#include "fullmatrix.h"
-
/**************************************************************************/
//This constructor reads a distance matrix file and stores the data in the matrix.
-FullMatrix::FullMatrix(ifstream& f) {
+FullMatrix::FullMatrix(ifstream& filehandle) {
try{
- f >> numSeqs;
+ globaldata = GlobalData::getInstance();
+ groupmap = globaldata->gGroupmap;
-
+ string name, group;
+ filehandle >> numSeqs >> name;
+
+ //make the matrix filled with zeros
+ matrix.resize(numSeqs);
+ for(int i = 0; i < numSeqs; i++) {
+ matrix[i].resize(numSeqs, 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;
+ 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;
+ while((d=filehandle.get()) != EOF){
+
+ //is d a number meaning its square
+ if(isalnum(d)){
+ square = true;
+ filehandle.putback(d);
+
+ for(int i=0;i<numSeqs;i++){
+ filehandle >> matrix[0][i];
+ }
+ break;
+ }
+
+ //is d a line return meaning its lower triangle
+ if(d == '\n'){
+ square = false;
+ break;
+ }
+ }
+
+ //read rest of matrix
+ if (square == true) { readSquareMatrix(filehandle); }
+ else { readLTMatrix(filehandle); }
+
+ //sort sequences so they are gathered in groups for processing
+ 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);
}
}
+/**************************************************************************/
+void FullMatrix::readSquareMatrix(ifstream& filehandle) {
+ try {
+
+ Progress* reading;
+ reading = new Progress("Reading matrix: ", numSeqs * numSeqs);
+
+ int count = 0;
+ float distance;
+
+ string group, name;
+
+ for(int i=1;i<numSeqs;i++){
+ filehandle >> name;
+
+ group = groupmap->getGroup(name);
+ 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); }
+
+ for(int j=0;j<numSeqs;j++){
+ filehandle >> distance;
+
+ matrix[i][j] = distance;
+ count++;
+ reading->update(count);
+ }
+ }
+ reading->finish();
+ delete reading;
+ }
+ 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";
+ 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) {
+ try {
+ Progress* reading;
+ reading = new Progress("Reading matrix: ", numSeqs * (numSeqs - 1) / 2);
+
+ int count = 0;
+ float distance;
+
+ string group, name;
+
+ for(int i=1;i<numSeqs;i++){
+ filehandle >> name;
+
+ group = groupmap->getGroup(name);
+ 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); }
+
+ for(int j=0;j<i;j++){
+ filehandle >> distance;
+
+ matrix[i][j] = distance; matrix[j][i] = distance;
+ count++;
+ reading->update(count);
+ }
+
+ }
+ reading->finish();
+ delete reading;
+ }
+ 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";
+ 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;
+ int 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(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;
+ }
+
+ /* swap columns*/
+ for (int b = 0; b < numSeqs; b++) {
+ y = matrix[b][i];
+ matrix[b][i] = matrix[b][j];
+ matrix[b][j] = y;
+ }
+
+ //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);
+
+
+ }
+ 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";
+ exit(1);
+ }
+
+}
+
/**************************************************************************/
int FullMatrix::getNumSeqs(){ return numSeqs; }
-/**************************************************************************/
\ No newline at end of file
+/**************************************************************************/
+//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::getMinsForRowsVectors(){
+ 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());
+
+ /*************************************************/
+ //find where in matrix each group starts and stops
+ /*************************************************/
+ vector<int> bounds; //bounds[1] = starting row in matrix from group B, bounds[2] = starting row in matrix from group C, bounds[3] = no need to find upper bound of C because its numSeqs.
+ bounds.resize(numGroups);
+
+ bounds[0] = 0;
+ bounds[numGroups] = numSeqs-1;
+ //for each group find bounds of subgroup/comparison
+ for (int i = 1; i < numGroups; i++) {
+ getBounds(bounds[i], globaldata->gGroupmap->namesOfGroups[i]);
+ }
+
+ /************************************************************/
+ //fill the minsForRows vectors for each group the user wants
+ /************************************************************/
+ int countx = bounds[1]; //where second group starts
+ int county = bounds[1];
+
+ //go through the entire matrix
+ for (int x = 0; x < numSeqs; x++) {
+ for (int y = 0; y < numSeqs; y++) {
+ //if have not changed groups
+ if ((x < countx) && (y < county)) {
+
+ }
+ }
+ }
+
+
+
+
+ }
+ 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);
+ }
+
+}
+
+/**************************************************************************/
+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) {
+ if (gotLower != true) { 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);
+ }
+
+}
+
projects / mothur.git / blobdiff