X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unweighted.cpp;h=431323f066665bd07edce8da80c32dadb1600cf2;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=d0eea3dc2b9f1f507213627e6d18df9a4e6afe68;hpb=f40e9e38c5604fdbe90f964fc26eca7758e6257f;p=mothur.git diff --git a/unweighted.cpp b/unweighted.cpp index d0eea3d..431323f 100644 --- a/unweighted.cpp +++ b/unweighted.cpp @@ -13,12 +13,11 @@ EstOutput Unweighted::getValues(Tree* t, int p, string o) { try { - globaldata = GlobalData::getInstance(); processors = p; outputDir = o; //if the users enters no groups then give them the score of all groups - int numGroups = globaldata->Groups.size(); + int numGroups = m->getNumGroups(); //calculate number of comparsions int numComp = 0; @@ -26,7 +25,7 @@ EstOutput Unweighted::getValues(Tree* t, int p, string o) { for (int r=0; r groups; groups.push_back(globaldata->Groups[r]); groups.push_back(globaldata->Groups[l]); + vector groups; groups.push_back((m->getGroups())[r]); groups.push_back((m->getGroups())[l]); namesOfGroupCombos.push_back(groups); } } @@ -35,15 +34,15 @@ EstOutput Unweighted::getValues(Tree* t, int p, string o) { vector groups; if (numGroups == 0) { //get score for all users groups - for (int i = 0; i < tmap->namesOfGroups.size(); i++) { - if (tmap->namesOfGroups[i] != "xxx") { - groups.push_back(tmap->namesOfGroups[i]); + for (int i = 0; i < (tmap->getNamesOfGroups()).size(); i++) { + if ((tmap->getNamesOfGroups())[i] != "xxx") { + groups.push_back((tmap->getNamesOfGroups())[i]); } } namesOfGroupCombos.push_back(groups); }else { - for (int i = 0; i < globaldata->Groups.size(); i++) { - groups.push_back(globaldata->Groups[i]); + for (int i = 0; i < m->getNumGroups(); i++) { + groups.push_back((m->getGroups())[i]); } namesOfGroupCombos.push_back(groups); } @@ -152,7 +151,7 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector > namesOfG m->gobble(in); } in.close(); - remove(s.c_str()); + m->mothurRemove(s); } m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine(); @@ -199,13 +198,14 @@ EstOutput Unweighted::driver(Tree* t, vector< vector > namesOfGroupCombo m->mothurOut(namesOfGroupCombos[h][namesOfGroupCombos[h].size()-1]); m->mothurOut(", skipping."); m->mothurOutEndLine(); results[count] = UW; }else{ - + //cout << "trying to get root" << endl; + //if including the root this clears rootForGrouping[namesOfGroupCombos[h]] getRoot(t, nodeBelonging, namesOfGroupCombos[h]); - + //cout << "here" << endl; for(int i=0;igetNumNodes();i++){ if (m->control_pressed) { return data; } - + //cout << i << endl; //pcountSize = 0, they are from a branch that is entirely from a group the user doesn't want //pcountSize = 2, not unique to one group //pcountSize = 1, unique to one group @@ -215,19 +215,19 @@ EstOutput Unweighted::driver(Tree* t, vector< vector > namesOfGroupCombo map::iterator itGroup = t->tree[i].pcount.find(namesOfGroupCombos[h][j]); if (itGroup != t->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } } } - + + //unique calc if (pcountSize == 0) { } else if ((t->tree[i].getBranchLength() != -1) && (pcountSize == 1) && (rootForGrouping[namesOfGroupCombos[h]].count(i) == 0)) { //you have a unique branch length and you are not the root UniqueBL += abs(t->tree[i].getBranchLength()); } - + //total calc if (pcountSize == 0) { } else if ((t->tree[i].getBranchLength() != -1) && (pcountSize != 0) && (rootForGrouping[namesOfGroupCombos[h]].count(i) == 0)) { //you have a branch length and you are not the root totalBL += abs(t->tree[i].getBranchLength()); } - } //cout << UniqueBL << '\t' << totalBL << endl; UW = (UniqueBL / totalBL); @@ -256,13 +256,11 @@ EstOutput Unweighted::driver(Tree* t, vector< vector > namesOfGroupCombo EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB, int p, string o) { try { - globaldata = GlobalData::getInstance(); processors = p; outputDir = o; - //if the users enters no groups then give them the score of all groups - int numGroups = globaldata->Groups.size(); + int numGroups = m->getNumGroups(); //calculate number of comparsions int numComp = 0; @@ -270,7 +268,7 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB, int p, st for (int r=0; r groups; groups.push_back(globaldata->Groups[r]); groups.push_back(globaldata->Groups[l]); + vector groups; groups.push_back((m->getGroups())[r]); groups.push_back((m->getGroups())[l]); namesOfGroupCombos.push_back(groups); } } @@ -279,15 +277,15 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB, int p, st vector groups; if (numGroups == 0) { //get score for all users groups - for (int i = 0; i < tmap->namesOfGroups.size(); i++) { - if (tmap->namesOfGroups[i] != "xxx") { - groups.push_back(tmap->namesOfGroups[i]); + for (int i = 0; i < (tmap->getNamesOfGroups()).size(); i++) { + if ((tmap->getNamesOfGroups())[i] != "xxx") { + groups.push_back((tmap->getNamesOfGroups())[i]); } } namesOfGroupCombos.push_back(groups); }else { - for (int i = 0; i < globaldata->Groups.size(); i++) { - groups.push_back(globaldata->Groups[i]); + for (int i = 0; i < m->getNumGroups(); i++) { + groups.push_back((m->getGroups())[i]); } namesOfGroupCombos.push_back(groups); } @@ -395,7 +393,7 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector > namesOfG m->gobble(in); } in.close(); - remove(s.c_str()); + m->mothurRemove(s); } return results; @@ -414,7 +412,7 @@ EstOutput Unweighted::driver(Tree* t, vector< vector > namesOfGroupCombo int count = 0; - Tree* copyTree = new Tree; + Tree* copyTree = new Tree(tmap); for (int h = start; h < (start+num); h++) { @@ -443,6 +441,7 @@ EstOutput Unweighted::driver(Tree* t, vector< vector > namesOfGroupCombo m->mothurOut(", skipping."); m->mothurOutEndLine(); results[count] = UW; }else{ + //if including the root this clears rootForGrouping[namesOfGroupCombos[h]] getRoot(copyTree, nodeBelonging, namesOfGroupCombos[h]); for(int i=0;igetNumNodes();i++){ @@ -496,49 +495,54 @@ EstOutput Unweighted::driver(Tree* t, vector< vector > namesOfGroupCombo int Unweighted::getRoot(Tree* t, int v, vector grouping) { try { //you are a leaf so get your parent - int index = t->tree[index].getParent(); + int index = t->tree[v].getParent(); - //my parent is a potential root - rootForGrouping[grouping].insert(index); - - //while you aren't at root - while(t->tree[index].getParent() != -1){ - - if (m->control_pressed) { return 0; } + if (includeRoot) { + rootForGrouping[grouping].clear(); + }else { - //am I the root for this grouping? if so I want to stop "early" - //does my sibling have descendants from the users groups? - //if so I am not the root - int parent = t->tree[index].getParent(); - int lc = t->tree[parent].getLChild(); - int rc = t->tree[parent].getRChild(); + //my parent is a potential root + rootForGrouping[grouping].insert(index); - int sib = lc; - if (lc == index) { sib = rc; } - - map::iterator itGroup; - int pcountSize = 0; - for (int j = 0; j < grouping.size(); j++) { - map::iterator itGroup = t->tree[sib].pcount.find(grouping[j]); - if (itGroup != t->tree[sib].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } } + //while you aren't at root + while(t->tree[index].getParent() != -1){ + //cout << index << endl; + if (m->control_pressed) { return 0; } + + //am I the root for this grouping? if so I want to stop "early" + //does my sibling have descendants from the users groups? + //if so I am not the root + int parent = t->tree[index].getParent(); + int lc = t->tree[parent].getLChild(); + int rc = t->tree[parent].getRChild(); + + int sib = lc; + if (lc == index) { sib = rc; } + + map::iterator itGroup; + int pcountSize = 0; + for (int j = 0; j < grouping.size(); j++) { + map::iterator itGroup = t->tree[sib].pcount.find(grouping[j]); + if (itGroup != t->tree[sib].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } } + } + + //if yes, I am not the root + if (pcountSize != 0) { + rootForGrouping[grouping].clear(); + rootForGrouping[grouping].insert(parent); + } + + index = parent; } - //if yes, I am not the root - if (pcountSize != 0) { - rootForGrouping[grouping].clear(); + //get all nodes above the root to add so we don't add their u values above + index = *(rootForGrouping[grouping].begin()); + while(t->tree[index].getParent() != -1){ + int parent = t->tree[index].getParent(); rootForGrouping[grouping].insert(parent); + //cout << parent << " in root" << endl; + index = parent; } - - index = parent; - } - - //get all nodes above the root to add so we don't add their u values above - index = *(rootForGrouping[grouping].begin()); - while(t->tree[index].getParent() != -1){ - int parent = t->tree[index].getParent(); - rootForGrouping[grouping].insert(parent); - //cout << parent << " in root" << endl; - index = parent; } return 0;