X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=fullmatrix.cpp;fp=fullmatrix.cpp;h=bc53b7db926cca543449fe58b5182d7d1ed6af67;hb=197c6d3303439582502840980d6a85cf3aab2314;hp=f4acd78c1132022b9bc22a6c878febe5a4df8c1c;hpb=3329385a816a97bdde934d98a615865c29eaacad;p=mothur.git diff --git a/fullmatrix.cpp b/fullmatrix.cpp index f4acd78..bc53b7d 100644 --- a/fullmatrix.cpp +++ b/fullmatrix.cpp @@ -10,6 +10,7 @@ #include "fullmatrix.h" /**************************************************************************/ + //This constructor reads a distance matrix file and stores the data in the matrix. FullMatrix::FullMatrix(ifstream& filehandle) { try{ @@ -27,12 +28,14 @@ FullMatrix::FullMatrix(ifstream& filehandle) { 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; + index.resize(numSeqs); + index[0].groupName = group; index[0].seqName = name; //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 @@ -59,7 +62,20 @@ FullMatrix::FullMatrix(ifstream& filehandle) { //sort sequences so they are gathered in groups for processing sortGroups(0, numSeqs-1); - + + groups.push_back(index[0].groupName); + sizes.push_back(1); + int groupCount = 0; + + for(int i=1;i> name; group = groupmap->getGroup(name); - index[i].groupname = group; + index[i].groupName = group; index[i].seqName = name; if(group == "not found") { cout << "Error: Sequence '" << name << "' was not found in the group file, please correct." << endl; exit(1); } @@ -125,7 +141,7 @@ void FullMatrix::readLTMatrix(ifstream& filehandle) { filehandle >> name; group = groupmap->getGroup(name); - index[i].groupname = group; + index[i].groupName = group; index[i].seqName = name; if(group == "not found") { cout << "Error: Sequence '" << name << "' was not found in the group file, please correct." << endl; exit(1); } @@ -154,6 +170,7 @@ void FullMatrix::readLTMatrix(ifstream& filehandle) { } /**************************************************************************/ + void FullMatrix::sortGroups(int low, int high){ try{ @@ -164,15 +181,15 @@ void FullMatrix::sortGroups(int low, int high){ /* compare value */ //what group does this row belong to - string z = index[(low + high) / 2].groupname; + string z = index[(low + high) / 2].groupName; /* partition */ do { /* find member above ... */ - while(index[i].groupname < z) i++; + while(index[i].groupName < z) i++; /* find element below ... */ - while(index[j].groupname > z) j--; + while(index[j].groupName > z) j--; if(i <= j) { /* swap rows*/ @@ -190,9 +207,9 @@ void FullMatrix::sortGroups(int low, int high){ } //swap map elements - z = index[i].groupname; - index[i].groupname = index[j].groupname; - index[j].groupname = z; + z = index[i].groupName; + index[i].groupName = index[j].groupName; + index[j].groupName = z; name = index[i].seqName; index[i].seqName = index[j].seqName; @@ -225,345 +242,47 @@ void FullMatrix::sortGroups(int low, int high){ } /**************************************************************************/ -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); - - bounds[0] = 0; - bounds[numGroups] = numSeqs; +float FullMatrix::get(int i, int j){ return matrix[i][j]; } - //for each group find bounds of subgroup/comparison - for (int i = 1; i < numGroups; i++) { - getBounds(bounds[i], globaldata->gGroupmap->namesOfGroups[i-1]); - } - - } - 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]; - - int countx = 1; //index in bound - int county = 1; //index in bound - - //find the bounds for the box the user wants - for (int i = 0; i < (numGroups * numGroups); i++) { - - //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"; - exit(1); - } +vector FullMatrix::getGroups(){ return groups; } -} +/**************************************************************************/ -/**************************************************************************/ -//print out matrix -void FullMatrix::printMinsForRows(ostream& out) { - try{ - for (int j = 0; j < minsForRows.size(); j++) { - out << minsForRows[j] << " "; - } - out << endl; +vector FullMatrix::getSizes(){ return sizes; } - } - 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); - } +/**************************************************************************/ -} +int FullMatrix::getNumGroups(){ return groups.size(); } -/**************************************************************************/ -//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; +int FullMatrix::getNumSeqs(){ return numSeqs; } - } - } - 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 */ - - 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; - } - - //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) { +void FullMatrix::printMatrix(ostream& out) { 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]; + 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; } - - //store distances in users vector - for (it = dist.begin(); it != dist.end(); it++) { - distances.push_back(it->first); - } - } 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"; + 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 restore. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + cout << "An unknown error has occurred in the FullMatrix class function printMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; exit(1); } + } +/**************************************************************************/ +