//if i's children are from the same group then i's pcount size will be 1
//if copyIpcount.size() = 0 they are from a branch that is entirely from a group the user doesn't want
if (copyIpcount.size() == 0) { }
- else if ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() == 1)) { UniqueBL += t->tree[i].getBranchLength(); }
+ else if ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() == 1)) { UniqueBL += abs(t->tree[i].getBranchLength()); }
//add i's BL to total if it is from the groups the user wants
if ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {
- totalBL += t->tree[i].getBranchLength();
+ totalBL += abs(t->tree[i].getBranchLength());
}
/**********************************************************************/
if (t->tree[rc].getRChild() == -1) {
//if rc is a valid group and rc has a BL
if ((inUsersGroups(t->tree[rc].getGroup(), groups) == true) && (t->tree[rc].getBranchLength() != -1)) {
- UniqueBL += t->tree[rc].getBranchLength();
- totalBL += t->tree[rc].getBranchLength();
+ UniqueBL += abs(t->tree[rc].getBranchLength());
+ totalBL += abs(t->tree[rc].getBranchLength());
}
}
if (t->tree[lc].getLChild() == -1) {
//if lc is a valid group and lc has a BL
if ((inUsersGroups(t->tree[lc].getGroup(), groups) == true) && (t->tree[lc].getBranchLength() != -1)) {
- UniqueBL += t->tree[lc].getBranchLength();
- totalBL += t->tree[lc].getBranchLength();
+ UniqueBL += abs(t->tree[lc].getBranchLength());
+ totalBL += abs(t->tree[lc].getBranchLength());
}
}
//if i's children are from the same group then i's pcount size will be 1
//if copyIpcount.size() = 0 they are from a branch that is entirely from a group the user doesn't want
if (copyIpcount.size() == 0) { }
- else if ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() == 1)) { UniqueBL += t->tree[i].getBranchLength(); }
+ else if ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() == 1)) { UniqueBL += abs(t->tree[i].getBranchLength()); }
//add i's BL to total if it is from the groups the user wants
if ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {
- totalBL += t->tree[i].getBranchLength();
+ totalBL += abs(t->tree[i].getBranchLength());
}
/**********************************************************************/
if (t->tree[rc].getRChild() == -1) {
//if rc is a valid group and rc has a BL
if ((inUsersGroups(t->tree[rc].getGroup(), groups) == true) && (t->tree[rc].getBranchLength() != -1)) {
- UniqueBL += t->tree[rc].getBranchLength();
- totalBL += t->tree[rc].getBranchLength();
+ UniqueBL += abs(t->tree[rc].getBranchLength());
+ totalBL += abs(t->tree[rc].getBranchLength());
}
}
if (t->tree[lc].getLChild() == -1) {
//if lc is a valid group and lc has a BL
if ((inUsersGroups(t->tree[lc].getGroup(), groups) == true) && (t->tree[lc].getBranchLength() != -1)) {
- UniqueBL += t->tree[lc].getBranchLength();
- totalBL += t->tree[lc].getBranchLength();
+ UniqueBL += abs(t->tree[lc].getBranchLength());
+ totalBL += abs(t->tree[lc].getBranchLength());
}
}
//if i's children are from the same group then i's pcount size will be 1
//if copyIpcount.size() = 0 they are from a branch that is entirely from a group the user doesn't want
if (copyIpcount.size() == 0) { }
- else if ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() == 1)) { UniqueBL += copyTree->tree[i].getBranchLength(); }
+ else if ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() == 1)) { UniqueBL += abs(copyTree->tree[i].getBranchLength()); }
//add i's BL to total if it is from the groups the user wants
if ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {
- totalBL += copyTree->tree[i].getBranchLength();
+ totalBL += abs(copyTree->tree[i].getBranchLength());
}
/**********************************************************************/
if (copyTree->tree[rc].getRChild() == -1) {
//if rc is a valid group and rc has a BL
if ((inUsersGroups(copyTree->tree[rc].getGroup(), groups) == true) && (copyTree->tree[rc].getBranchLength() != -1)) {
- UniqueBL += copyTree->tree[rc].getBranchLength();
- totalBL += copyTree->tree[rc].getBranchLength();
+ UniqueBL += abs(copyTree->tree[rc].getBranchLength());
+ totalBL += abs(copyTree->tree[rc].getBranchLength());
}
}
if (copyTree->tree[lc].getLChild() == -1) {
//if lc is a valid group and lc has a BL
if ((inUsersGroups(copyTree->tree[lc].getGroup(), groups) == true) && (copyTree->tree[lc].getBranchLength() != -1)) {
- UniqueBL += copyTree->tree[lc].getBranchLength();
- totalBL += copyTree->tree[lc].getBranchLength();
+ UniqueBL += abs(copyTree->tree[lc].getBranchLength());
+ totalBL += abs(copyTree->tree[lc].getBranchLength());
}
}
//if i's children are from the same group then i's pcount size will be 1
//if copyIpcount.size() = 0 they are from a branch that is entirely from a group the user doesn't want
if (copyIpcount.size() == 0) { }
- else if ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() == 1)) { UniqueBL += copyTree->tree[i].getBranchLength(); }
+ else if ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() == 1)) { abs(UniqueBL += copyTree->tree[i].getBranchLength()); }
//add i's BL to total if it is from the groups the user wants
if ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {
- totalBL += copyTree->tree[i].getBranchLength();
+ totalBL += abs(copyTree->tree[i].getBranchLength());
}
/**********************************************************************/
if (copyTree->tree[rc].getRChild() == -1) {
//if rc is a valid group and rc has a BL
if ((inUsersGroups(copyTree->tree[rc].getGroup(), groups) == true) && (copyTree->tree[rc].getBranchLength() != -1)) {
- UniqueBL += copyTree->tree[rc].getBranchLength();
- totalBL += copyTree->tree[rc].getBranchLength();
+ UniqueBL += abs(copyTree->tree[rc].getBranchLength());
+ totalBL += abs(copyTree->tree[rc].getBranchLength());
}
}
if (copyTree->tree[lc].getLChild() == -1) {
//if lc is a valid group and lc has a BL
if ((inUsersGroups(copyTree->tree[lc].getGroup(), groups) == true) && (copyTree->tree[lc].getBranchLength() != -1)) {
- UniqueBL += copyTree->tree[lc].getBranchLength();
- totalBL += copyTree->tree[lc].getBranchLength();
+ UniqueBL += abs(copyTree->tree[lc].getBranchLength());
+ totalBL += abs(copyTree->tree[lc].getBranchLength());
}
}
//if you have a BL
if(t->tree[index].getBranchLength() != -1){
- sum += t->tree[index].getBranchLength();
+ sum += abs(t->tree[index].getBranchLength());
}
index = t->tree[index].getParent();
}
//get last breanch length added
if(t->tree[index].getBranchLength() != -1){
- sum += t->tree[index].getBranchLength();
+ sum += abs(t->tree[index].getBranchLength());
}
//is this sum from a sequence which is in one of the users groups
u -= (double) t->tree[i].pcount[globaldata->Groups[l]] / (double) tmap->seqsPerGroup[globaldata->Groups[l]];
}
- u = abs(u) * t->tree[i].getBranchLength();
+ u = abs(u * t->tree[i].getBranchLength());
//save groupcombs u value
WScore[globaldata->Groups[b]+globaldata->Groups[l]] += u;
//if you have a BL
if(t->tree[index].getBranchLength() != -1){
- sum += t->tree[index].getBranchLength();
+ sum += abs(t->tree[index].getBranchLength());
}
index = t->tree[index].getParent();
}
//get last breanch length added
if(t->tree[index].getBranchLength() != -1){
- sum += t->tree[index].getBranchLength();
+ sum += abs(t->tree[index].getBranchLength());
}
if ((t->tree[v].getGroup() == groupA) || (t->tree[v].getGroup() == groupB)) {
u -= (double) t->tree[i].pcount[groupB] / (double) tmap->seqsPerGroup[groupB];
}
- u = abs(u) * t->tree[i].getBranchLength();
+ u = abs(u * t->tree[i].getBranchLength());
//save groupcombs u value
WScore[(groupA+groupB)] += u;