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;
+ 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
if(isalnum(d)){
square = true;
filehandle.putback(d);
+
for(int i=0;i<numSeqs;i++){
filehandle >> matrix[0][i];
}
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);
-
+ 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";
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].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); }
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].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); }
count++;
reading->update(count);
}
+
}
reading->finish();
delete reading;
}
/**************************************************************************/
-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);
- }
- }
- 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);
- }
-
-}
-/**************************************************************************/
-//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) {
- 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];
+ string z = index[(low + high) / 2].groupname;
/* partition */
do {
/* find member above ... */
- while(index[i] < z) i++;
+ while(index[i].groupname < z) i++;
/* find element below ... */
- while(index[j] > z) j--;
+ while(index[j].groupname > 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 rows*/
+ for (int h = 0; h < numSeqs; h++) {
+ y = matrix[i][h];
+ matrix[i][h] = matrix[j][h];
+ matrix[j][h] = y;
+ }
- /* swap two elements in column*/
- y = matrix[i][row];
- matrix[i][row] = matrix[j][row];
- matrix[j][row] = 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];
- index[i] = index[j];
- index[j] = 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;
+ index[j].seqName = name;
+
i++;
j--;
-//cout << "swapping elements " << i << " " << j << endl;
-//printMatrix(cout); cout << endl;
}
} while(i <= j);
/* recurse */
if(low < j)
- quicksort(low, j, row);
+ sortGroups(low, j);
if(i < high)
- quicksort(i, high, row);
+ sortGroups(i, high);
+
+
}
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";
+ 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 quicksort. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "An unknown error has occurred in the FullMatrix class function sortGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
+
}
/**************************************************************************/
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] << " ";
}
}
}
+
/**************************************************************************/
+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