X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unweighted.cpp;h=56694e32e3a977b08df087dfc8deeabb2524564c;hb=1a968f34ae2d2680eaf189a197d1a21b8dfd6c03;hp=f0c7c4051a7f7d83214cb921ae40570e7f4f8dd7;hpb=7762fd5ec7582a78a31bb690a5c05b76e5b899c2;p=mothur.git diff --git a/unweighted.cpp b/unweighted.cpp index f0c7c40..56694e3 100644 --- a/unweighted.cpp +++ b/unweighted.cpp @@ -13,12 +13,13 @@ EstOutput Unweighted::getValues(Tree* t, int p, string o) { try { - globaldata = GlobalData::getInstance(); processors = p; outputDir = o; - + + CountTable* ct = t->getCountTable(); + //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 +27,7 @@ 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); } } @@ -35,23 +36,23 @@ 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 < (ct->getNamesOfGroups()).size(); i++) { + if ((ct->getNamesOfGroups())[i] != "xxx") { + groups.push_back((ct->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); } } - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) if(processors == 1){ - data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size()); + data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), ct); }else{ int numPairs = namesOfGroupCombos.size(); @@ -66,11 +67,11 @@ EstOutput Unweighted::getValues(Tree* t, int p, string o) { lines.push_back(linePair(startPos, numPairsPerProcessor)); } - data = createProcesses(t, namesOfGroupCombos); + data = createProcesses(t, namesOfGroupCombos, ct); lines.clear(); } #else - data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size()); + data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), ct); #endif return data; @@ -82,9 +83,9 @@ EstOutput Unweighted::getValues(Tree* t, int p, string o) { } /**************************************************************************************************/ -EstOutput Unweighted::createProcesses(Tree* t, vector< vector > namesOfGroupCombos) { +EstOutput Unweighted::createProcesses(Tree* t, vector< vector > namesOfGroupCombos, CountTable* ct) { try { -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) int process = 1; vector processIDS; @@ -99,11 +100,11 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector > namesOfG process++; }else if (pid == 0){ EstOutput myresults; - myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num); + myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, ct); if (m->control_pressed) { exit(0); } - m->mothurOut("Merging results."); m->mothurOutEndLine(); + //m->mothurOut("Merging results."); m->mothurOutEndLine(); //pass numSeqs to parent ofstream out; @@ -121,7 +122,7 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector > namesOfG } } - results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num); + results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, ct); //force parent to wait until all the processes are done for (int i=0;i<(processors-1);i++) { @@ -152,10 +153,10 @@ 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(); + //m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine(); return results; #endif @@ -166,7 +167,7 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector > namesOfG } } /**************************************************************************************************/ -EstOutput Unweighted::driver(Tree* t, vector< vector > namesOfGroupCombos, int start, int num) { +EstOutput Unweighted::driver(Tree* t, vector< vector > namesOfGroupCombos, int start, int num, CountTable* ct) { try { @@ -199,13 +200,14 @@ 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 +217,19 @@ 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); @@ -256,12 +258,13 @@ 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; + CountTable* ct = t->getCountTable(); + //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; @@ -269,7 +272,7 @@ 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); } } @@ -278,23 +281,23 @@ 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 < (ct->getNamesOfGroups()).size(); i++) { + if ((ct->getNamesOfGroups())[i] != "xxx") { + groups.push_back((ct->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); } } - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) if(processors == 1){ - data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true); + data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true, ct); }else{ int numPairs = namesOfGroupCombos.size(); @@ -308,12 +311,12 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB, int p, st lines.push_back(linePair(startPos, numPairsPerProcessor)); } - data = createProcesses(t, namesOfGroupCombos, true); + data = createProcesses(t, namesOfGroupCombos, true, ct); lines.clear(); } #else - data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true); + data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true, ct); #endif return data; @@ -325,9 +328,9 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB, int p, st } /**************************************************************************************************/ -EstOutput Unweighted::createProcesses(Tree* t, vector< vector > namesOfGroupCombos, bool usingGroups) { +EstOutput Unweighted::createProcesses(Tree* t, vector< vector > namesOfGroupCombos, bool usingGroups, CountTable* ct) { try { -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) int process = 1; vector processIDS; @@ -342,7 +345,7 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector > namesOfG process++; }else if (pid == 0){ EstOutput myresults; - myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, usingGroups); + myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, usingGroups, ct); if (m->control_pressed) { exit(0); } @@ -362,7 +365,7 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector > namesOfG } } - results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, usingGroups); + results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, usingGroups, ct); //force parent to wait until all the processes are done for (int i=0;i<(processors-1);i++) { @@ -394,7 +397,7 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector > namesOfG m->gobble(in); } in.close(); - remove(s.c_str()); + m->mothurRemove(s); } return results; @@ -406,14 +409,14 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector > namesOfG } } /**************************************************************************************************/ -EstOutput Unweighted::driver(Tree* t, vector< vector > namesOfGroupCombos, int start, int num, bool usingGroups) { +EstOutput Unweighted::driver(Tree* t, vector< vector > namesOfGroupCombos, int start, int num, bool usingGroups, CountTable* ct) { try { EstOutput results; results.resize(num); int count = 0; - Tree* copyTree = new Tree; + Tree* copyTree = new Tree(ct); for (int h = start; h < (start+num); h++) { @@ -442,6 +445,7 @@ 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++){ @@ -495,49 +499,54 @@ 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;