3 == true) {
if ((fabs((peakList[j].mass - peakList[i].mass) - 0.333333333333333333) < runManParam->FRAGMENT_ERROR1)
&& (peakList[j].intensity < peakList[i].intensity)) {
// je prends l'erreur 1 car je compare des isotopes
// exiger que l'intensite soit plus petite fait qu'on va manquer d'oter certains isotopes (hautes masses)
// mais je prefere en garder trop que pas assez
peakList[j].used = true;
}
}
// +0.5
if (peakList[i].CHARGE2 == true) {
if ((fabs((peakList[j].mass - peakList[i].mass) - 0.5) < runManParam->FRAGMENT_ERROR1)
&& (peakList[j].intensity < peakList[i].intensity)) {
peakList[j].used = true;
}
}
// +1
if (peakList[i].CHARGE1 == true) {
if ((fabs((peakList[j].mass - peakList[i].mass) - 1) < runManParam->FRAGMENT_ERROR1)
&& (peakList[j].intensity < peakList[i].intensity)) {
peakList[j].used = true;
}
}
if (peakList[j].mass - peakList[i].mass > 4) {
break;
}
}
}
// vire les pics doubles (je garde a chaque fois le pic de plus grande intensite)
for (int i = 0; i < peakNb; i++) {
for (int j = i+1; j < peakNb; j++) {
if (fabs(peakList[j].mass - peakList[i].mass) < runManParam->FRAGMENT_ERROR1) {
// repere le pic de + grande intensite
if (peakList[i].intensity > peakList[j].intensity) {
peakList[j].used = true;
}
else {
peakList[i].used = true;
}
}
}
}
}
