/**************************************************************************/
//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] = 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
if(isalnum(d)){
square = true;
filehandle.putback(d);
+
for(int i=0;i<numSeqs;i++){
filehandle >> matrix[0][i];
+ if (sim) { matrix[0][i] = 1.0 - matrix[0][i]; }
}
break;
}
break;
}
}
-
+
//read rest of matrix
- if (square == true) { readSquareMatrix(filehandle); }
- else { readLTMatrix(filehandle); }
-
-
+ if (square == true) { readSquareMatrix(filehandle); }
+ else { readLTMatrix(filehandle); }
- printMatrix(cout);
- //sort sequences so they are gathered in groups for processing
- sortGroups();
- cout << "after sort" << endl;
- printMatrix(cout);
+ 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;
- reading = new Progress("Reading matrix: ", numSeqs * numSeqs);
+ reading = new Progress("Reading matrix: ", numSeqs * numSeqs);
int count = 0;
- float distance;
- string group, name;
+ string group, name;
+
for(int i=1;i<numSeqs;i++){
filehandle >> name;
group = groupmap->getGroup(name);
- index[i] = 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;j<numSeqs;j++){
- filehandle >> distance;
-
- matrix[i][j] = distance;
+ if (m->control_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";
- 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";
+ m->errorOut(e, "FullMatrix", "readSquareMatrix");
exit(1);
}
-
}
/**************************************************************************/
-void FullMatrix::readLTMatrix(ifstream& filehandle) {
+int FullMatrix::readLTMatrix(ifstream& filehandle) {
try {
+
Progress* reading;
- reading = new Progress("Reading matrix: ", numSeqs * (numSeqs - 1) / 2);
+ 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] = 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;j<i;j++){
+ if (m->control_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";
- 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";
+ m->errorOut(e, "FullMatrix", "readLTMatrix");
exit(1);
}
-
}
/**************************************************************************/
-void FullMatrix::sortGroups(){
+
+void FullMatrix::sortGroups(int low, int high){
try{
- //sort each row by group and when you do, swap rows too.
- for (int i = 0; i < numSeqs; i++) {
- quicksort(0, numSeqs-1, i);
+
+ if (low < high) {
+ int i = low+1;
+ int j = high;
+ int pivot = (low+high) / 2;
+
+ 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++; }
+
+ /* find element below ... */
+ while((j >= low) && (index[j].groupName > key)) { j--; }
+
+ if(i < j) {
+ swapRows(i, j);
+ }
+ }
+
+ 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);
}
-
}
-/**************************************************************************/
-//this is a version of quicksort taken from http://www.c.happycodings.com/Sorting_Searching/code13.html
-/* sort everything inbetween `low' <-> `high' */
-void FullMatrix::quicksort(int low, int high, int row) {
+
+/**************************************************************************/
+void FullMatrix::swapRows(int i, int j) {
try {
- int i = low;
- int j = high;
- int y = 0;
+
+ float y;
+ string z, name;
+
+ /* 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;
+
- /* compare value */
- //what group does this row belong to
- string z = index[(low + high) / 2];
-
- /* partition */
- do {
- /* find member above ... */
- while(index[i] < z) i++;
-
- /* find element below ... */
- while(index[j] > z) j--;
-
- if(i <= j) {
- /* swap two elements in row*/
- y = matrix[row][i];
- matrix[row][i] = matrix[row][j];
- matrix[row][j] = y;
-
- /* swap two elements in column*/
- y = matrix[i][row];
- matrix[i][row] = matrix[j][row];
- matrix[j][row] = y;
-
- //swap map elements
- z = index[i];
- index[i] = index[j];
- index[j] = z;
-
- i++;
- j--;
-//cout << "swapping elements " << i << " " << j << endl;
-//printMatrix(cout); cout << endl;
- }
- } while(i <= j);
-
- /* recurse */
- if(low < j)
- quicksort(low, j, row);
-
- if(i < high)
- quicksort(i, high, row);
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function quicksort. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the FullMatrix class function quicksort. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "FullMatrix", "swapRows");
exit(1);
}
}
+/**************************************************************************/
+
+float FullMatrix::get(int i, int j){ return matrix[i][j]; }
+
+/**************************************************************************/
+
+vector<string> FullMatrix::getGroups(){ return groups; }
+
+/**************************************************************************/
+
+vector<int> FullMatrix::getSizes(){ return sizes; }
+
+/**************************************************************************/
+
+int FullMatrix::getNumGroups(){ return groups.size(); }
/**************************************************************************/
-int FullMatrix::getNumSeqs(){ return numSeqs; }
+
+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] << endl;
+ out << "row " << i << " group = " << index[i].groupName << " name = " << index[i].seqName << endl;
for (int j = 0; j < numSeqs; j++) {
- out << matrix[i][j] << " ";
+ out << i << '\t' << j << '\t' << matrix[i][j] << endl;
}
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 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";
+ m->errorOut(e, "FullMatrix", "printMatrix");
exit(1);
}
-
}
+
/**************************************************************************/