X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=fullmatrix.cpp;h=4451d6645ea8691b941ebbc991f82cc4ce8b4706;hb=1a968f34ae2d2680eaf189a197d1a21b8dfd6c03;hp=f4acd78c1132022b9bc22a6c878febe5a4df8c1c;hpb=cd10743907df223b7dd5b3a3deb20fde758b8ed7;p=mothur.git diff --git a/fullmatrix.cpp b/fullmatrix.cpp index f4acd78..4451d66 100644 --- a/fullmatrix.cpp +++ b/fullmatrix.cpp @@ -11,28 +11,29 @@ /**************************************************************************/ //This constructor reads a distance matrix file and stores the data in the matrix. -FullMatrix::FullMatrix(ifstream& filehandle) { +FullMatrix::FullMatrix(ifstream& filehandle, GroupMap* g, bool s) : groupmap(g), sim(s) { try{ - globaldata = GlobalData::getInstance(); - groupmap = globaldata->gGroupmap; + m = MothurOut::getInstance(); string name, group; - filehandle >> numSeqs >> name; + filehandle >> numSeqs >> name; + //make the matrix filled with zeros matrix.resize(numSeqs); for(int i = 0; i < numSeqs; i++) { - matrix[i].resize(numSeqs, 0); + matrix[i].resize(numSeqs, 0.0); } - group = groupmap->getGroup(name); - if(group == "not found") { cout << "Error: Sequence '" << name << "' was not found in the group file, please correct." << endl; exit(1); } - index[0].groupname = group; + if(group == "not found") { m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); } + index.resize(numSeqs); index[0].seqName = name; + index[0].groupName = group; //determine if matrix is square or lower triangle //if it is square read the distances for the first sequence char d; + bool square; while((d=filehandle.get()) != EOF){ //is d a number meaning its square @@ -42,6 +43,7 @@ FullMatrix::FullMatrix(ifstream& filehandle) { for(int i=0;i> matrix[0][i]; + if (sim) { matrix[0][i] = 1.0 - matrix[0][i]; } } break; } @@ -52,26 +54,23 @@ FullMatrix::FullMatrix(ifstream& filehandle) { break; } } - + //read rest of matrix - if (square == true) { readSquareMatrix(filehandle); } - else { readLTMatrix(filehandle); } + if (square == true) { readSquareMatrix(filehandle); } + else { readLTMatrix(filehandle); } - //sort sequences so they are gathered in groups for processing - sortGroups(0, numSeqs-1); - + filehandle.close(); + + if (!m->control_pressed) { sortGroups(0, numSeqs-1); } + } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function FullMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the FullMatrix class function FullMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "FullMatrix", "FullMatrix"); exit(1); } } /**************************************************************************/ -void FullMatrix::readSquareMatrix(ifstream& filehandle) { +int FullMatrix::readSquareMatrix(ifstream& filehandle) { try { Progress* reading; @@ -80,39 +79,43 @@ void FullMatrix::readSquareMatrix(ifstream& filehandle) { int count = 0; string group, name; - + for(int i=1;i> name; group = groupmap->getGroup(name); - index[i].groupname = group; index[i].seqName = name; + index[i].groupName = group; - if(group == "not found") { cout << "Error: Sequence '" << name << "' was not found in the group file, please correct." << endl; exit(1); } + if(group == "not found") { m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); } for(int j=0;jcontrol_pressed) { delete reading; return 0; } + filehandle >> matrix[i][j]; + if (sim) { matrix[i][j] = 1.0 - matrix[i][j]; } count++; reading->update(count); } } + + if (m->control_pressed) { delete reading; return 0; } + reading->finish(); delete reading; + + return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function readSquareMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "FullMatrix", "readSquareMatrix"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the FullMatrix class function readSquareMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - } /**************************************************************************/ -void FullMatrix::readLTMatrix(ifstream& filehandle) { +int FullMatrix::readLTMatrix(ifstream& filehandle) { try { + Progress* reading; reading = new Progress("Reading matrix: ", numSeqs * (numSeqs - 1) / 2); @@ -120,450 +123,161 @@ void FullMatrix::readLTMatrix(ifstream& filehandle) { float distance; string group, name; - + for(int i=1;i> name; - + group = groupmap->getGroup(name); - index[i].groupname = group; index[i].seqName = name; + index[i].groupName = group; - if(group == "not found") { cout << "Error: Sequence '" << name << "' was not found in the group file, please correct." << endl; exit(1); } + if(group == "not found") { m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); } for(int j=0;jcontrol_pressed) { delete reading; return 0; } + filehandle >> distance; - + if (sim) { distance = 1.0 - distance; } + matrix[i][j] = distance; matrix[j][i] = distance; + count++; reading->update(count); } - } + + if (m->control_pressed) { delete reading; return 0; } + reading->finish(); delete reading; + + return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function readLTMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "FullMatrix", "readLTMatrix"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the FullMatrix class function readLTMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - } /**************************************************************************/ + void FullMatrix::sortGroups(int low, int high){ try{ - - int i = low; - int j = high; - float y = 0; - string name; - /* compare value */ - //what group does this row belong to - string z = index[(low + high) / 2].groupname; - - /* partition */ - do { - /* find member above ... */ - while(index[i].groupname < z) i++; - - /* find element below ... */ - while(index[j].groupname > z) j--; + if (low < high) { + int i = low+1; + int j = high; + int pivot = (low+high) / 2; - if(i <= j) { - /* swap rows*/ - for (int h = 0; h < numSeqs; h++) { - y = matrix[i][h]; - matrix[i][h] = matrix[j][h]; - matrix[j][h] = y; - } + swapRows(low, pivot); //puts pivot in final spot + + /* compare value */ + //what group does this row belong to + string key = index[low].groupName; + + /* partition */ + while(i <= j) { + /* find member above ... */ + while((i <= high) && (index[i].groupName <= key)) { i++; } - /* swap columns*/ - for (int b = 0; b < numSeqs; b++) { - y = matrix[b][i]; - matrix[b][i] = matrix[b][j]; - matrix[b][j] = y; + /* find element below ... */ + while((j >= low) && (index[j].groupName > key)) { j--; } + + if(i < j) { + swapRows(i, j); } - - //swap map elements - z = index[i].groupname; - index[i].groupname = index[j].groupname; - index[j].groupname = z; - - name = index[i].seqName; - index[i].seqName = index[j].seqName; - index[j].seqName = name; - - - i++; - j--; - } - } while(i <= j); - - /* recurse */ - if(low < j) - sortGroups(low, j); - - if(i < high) - sortGroups(i, high); - + } + + swapRows(low, j); + + /* recurse */ + sortGroups(low, j-1); + sortGroups(j+1, high); + } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function sortGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the FullMatrix class function sortGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "FullMatrix", "sortGroups"); exit(1); } - } /**************************************************************************/ -int FullMatrix::getNumSeqs(){ return numSeqs; } -/**************************************************************************/ -//print out matrix -void FullMatrix::printMatrix(ostream& out) { - try{ - for (int i = 0; i < numSeqs; i++) { - out << "row " << i << " group = " << index[i].groupname << " name = " << index[i].seqName << endl; - for (int j = 0; j < numSeqs; j++) { - out << matrix[i][j] << " "; - } - out << endl; - } - } - catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function printMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the FullMatrix class function printMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - -} - -/**************************************************************************/ -void FullMatrix::setBounds(){ - try{ - numGroups = globaldata->gGroupmap->namesOfGroups.size(); - - //sort globaldata->gGroupmap.namesOfGroups so that it will match the matrix - sort(globaldata->gGroupmap->namesOfGroups.begin(), globaldata->gGroupmap->namesOfGroups.end()); - - //one for each comparision - //minsForRows.resize(numGroups*numGroups); - - /*************************************************/ - //find where in matrix each group starts and stops - /*************************************************/ - bounds.resize(numGroups); +void FullMatrix::swapRows(int i, int j) { + try { + + float y; + string z, name; - bounds[0] = 0; - bounds[numGroups] = numSeqs; - - //for each group find bounds of subgroup/comparison - for (int i = 1; i < numGroups; i++) { - getBounds(bounds[i], globaldata->gGroupmap->namesOfGroups[i-1]); + /* swap rows*/ + for (int h = 0; h < numSeqs; h++) { + y = matrix[i][h]; + matrix[i][h] = matrix[j][h]; + matrix[j][h] = y; } - } - catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function getMinsForRowsVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the FullMatrix class function getMinsForRowsVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - -} -/**************************************************************************/ -vector FullMatrix::getMins(int x) { - try{ - //clear out old data - minsForRows.clear(); - - /************************************************************/ - //fill the minsForRows vector for the box the user wants - /************************************************************/ - int count = 0; - int lowBoundx = bounds[0]; //where first group starts - int lowBoundy = bounds[0]; - int highBoundx = bounds[1]; //where second group starts - int highBoundy = bounds[1]; + /* swap columns*/ + for (int b = 0; b < numSeqs; b++) { + y = matrix[b][i]; + matrix[b][i] = matrix[b][j]; + matrix[b][j] = y; + } - int countx = 1; //index in bound - int county = 1; //index in bound + //swap map elements + z = index[i].groupName; + index[i].groupName = index[j].groupName; + index[j].groupName = z; - //find the bounds for the box the user wants - for (int i = 0; i < (numGroups * numGroups); i++) { + name = index[i].seqName; + index[i].seqName = index[j].seqName; + index[j].seqName = name; - //are you at the box? - if (count == x) { break; } - else { count++; } - - //move to next box - if (county < numGroups) { - county++; - highBoundy = bounds[county]; - lowBoundy = bounds[county-1]; - }else{ //you are moving to a new row of "boxes" - county = 1; - countx++; - highBoundx = bounds[countx]; - lowBoundx = bounds[countx-1]; - highBoundy = bounds[county]; - lowBoundy = bounds[county-1]; - } - } - - //each row in the box - for (int x = lowBoundx; x < highBoundx; x++) { - float min4Row = 100000.0; - //each entry in that row - for (int y = lowBoundy; y < highBoundy; y++) { - //if you are not on the diagonal and you are less than previous minimum - if ((x != y) && (matrix[x][y] < min4Row)) { - min4Row = matrix[x][y]; - } - } - //save minimum value for that row in minsForRows vector of vectors - minsForRows.push_back(min4Row); - } - - return minsForRows; - } - catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function getMins. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the FullMatrix class function getMins. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } -} -/**************************************************************************/ -void FullMatrix::getBounds(int& higher, string group) { - try{ - bool gotLower = false; - //for each group find bounds of subgroup/comparison - for (it = index.begin(); it != index.end(); it++) { - if (it->second.groupname == group) { - gotLower = true; - }else if ((gotLower == true) && (it->second.groupname != group)) { higher = it->first; break; } - } - } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function getBounds. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the FullMatrix class function getBounds. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "FullMatrix", "swapRows"); exit(1); } - } +/**************************************************************************/ -/**************************************************************************/ -//print out matrix -void FullMatrix::printMinsForRows(ostream& out) { - try{ - for (int j = 0; j < minsForRows.size(); j++) { - out << minsForRows[j] << " "; - } - out << endl; +float FullMatrix::get(int i, int j){ return matrix[i][j]; } - } - catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function printMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the FullMatrix class function printMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } +/**************************************************************************/ -} +vector FullMatrix::getGroups(){ return groups; } -/**************************************************************************/ -//shuffles the sequences in the 2 groups passed in. -void FullMatrix::shuffle(string groupA, string groupB){ - try{ - vector rows2Swap; - vector shuffled; - float y = 0; - string name = ""; - - - /********************************/ - //save rows you want to randomize - /********************************/ - //go through the matrix map to find the rows from groups you want to randomize - for (it = index.begin(); it != index.end(); it++) { - //is this row from group A or B? - if ((it->second.groupname == groupA) || (it->second.groupname == groupB)) { - rows2Swap.push_back(it->first); - shuffled.push_back(it->first); - } - } - - //randomize rows to shuffle in shuffled - random_shuffle(shuffled.begin(), shuffled.end()); - - /***************************************/ - //swap rows and columns to randomize box - /***************************************/ - for (int i = 0; i < shuffled.size(); i++) { +/**************************************************************************/ - //record the swaps you are making so you can undo them in restore function - restoreIndex[i].a = shuffled[i]; - restoreIndex[i].b = rows2Swap[i]; - - /* swap rows*/ - for (int h = 0; h < numSeqs; h++) { - y = matrix[shuffled[i]][h]; - matrix[shuffled[i]][h] = matrix[rows2Swap[i]][h]; - matrix[rows2Swap[i]][h] = y; - } - - /* swap columns */ - for (int b = 0; b < numSeqs; b++) { - y = matrix[b][shuffled[i]]; - matrix[b][shuffled[i]] = matrix[b][rows2Swap[i]]; - matrix[b][rows2Swap[i]] = y; - } - - //swap map elements - name = index[shuffled[i]].seqName; - index[shuffled[i]].seqName = index[rows2Swap[i]].seqName; - index[rows2Swap[i]].seqName = name; +vector FullMatrix::getSizes(){ return sizes; } - } - } - catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function shuffle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the FullMatrix class function shuffle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } -} -/**************************************************************************/ -//unshuffles the matrix. -void FullMatrix::restore(){ - try{ - float y = 0; - string name = ""; +/**************************************************************************/ - //reverse iterate through swaps and undo them to restore original matrix and index map. - for(it2 = restoreIndex.rbegin(); it2 != restoreIndex.rend(); it2++) { - /* swap rows */ +int FullMatrix::getNumGroups(){ return groups.size(); } - for (int h = 0; h < numSeqs; h++) { - y = matrix[it2->second.a][h]; - matrix[it2->second.a][h] = matrix[it2->second.b][h]; - matrix[it2->second.b][h] = y; - } - - /* swap columns */ - for (int b = 0; b < numSeqs; b++) { - y = matrix[b][it2->second.a]; - matrix[b][it2->second.a] = matrix[b][it2->second.b]; - matrix[b][it2->second.b] = y; - } - - - //swap map elements - name = index[it2->second.a].seqName; - index[it2->second.a].seqName = index[it2->second.b].seqName; - index[it2->second.b].seqName = name; +/**************************************************************************/ - } +int FullMatrix::getNumSeqs(){ return numSeqs; } - //clear restore for next shuffle - restoreIndex.clear(); - } - catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function restore. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the FullMatrix class function restore. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } -} /**************************************************************************/ -void FullMatrix::getDist(vector& distances) { - try{ - map dist; //holds the distances for the integral form - map::iterator it; - /************************************************************/ - //fill the minsForRows vectors for each group the user wants - /************************************************************/ - int lowBoundx = bounds[0]; //where first group starts - int lowBoundy = bounds[0]; - int highBoundx = bounds[1]; //where second group starts - int highBoundy = bounds[1]; - - int countx = 1; //index in bound - int county = 1; //index in bound - - //go through each "box" in the matrix - for (int i = 0; i < (numGroups * numGroups); i++) { - //each row in the box - for (int x = lowBoundx; x < highBoundx; x++) { - float min4Row = 100000.0; - //each entry in that row - for (int y = lowBoundy; y < highBoundy; y++) { - //if you are not on the diagonal and you are less than previous minimum - if ((x != y) && (matrix[x][y] < min4Row)){ - min4Row = matrix[x][y]; - } - } - //save minimum value - dist[min4Row] = min4Row; - } - - //****** reset bounds to process next "box" ******** - //if you still have more "boxes" in that row - if (county < numGroups) { - county++; - highBoundy = bounds[county]; - lowBoundy = bounds[county-1]; - }else{ //you are moving to a new row of "boxes" - county = 1; - countx++; - highBoundx = bounds[countx]; - lowBoundx = bounds[countx-1]; - highBoundy = bounds[county]; - lowBoundy = bounds[county-1]; +void FullMatrix::printMatrix(ostream& out) { + try{ + for (int i = 0; i < numSeqs; i++) { + out << "row " << i << " group = " << index[i].groupName << " name = " << index[i].seqName << endl; + for (int j = 0; j < numSeqs; j++) { + out << i << '\t' << j << '\t' << matrix[i][j] << endl; } - } - - //store distances in users vector - for (it = dist.begin(); it != dist.end(); it++) { - distances.push_back(it->first); + out << endl; } + for (int i = 0; i < numSeqs; i++) { out << i << '\t' << index[i].seqName << endl; } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function restore. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the FullMatrix class function restore. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "FullMatrix", "printMatrix"); exit(1); } } +/**************************************************************************/ +