X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unweighted.cpp;h=2a2a41cf0f6b823e3a781d9dabe53702e04d6f78;hb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;hp=b038f388af1c3ef027c66339523ce8bc87b55661;hpb=d9ec50b60719a907681a22acbe2469f1ea93facb;p=mothur.git diff --git a/unweighted.cpp b/unweighted.cpp index b038f38..2a2a41c 100644 --- a/unweighted.cpp +++ b/unweighted.cpp @@ -48,53 +48,30 @@ EstOutput Unweighted::getValues(Tree* t) { //groups in this combo groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]); - for(int i=t->getNumLeaves();igetNumNodes();i++){ - - int lc = t->tree[i].getLChild(); //lc = vector index of left child - int rc = t->tree[i].getRChild(); //rc = vector index of right child - - /**********************************************************************/ - //This section adds in all lengths that are non leaf - + for(int i=0;igetNumNodes();i++){ + if (m->control_pressed) { return data; } + copyIpcount = t->tree[i].pcount; - for (it = copyIpcount.begin(); it != copyIpcount.end(); it++) { - if (inUsersGroups(it->first, groups) != true) { copyIpcount.erase(it->first); } + for (it = copyIpcount.begin(); it != copyIpcount.end();) { + if (inUsersGroups(it->first, groups) != true) { + copyIpcount.erase(it++); + }else { it++; } } //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()); } - /**********************************************************************/ - //This section adds in all lengths that are leaf - - //if i's chidren are leaves - 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(); - } - } - - 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(); - } - } - - /**********************************************************************/ } UW = (UniqueBL / totalBL); + //cout << globaldata->Groups[a] << globaldata->Groups[l] << '\t' << UniqueBL << '\t' << totalBL << endl; if (isnan(UW) || isinf(UW)) { UW = 0; } @@ -109,7 +86,9 @@ EstOutput Unweighted::getValues(Tree* t) { if (numGroups == 0) { //get score for all users groups for (int i = 0; i < tmap->namesOfGroups.size(); i++) { - groups.push_back(tmap->namesOfGroups[i]); + if (tmap->namesOfGroups[i] != "xxx") { + groups.push_back(tmap->namesOfGroups[i]); + } } }else { for (int i = 0; i < globaldata->Groups.size(); i++) { @@ -122,50 +101,27 @@ EstOutput Unweighted::getValues(Tree* t) { UW = 0.00; //Unweighted Value = UniqueBL / totalBL; copyIpcount.clear(); - for(int i=t->getNumLeaves();igetNumNodes();i++){ - - int lc = t->tree[i].getLChild(); //lc = vector index of left child - int rc = t->tree[i].getRChild(); //rc = vector index of right child - - /**********************************************************************/ - //This section adds in all lengths that are non leaf + for(int i=0;igetNumNodes();i++){ + if (m->control_pressed) { return data; } + copyIpcount = t->tree[i].pcount; - for (it = copyIpcount.begin(); it != copyIpcount.end(); it++) { - if (inUsersGroups(it->first, groups) != true) { copyIpcount.erase(it->first); } + for (it = copyIpcount.begin(); it != copyIpcount.end();) { + if (inUsersGroups(it->first, groups) != true) { + copyIpcount.erase(it++); + }else { it++; } } //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()); } - /**********************************************************************/ - //This section adds in all lengths that are leaf - - //if i's chidren are leaves - 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(); - } - } - - 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(); - } - } - - /**********************************************************************/ } UW = (UniqueBL / totalBL); @@ -179,14 +135,9 @@ EstOutput Unweighted::getValues(Tree* t) { } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the Unweighted class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the Unweighted class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "Unweighted", "getValues"); exit(1); } - } /**************************************************************************************************/ @@ -205,7 +156,7 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB) { //if the users enters no groups then give them the score of all groups int numGroups = globaldata->Groups.size(); - + //calculate number of comparsions int numComp = 0; for (int r=0; rgetCopy(t); + + //groups in this combo + groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]); //swap labels in the groups you want to compare - copyTree->assembleRandomUnifracTree(globaldata->Groups[a], globaldata->Groups[l]); + copyTree->assembleRandomUnifracTree(groups[0], groups[1]); - //groups in this combo - groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]); - - for(int i=t->getNumLeaves();igetNumNodes();i++){ - - int lc = t->tree[i].getLChild(); //lc = vector index of left child - int rc = t->tree[i].getRChild(); //rc = vector index of right child - + if (m->control_pressed) { delete copyTree; return data; } + + //copyTree->createNewickFile("random"+groupA+toString(count)); + + for(int i=0;igetNumNodes();i++){ + + if (m->control_pressed) { delete copyTree; return data; } + /**********************************************************************/ //This section adds in all lengths that are non leaf - - copyIpcount = t->tree[i].pcount; - for (it = copyIpcount.begin(); it != copyIpcount.end(); it++) { - if (inUsersGroups(it->first, groups) != true) { copyIpcount.erase(it->first); } + copyIpcount = copyTree->tree[i].pcount; + for (it = copyIpcount.begin(); it != copyIpcount.end();) { + if (inUsersGroups(it->first, groups) != true) { + copyIpcount.erase(it++); + }else { it++; } } //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 ((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 ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) { - totalBL += t->tree[i].getBranchLength(); + if ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) { + totalBL += abs(copyTree->tree[i].getBranchLength()); } - /**********************************************************************/ - //This section adds in all lengths that are leaf - - //if i's chidren are leaves - 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(); - } - } - - 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(); - } - } - - /**********************************************************************/ } UW = (UniqueBL / totalBL); @@ -295,7 +229,9 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB) { if (numGroups == 0) { //get score for all users groups for (int i = 0; i < tmap->namesOfGroups.size(); i++) { - groups.push_back(tmap->namesOfGroups[i]); + if (tmap->namesOfGroups[i] != "xxx") { + groups.push_back(tmap->namesOfGroups[i]); + } } }else { for (int i = 0; i < globaldata->Groups.size(); i++) { @@ -312,52 +248,30 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB) { copyTree->getCopy(t); //swap labels in all the groups you want to compare - copyTree->assembleRandomUnifracTree(); - - for(int i=t->getNumLeaves();igetNumNodes();i++){ - - int lc = t->tree[i].getLChild(); //lc = vector index of left child - int rc = t->tree[i].getRChild(); //rc = vector index of right child + copyTree->assembleRandomUnifracTree(groups); - /**********************************************************************/ - //This section adds in all lengths that are non leaf - - copyIpcount = t->tree[i].pcount; - for (it = copyIpcount.begin(); it != copyIpcount.end(); it++) { - if (inUsersGroups(it->first, groups) != true) { copyIpcount.erase(it->first); } + if (m->control_pressed) { delete copyTree; return data; } + + for(int i=0;igetNumNodes();i++){ + if (m->control_pressed) { delete copyTree; return data; } + + copyIpcount = copyTree->tree[i].pcount; + for (it = copyIpcount.begin(); it != copyIpcount.end();) { + if (inUsersGroups(it->first, groups) != true) { + copyIpcount.erase(it++); + }else { it++; } } //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 ((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 ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) { - totalBL += t->tree[i].getBranchLength(); - } - - /**********************************************************************/ - //This section adds in all lengths that are leaf - - //if i's chidren are leaves - 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(); - } + if ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) { + totalBL += abs(copyTree->tree[i].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(); - } - } - - /**********************************************************************/ } UW = (UniqueBL / totalBL); @@ -366,16 +280,14 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB) { data[count] = UW; } - + + delete copyTree; + return data; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the Unweighted class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the Unweighted class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "Unweighted", "getValues"); exit(1); } }